DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1-7, 9, 17, and 20 are pending.
Election/Restrictions
Applicant previously elected the species SEQ ID NO 13 (ICOS) in the reply filed on 02 October 2025. SEQ ID NO 2 was also examined.
Since art was found for those species, the next examined species are SEQ ID NOs 3, 7-8, and 14-16. Note that multiple species are being rejoined as a courtesy and in the interest of compact prosecution. The requirement for election of those species is withdrawn but other requirements for election of species are maintained.
Status of the Application
Applicant’s response and amendment filed 27 April 2026 are acknowledged and entered.
Applicant has amended Claims 1-4, 6, 17, and 20. Applicant has cancelled Claims 8 and 25-30.
Response to Amendment
The objections to the Drawings are withdrawn in view of amendments to the Drawings.
Applicant has amended the Spec. to overcome Objections; the objections are withdrawn over some aspects but maintained over the absence of ® and TM symbols.
The Objections to the Claims are withdrawn in view of the claim amendments.
Applicant has amended the claims to overcome the 112(a) rejection; the 112(a) rejection partially withdrawn in view of Applicant’s arguments and partially maintained.
The 101 rejection over a claim that reads on a human organism is withdrawn in view of the claim amendments. The previous 101 rejections over noneligible subject matter are withdrawn in view of the claim amendments but new 101 rejections are applied.
The previous 102 and 103 rejections are withdrawn in view of the claim amendments but new 102 and 103 rejections are applied.
Claims 1-7, 9, 17, and 20 are examined.
Arguments applicable to newly applied rejections to amended or newly presented claims are addressed below. Arguments that are no longer relevant are not addressed.
Rejections not reiterated here are withdrawn.
Specification
The use of the following terms, which are trade names or marks used in commerce, has been noted in this application in the §Examples:
PEIPro®
PolyPlus®
HYDROSORT (should be HYDROSART®)
Dynabeads™
Attune™
Alexa Fluor® (AF)
Brilliant Violet™ (BV)
Zombie NIR™
FICOLL®
Gibco™
CellFix™
PE/Dazzle™
NOTE: Applicant is responsible for identifying and fixing any and all such instances for the terms listed above and any other terms that are trade names or trademarks. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever it/they appear(s) or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Interpretation
Claims that recite a promoter sequence for use are interpreted as reciting an intended use that does not affect the structure of the claimed promoter sequence. Therefore an intended use provides no patentable weight.
CD+ cells are understood to be any kind of cell that expresses CD3 including all Tcells because all Tcells are known to express CD3. See Wikipedia (“CD3 [immunology”. Available at en.wikipedia.org/wiki/CD3_(immunology). Accessed on 21 October 2025, of record).
The claims recite the promoter sequence comprises a fragment of any of SEQ ID NOS…, the fragment consisting of nt… of any of SEQ ID NOS…., or a variant thereof having at least 95% identity to said fragment. That is interpreted as requiring that the promoter comprise a fragment that consists of nt [#]… of any of SEQ ID NOs [#] or a variant that has at least 95% identity to a fragment of SEQ ID NOs [#]. Since the claim recites that the promoter sequence compris[es] the fragment, the claim is interpreted as allowing the promoter to comprise more than just the fragment consisting of the recited nt.
The Spec. does not define a transgene. A transgene is interpreted in its broadest reasonable sense: any gene that has been transferred from one organism to another. One organism is interpreted to be one individual organism.
The Spec. does not define a vector. A vector is interpreted in its broadest reasonable sense: an agent that allows for gene transfer. That interpretation is in part based on the fact that the Spec. clarifies (p. 1 L20-25) that viral vectors are just one exemplary kind of vector.
Claim Objections
Claim 17 is rejected for minor informalities: Claim 17 should recite An isolated cell...
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-7, 9, 17, and 20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
Claims 1-4 (and claims depending therefrom) recite a promoter sequence for use in expression of a transgene under control of the promoter sequence in a CD3+ cell, the promoter sequence comprising a fragment consisting of nucleotides 1501-2000, 1001-2000, or 501-2000 of any of SEQ ID NOs: 3, 7-8, or 14-16, or comprising SEQ ID NOs 3, 7-8, or 14-16, or a variant thereof having at least 95% identity to said fragment or said sequence.
Those broad claims encompass the large genus and sub-genera of sequences that have at least 95% identity to SEQ ID NOs 3, 7-8, or 14-16 or to nucleotides 1501-2000, 1001-2000, or 501-2000 of any of SEQ ID NOs: 3, 7-8, or 14-16. Any nucleic acid sequence having at least 95% identity to SEQ ID NOs 3, 7-8, or 14-16 or any of the portions thereof (i.e., nucleotides 1501-2000, 1001-2000, or 501-2000 of any of SEQ ID NOs: 3, 7-8, or 14-16) would be encompassed by the claims as instantly presented. Claims 1-4 recite the large genus/subgenera of promoter sequences and variants that are used to express any transgene.
Claim 6 recites that the promoter is capable of expressing the transgene at a higher level in CD3+ cells compare to CD3- cells. Claim 6 recites a genus of items identified solely by their function: the promoter is capable of expressing the transgene at a higher level in CD3+ cells compare to CD3- cells.
Claims 9 and 17 recite a nucleic acid molecule comprising the promoter sequences of Claim 1 and a cell comprising the nucleic acid molecule of Claim 9. Those broad claims encompass the large genus of nucleic acid molecules comprising the promoter sequences of Claim 1. Any nucleic acid molecule comprising the promoter sequences of Claim 1 (including having at least 95% identity to SEQ ID NOs 3, 7-8, or 14-16) would be encompassed by the claims as instantly presented.
Claim 20 recites a nanoparticle (NP) comprising the vector of Claim 9 wherein the NP is capable of delivery of the vector into a CD3+ cell. The broad claim encompasses the large genus of NP that are capable of delivery of the vector. Claim 20 recites a genus of items identified solely by their function: the NP is capable of delivery of the vector into a CD3+ cell.
An original claim may lack written description support when a broad genus claim is presented but the disclosure only describes a narrow species with no evidence that the genus is contemplated. See Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1349-50 (Fed. Cir. 2010) (en banc). The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. See MPEP 2163.
Regarding Claims 1-4, sequences that have at least 95% identity to either SEQ ID NOs 3, 7-8, or 14-16 or to nucleotides 1501-2000, 1001-2000, or 501-2000 of any of SEQ ID NOs: 3, 7-8, or 14-16 encompasses a large genus of nt sequences that may be ≤5% different from SEQ ID NOs 3, 7-8, or 14-16. A nt sequence could be or have:
up to 5% of the nts removed from SEQ ID NOs 3, 7-8, or 14-16,
a single chunk comprising ≤5% of the nts different from SEQ ID NOs 3, 7-8, or 14-16,
every 20th nt (starting at any position) different from SEQ ID NOs 3, 7-8, or 14-16,
every 20th nt (starting at any position) removed from SEQ ID NOs 3, 7-8, or 14-16,
any other combination of nts mutated or removed from SEQ ID NOs 3, 7-8, or 14-16 as long as the total adds up to ≤5% of total nts.
Each of those categories comprises a broad subgenus with diverse members and different structures that affect their functions. Since SEQ ID NOs 3, 7-8, or 14-16 are each 2000 nt, that means as many as 100 nt could be altered or absent or added to SEQ ID NOs 3, 7-8, or 14-16. Some of those sequence structures may have altered promoter activity or other altered function(s) (e.g., when it comes to expressing a transgene). For example, Smale (and Kadonaga. 2003. The RNA Polymerase II Core Promoter. Annu. Rev. Biochem. 72:449-479, “Smale”, of record) teaches (§PROPERTIES OF RNA POLYMERASE II CORE PROMOTER ELEMENTS) core elements that are required for transcription. 5% alteration to the claimed SEQ ID NOs 3, 7-8, or 14-16 or truncated sequences could result in those necessary elements being lost. At the same time, Wikipedia (“Promoter (genetics)”. Available online at en.wikipedia.org. Accessed on 22 October 2025, “Wikipedia”, of record) teaches (§Eukaryotic) there is no such thing as a set of “universal elements” found in every core promoter. Since the required elements can vary, an adequate written description describing those elements is required to substantiate that the full scope of the claims was in Applicant’s possession at time of filing.
Aside from disclosing (starting at p. 23) SEQ ID NOs 3, 7-8, or 14-16 themselves, the Spec. does not provide any guidance on what portions of SEQ ID NOs 3, 7-8, or 14-16 may or may not be altered. Regarding what structure is encompassed by the sequences that have at least 95% identity to either SEQ ID NOs 3, 7-8, or 14-16 or to nucleotides 1501-2000, 1001-2000, or 501-2000 of any of SEQ ID NOs: 3, 7-8, or 14-16, the Spec. does not provide information describing requisite features. The Spec. does not disclose what physical structure(s) are required for their invention. Furthermore, the claims recite the intended use of expressing a transgene. But the Spec. does not disclose what structures may or may not be altered or how any alterations may or may not affect transgene expression.
Applicant’s examples show possession of the claimed SEQ ID NOs 3, 7-8, or 14-16 and portions of them (i.e., nucleotides 1501-2000, 1001-2000, or 501-2000 of any of SEQ ID NOs: 3, 7-8, or 14-16), but not sequences having 95% identity to those sequences. The examples shown/discussed are not sufficient to provide written description support for sequences having 95% identity to the claimed sequences.
Although the Specification teaches the examples discussed above, it does not identify a core structure or nucleotide sequence (or way to identify such a sequence) of which at least 95% must be preserved and which is common among various members of the claimed genus. No core structure, partial structure, physical or chemical property, or functional characteristic coupled with a known or disclosed structure/function relationship of a promoter sequence comprising a sequence having at least 95% identity to nts 1501-2000, 1001-2000, or 501-2000 of SEQ ID NOs 3, 7-8, or 14-16, or a sequence having at least 95% identity to SEQ ID NOs 3, 7-8, or 14-16 is disclosed in such a way to demonstrate possession of the full invention as claimed at time of filing.
The specification teaches only these species within the claimed genus/genera: SEQ ID NOs 3, 7-8, or 14-16 themselves. But those are only a paltry number compared with the breadth of what is claimed. Altogether, the number of species disclosed by complete structure is not sufficient to provide the written description support for the huge genera and subgenera that are encompassed by the claims: a promoter sequence comprising a sequence having at least 95% identity to nts 1501-2000, 1001-2000, or 501-2000 of SEQ ID NOs 3, 7-8, or 14-16, or a sequence having at least 95% identity to SEQ ID NOs 3, 7-8, or 14-16.
Regarding Claim 6, the Spec. discloses (starts on p. 5, final ¶) the promoter sequence is capable of selectively promoting expression of a transgene in CD3+ cells compared to CD3- cells. However, the Spec. does not disclose what structure(s) makes the promoter capable of expressing the transgene at a higher level in CD3+ cells compared to CD3- cells.
Claim 6 recites a functional characteristics (i.e., the promoter sequence is capable of selectively promoting expression of a transgene in CD3+ cells compared to CD3- cells), but the functional characteristic is not coupled with any known structure. An artisan therefore would not know whether or not a promoter having a truncated/altered sequence or having at least 95% identity to the claimed SEQ ID NOs is capable of expressing the transgene at a higher level in a CD3+ cell compared to a CD3- cell.
The Spec. does not identify a core structure necessary for performing the claimed function(s) of selectively promoting expression of a transgene in CD3+ cells compared to CD3- cells. The Spec. does not disclose any core structure, partial structure, physical or chemical property, or functional characteristic coupled with a known or disclosed structure/function relationship responsible for selectively promoting expression of a transgene in CD3+ cells compared to CD3- cells in such a way to demonstrate possession of the full invention as claimed at time of filing.
Regarding Claims 9 and 17, the Spec. does not disclose any nucleic acid molecules that comprise the promoter sequence of Claim 1 aside from SEQ ID NOs 3, 7-8, or 14-16 themselves.
Although Claims 9 and 17 recite the huge genera of nucleic acid molecules comprising the promoter sequence of Claim 1, they have not demonstrated possession of the full invention as claimed at time of filing.
Regarding Claim 20, the Spec. does not disclose what structure makes the NP deliver the vector into a CD3+ cell. Although Claim 20 recites a functional characteristics (i.e., wherein the NP delivers the vector into a CD3+ cell), the functional characteristic is not coupled with any known structure. The Examples teach that (p. 22) NP comprising “bald” lentiviral vectors (LV) resulted in no expression of GFP, and they describe that nanoparticles comprising poly(beta-amino ester)s (PBAEs) restored their transduction efficiency. That indicates that the NP comprising PBAE were capable of delivery of the vector into a CD3+ cell. However, the Spec. has described no core structure responsible for the claimed function. An artisan therefore would not know whether a NP is or is not capable of delivering the vector into a CD3+ cell.
Although the Specification teaches the examples discussed above, it does not identify a core structure necessary for performing the claimed function(s) of delivering the vector into a CD3+ cell. The Spec. does not disclose any core structure, partial structure, physical or chemical property, or functional characteristic coupled with a known or disclosed structure/function relationship responsible for delivering the vector into a CD3+ cell in such a way to demonstrate possession of the full invention as claimed at time of filing.
The specification teaches only these species within the claimed genus/genera: PBAEs. But those are only a paltry number compared with the breadth of what is claimed. Altogether, the Spec. has not described what makes a NP capable or not capable of delivering a vector into a CD3+ cell. The number of species of things that make a NP deliver a vector into a CD3+ cell disclosed by complete structure is not sufficient to provide the written description support for the huge genera encompassed by the claims.
Altogether, the Spec. does not disclose: what structures must be preserved from SEQ ID NOs 3, 7-8, or 14-16, the structure that makes the promoter express the transgene at a higher level in CD3+ cells compared to CD3- cells, or the structure that makes a NP deliver the vector into a CD3+ cell. The Spec. has not disclosed a representative number of transgenes or nucleic acid molecules comprising the promoter.
While none of these elements is specifically required to demonstrate possession, in combination their absence means that one skilled in the art at the time of filing would conclude that the inventors lacked possession of the full breadth of the invention claimed. Claims 1-4, 6, 9, and 20 are rejected for failing to demonstrate possession of the claimed invention. Claims 2-7, 9, 17, and 20 are rejected because they depend from Claim(s) 1-3 and/or 9 and do not remedy the issues.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Section 33(a) of the America Invents Act reads as follows:
Notwithstanding any other provision of law, no patent may issue on a claim directed to or encompassing a human organism.
Claims 1-7, 9, 17, and 20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a product of nature without significantly more.
The claim(s) recite(s) a promoter sequence for use in expression of a transgene under control of the promoter sequence in a CD3+ cell, the promoter sequence comprising a fragment of any of SEQ ID NOs 3, 7-8, or 14-16, the fragment consisting of nucleotides 1501-2000, 1001-2000, or 501-2000 of any of SEQ ID NOs 3, 7-8, or 14-16, or a variant thereof having at least 95% identity to said fragment, or comprising a variant of any one of SEQ ID NOs 3, 7-8, or 14-16, wherein the variant has at least 95% identity to said sequence (Claims 1-4); wherein the promoter sequence comprises a binding sequence for one or more transcription factors selected from the group consisting of… (Claim 5); wherein the promoter expresses the transgene at a higher level in CD3+ cells compared to CD3- cells (Claim 6); wherein the ratio of expression in CD3+ cells to CD3- cells is at least 2:1 (Claim 7); a… nucleic acid molecule comprising the promoter sequence of Claim 1 (Claim 9); an isolated cell comprising the nucleic acid molecule of Claim 9 (Claim 17); and a nanoparticle comprising the vector of Claim 9, wherein the nanoparticle delivers the vector into a CD3+ cell (Claim 20).
This judicial exception is not integrated into a practical application because the recited sequences exist in cells in Nature. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the sequences exist within cells in Nature.
Claims 1-4 recite a promoter sequence for use in expression of a transgene under control of a promoter sequence in a CD3+ cell, the promoter sequence comprising nucleotides 1501-2000, 1001-2000, or 501-2000 of SEQ ID NOs 3, 7-8, or 14-16, or a variant having at least 95% identity to any of those sequences, or comprising SEQ ID NO 2.
Claim 5 recites that the promoter comprises binding sequences for a number of transcription factors.
Claims 6 and 7 recite that the promoter expresses the transgene at a higher level in CD3+ cells vs CD3- cells, including at a ratio of 2:1 higher expression in CD3+ cells.
Claim 9 recites a vector/plasmid/nucleic acid molecule comprising the promoter sequence; Claim 17 recites a cell comprising a vector/plasmid/nucleic acid molecule comprising the promoter sequence; and Claim 20 recites a nanoparticle comprising the promoter sequence.
The claimed characteristics are not markedly different from the product’s naturally occurring counterpart in the natural state. This judicial exception is not integrated into a practical application because the claims do not provide a promoter that is markedly different from its naturally occurring counterpart (Claims 1-7, 9, and 17) or a promoter that is markedly different from something routine and conventional (Claim 20).
Step 1 – Statutory Category: The claimed invention is either a composition of matter or a manufacture. Under 35 USC 101, the claimed invention must be “any new and useful process, machine, manufacture, or composition of matter.” The composition comprising a promoter sequence comprising a fragment of any one of SEQ ID NOs 3, 7-8, or 14-16 [wherein the fragment consists of nt 1501-2000, 1101-2000, or 501-2000 of those SEQ ID NOs] or a variant thereof having at least 95% identity to said fragment, or a promoter sequence comprising a variant of the nt sequence of any one of SEQ ID NOs 3, 7-8, or 14-16, wherein the variant has at least 95% identity to said sequence can be considered a composition of matter or a manufactured product. Therefore, the composition falls under one of the statutory categories identified in 35 USC 101.
Step 2A Judicial Exception – Prong 1 (Nature of the claim recitation & Markedly different characteristics analysis): Prong 1 asks whether the claim recites an abstract idea, law of nature, or natural phenomenon (product of nature). Even a composition or a manufactured product may not be patent-eligible if it falls under a judicial exception. Nature-based products falling within the judicial exception can include 1) naturally occurring products or 2) those that are not naturally occurring but have characteristics that are not markedly different from a naturally occurring counterpart. The Federal Circuit in University of Utah Research Foundation v. Ambry Genetics (Fed. Circ. December 2014) held claimed synthetically made primers that have the identical nucleotide sequences as portions (i.e., fragments) of naturally occurring nucleic acids are ineligible nature-based products. The court reasoned that simply being synthetic or non-naturally created is not enough for eligibility when the identical sequences occur in nature.
The instantly claimed invention is a composition but recites the promoter comprises a variant of a fragment of certain SEQ ID NOs wherein the variant has at least 95% identity to the fragment or sequence, and those fragments are found within the human genome. The following sequence alignment demonstrates that a sequence at least 95% identical to SEQ ID NO 3 is found within the human genome:.
RESULT 2
OZ163366s2
LOCUS OZ163366s2 6526234 bp DNA linear PRI 25-AUG-2024
COMMENT segment of length 6526234: from 12000001 to 18526234
DEFINITION Homo sapiens genome assembly, chromosome: contig-478.
ACCESSION OZ163366
VERSION OZ163366.1
DBLINK BioProject: PRJEB78558
BioSample: SAMEA115885572
KEYWORDS .
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
REFERENCE 1
AUTHORS Yilmaz,F.
TITLE Direct Submission
JOURNAL Submitted (03-AUG-2024) THE JACKSON LABORATORY, Charle Lee Lab, 10
Discovery Drive, Farmington, CT, USA
FEATURES Location/Qualifiers
source 1..18526234
/organism="Homo sapiens"
/mol_type="genomic DNA"
/db_xref="taxon:9606"
/chromosome="contig-478
Query Match 99.9%; Score 1998.4; Length 6526234;
Best Local Similarity 99.9%;
Matches 1999; Conservative 0; Mismatches 1; Indels 0; Gaps 0;
Qy 1 TTTTCCACTGCCCTTCTCAGCCCCACAGGCCTTCAGGAAGACCCGAACTTCAAGCAAAGC 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2316911 TTTTCCACTGCCCTTCTCAGCCCCACAGGCCTTCAGGAAGACCCGAACTTCAAGCAAAGC 2316970
Qy 61 CTTTTTATTTTTCAACACCCACAGCTTCCATTCAACAATCAGAAGTTTTCCACTTTGATC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2316971 CTTTTTATTTTTCAACACCCACAGCTTCCATTCAACAATCAGAAGTTTTCCACTTTGATC 2317030
Qy 121 AAAGAGGCTGAACAAGAGGGCCAAGGGAGCAGCTGGTTCTCAGCAACTCTGGGCAGACCA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317031 AAAGAGGCTGAACAAGAGGGCCAAGGGAGCAGCTGGTTCTCAGCAACTCTGGGCAGACCA 2317090
Qy 181 CAGAGCCCTTGCTACCCACTCACTGTCCGTGCCCACCAGAGGACACAGCCTTCTCCCCAA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317091 CAGAGCCCTTGCTACCCACTCACTGTCCGTGCCCACCAGAGGACACAGCCTTCTCCCCAA 2317150
Qy 241 ATCAGCCAGGTACATGCCCCAGAAAACACTGGCTTGCCTCGTTCCCACCTTAATTACCGG 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317151 ATCAGCCAGGTACATGCCCCAGAAAACACTGGCTTGCCTCGTTCCCACCTTAATTACCGG 2317210
Qy 301 ACCAAACGAACGTGAACACACTGTTTTCAAAACCAAACTCAATTGGGATCACGGGGGCCT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317211 ACCAAACGAACGTGAACACACTGTTTTCAAAACCAAACTCAATTGGGATCACGGGGGCCT 2317270
Qy 361 CGGTTTCCTTGATTGTAAAATGGGTATATCGCCCCCCACTCTATTTAGCCCAAGAAAACA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317271 CGGTTTCCTTGATTGTAAAATGGGTATATCGCCCCCCACTCTATTTAGCCCAAGAAAACA 2317330
Qy 421 ATTTATCTCTTGATGTCTCTTTCGTCTCCAGGATCTATGCTTTTACAGACTCACTGGGAG 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317331 ATTTATCTCTTGATGTCTCTTTCGTCTCCAGGATCTATGCTTTTACAGACTCACTGGGAG 2317390
Qy 481 GAAATATCCAGACCAAATCCTAAAGCCTGATCTAATTTGGGAGATGCTCAGAAGTTTTGG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317391 GAAATATCCAGACCAAATCCTAAAGCCTGATCTAATTTGGGAGATGCTCAGAAGTTTTGG 2317450
Qy 541 TTCTATGCAAGAACAGCAGTGGTAATAATCCAAGCTTGGCTTTAGACACAGGACGTTTCC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317451 TTCTATGCAAGAACAGCAGTGGTAATAATCCAAGCTTGGCTTTAGACACAGGACGTTTCC 2317510
Qy 601 TTAGGGGCATCTGGGATCTCTGCTGGCTCAAAGTGATGCGCTGCAGACAAAAAGTGAGCA 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317511 TTAGGGGCATCTGGGATCTCTGCTGGCTCAAAGTGATGCGCTGCAGACAAAAAGTGAGCA 2317570
Qy 661 GAAAGGAAAGGAGGTGCTATGCAGAATGAGCTTCTTCCACGGTGATACCAAATGGAGCTT 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317571 GAAAGGAAAGGAGGTGCTATGCAGAATGAGCTTCTTCCACGGTGATACCAAATGGAGCTT 2317630
Qy 721 TCAAAGGCCCACATCTGGAGGCAGCAGCTATGCAGTGATTAACATTTTAAACGGTATTTT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317631 TCAAAGGCCCACATCTGGAGGCAGCAGCTATGCAGTGATTAACATTTTAAACGGTATTTT 2317690
Qy 781 GAAATGGAGATCATTAGTAACCACAGATGTGATCTGACTCTGTCCCCCAGGTAATCTGTC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317691 GAAATGGAGATCATTAGTAACCACAGATGTGATCTGACTCTGTCCCCCAGGTAATCTGTC 2317750
Qy 841 TATTGTATCTAAATTCCAGACTTAGCCCAGTAGACAGCTTGGGATGTTTAACAGGAATTG 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317751 TATTGTATCTAAATTCCAGACTTAGCCCAGTAGACAGCTTGGGATGTTTAACAGGAATTG 2317810
Qy 901 TCCAACACCATCCCCAAATCTATTTTTATTCATGGAGTACTCTGACATCATCTCGCTTGG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317811 TCCAACACCATCCCCAAATCTATTTTTATTCATGGAGTACTCTGACATCATCTCGCTTGG 2317870
Qy 961 TCTTCCTGATGACTGTAATGCAGATTGGGAACAGAGAAAGCCATAAAGACTTGTATGATG 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317871 TCTTCCTGATGACTGTAATGCAGATTGGGAACAGAGAAAGCCATAAAGACTTGTATGATG 2317930
Qy 1021 GCCCAAGGCTAAGAAGGGAAAGGGCTGAGACCACACTTCAGGTTTTAGCTTTCAGGTGCA 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317931 GCCCAAGGCTAAGAAGGGAAAGGGCTGAGACCACACTTCAGGTTTTAGCTTTCAGGTGCA 2317990
Qy 1081 GTGAAGATTGAATGACTTAGCACGAGCTTTCAGCCAGGCAGGCTGCAAAGTGCACCCAAG 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2317991 GTGAAGATTGAATGACTTAGCACGAGCTTTCAGCCAGGCAGGCTGCAAAGTGCACCCAAG 2318050
Qy 1141 TTCTTTCAGTGATCGACACTTGCGACTTAGGTTGAGATAGTTTTCATCCTCCCTGAGCCT 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318051 TTCTTTCAGTGATCGACACTTGCGACTTAGGTTGAGATAGTTTTCATCCTCCCTGAGCCT 2318110
Qy 1201 CAGTTTTCCCATCTGTAAAAAATAAACATTGCCTGCCTCGGAGGGTGGAGGTGGAAGTGG 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318111 CAGTTTTCCCATCTGTAAAAAATAAACATTGCCTGCCTCGGAGGGTGGAGGTGGAAGTGG 2318170
Qy 1261 AATGAAGCCACATGTAACTCCTAGCGCTGTGCCTGAGACAGTAGAGGTTCAATTATAGTA 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318171 AATGAAGCCACATGTAACTCCTAGCGCTGTGCCTGAGACAGTAGAGGTTCAATTATAGTA 2318230
Qy 1321 GTCACATACACACACAACACATACATACACAAGACACAACACACCACACACAACACATAC 1380
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318231 GTCACATACACACACAACACATACATACACAAGACACAACACACCACACACAACACATAC 2318290
Qy 1381 ATACACACCACACACAACACTTACATACGCACCACACTCGGCATGCATTGCAGATCACAA 1440
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318291 ATACACACCACACACAACACTTACATACGCACCACACTCGGCATGCATTGCAGATCACAA 2318350
Qy 1441 ATGCACACCACACACACACTGCATACATATACCATAGAGAACACACAACACCTACACATA 1500
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318351 ATGCACACCACACACACACTGCATACATATACCATAGAGAACACACAACACCTACACATA 2318410
Qy 1501 ACCCCATACCACAAATACACACACACTACATAGTACACCACGCAGAACACACACAGCCCC 1560
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318411 CCCCCATACCACAAATACACACACACTACATAGTACACCACGCAGAACACACACAGCCCC 2318470
Qy 1561 CATATTCCACACCACACCATCTCACTGCCAATTCCTTCCCCTCTTCATGAGTTTTACGGC 1620
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318471 CATATTCCACACCACACCATCTCACTGCCAATTCCTTCCCCTCTTCATGAGTTTTACGGC 2318530
Qy 1621 AGGTCCAGGTTCATCTGCCAGTTTAACAGATCCCAAAACTTCTGCAGGAGTGTTTGTTCA 1680
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318531 AGGTCCAGGTTCATCTGCCAGTTTAACAGATCCCAAAACTTCTGCAGGAGTGTTTGTTCA 2318590
Qy 1681 AAAGATTGATATTTCCAGATTCCTGCTTTCTGACAGTATCTTTGAACCCCAAATTTCATA 1740
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318591 AAAGATTGATATTTCCAGATTCCTGCTTTCTGACAGTATCTTTGAACCCCAAATTTCATA 2318650
Qy 1741 CTGCCATGAGCCAGTCCCCCTTTGGAGAAATATCTCCATTTGTGTGCCCTTTTTCCCCCA 1800
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318651 CTGCCATGAGCCAGTCCCCCTTTGGAGAAATATCTCCATTTGTGTGCCCTTTTTCCCCCA 2318710
Qy 1801 GGGAACCTGCAGCATGTCCCTTTTTCAGCAGTAGCCTATCAAACCGAACCCTTTGGAGTT 1860
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318711 GGGAACCTGCAGCATGTCCCTTTTTCAGCAGTAGCCTATCAAACCGAACCCTTTGGAGTT 2318770
Qy 1861 ATTACACTGCAGTCCGAGGGATCCGGCCTCCCTGAGACCCAGCAAGGACTCATTATCTGG 1920
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318771 ATTACACTGCAGTCCGAGGGATCCGGCCTCCCTGAGACCCAGCAAGGACTCATTATCTGG 2318830
Qy 1921 GGAGGTCTTCTGAGCCACAGGCCTCGCTGAAAGAAGGTGCAGCTTCTTGAACAGGAAGGC 1980
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2318831 GGAGGTCTTCTGAGCCACAGGCCTCGCTGAAAGAAGGTGCAGCTTCTTGAACAGGAAGGC 2318890
Qy 1981 GTTTTGTGGCAGAGTCTAAA 2000
||||||||||||||||||||
Db 2318891 GTTTTGTGGCAGAGTCTAAA 2318910
A BLAST® (NCBI. BLAST® of claimed SEQ ID NOs 3, 8, and 15. Performed on 06 or 07 May 2026, “NCBI”) indicates that at least nt 1001-2000 or SEQ ID NO 3 have at least 95% identity to the gene CD30L (a.k.a. TNFSF8). In addition, data provided by The Human Protein Atlas (“CD30L/TNFSF8” and [see following ¶s] “CTLA4”, “TCF7”, “LCK”, “ITK”, “IL2RA”. Available at proteinatlas.org. Accessed on 06-07 May 2026, “Atlas2”) show that CD30L/TNFSF8 (which an artisan would understand is under the control of its own promoter sequence) is expressed in CD3+ cells, including at a ratio of at least 2:1 (see, e.g., data for § Immune Cell Type Expression [RNA]). Portions of those data are presented here:
PNG
media_image1.png
403
1202
media_image1.png
Greyscale
The following sequence alignment demonstrates that a sequence at least 95% identical to SEQ ID NO 7 is found within the human genome:
RESULT 1
AC010138
LOCUS AC010138 160970 bp DNA linear PRI 16-APR-2005
DEFINITION Homo sapiens BAC clone RP11-175H4 from 2, complete sequence.
ACCESSION AC010138
VERSION AC010138.6
KEYWORDS HTG.
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 160970)
AUTHORS Kozlowicz,A. and Waligorski,J.
TITLE The sequence of Homo sapiens BAC clone RP11-175H4
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 160970)
AUTHORS Waterston,R.H.
TITLE Direct Submission
JOURNAL Submitted (13-SEP-1999) Genome Sequencing Center, Washington
University School of Medicine, 4444 Forest Park Parkway, St. Louis,
MO 63108, USA
REFERENCE 3 (bases 1 to 160970)
AUTHORS Waterston,R.H.
TITLE Direct Submission
JOURNAL Submitted (11-JAN-2002) Genome Sequencing Center, Washington
University School of Medicine, 4444 Forest Park Parkway, St. Louis,
MO 63108, USA
REFERENCE 4 (bases 1 to 160970)
AUTHORS Waterston,R.
TITLE Direct Submission
JOURNAL Submitted (21-FEB-2002) Department of Genetics, Washington
University, 4444 Forest Park Avenue, St. Louis, Missouri 63108, USA
REFERENCE 5 (bases 1 to 160970)
AUTHORS Wilson,R.K.
TITLE Direct Submission
JOURNAL Submitted (16-APR-2005) Genome Sequencing Center, Washington
University School of Medicine, 4444 Forest Park Parkway, St. Louis,
MO 63108, USA
COMMENT On Jan 11, 2002 this sequence version replaced AC010138.5.
-------------- Genome Center
Center: Washington University Genome Sequencing Center
Center code: WUGSC
Web site: http://genome.wustl.edu
Contact: submissions\@watson.wustl.edu
-------------- Summary Statistics
Center project name: H_NH0175H04
--------------.
NOTICE:
This sequence was finished as follows unless otherwise noted:
all regions were double stranded, sequenced with an alternate
chemistry, or covered by high quality data (i.e., phred quality >=
30); an attempt was made to resolve all sequencing problems, such
as compressions and repeats; all regions were covered by sequence
from more than one subclone; and the assembly was confirmed by
restriction digest.
MAPPING INFORMATION:
Mapping information for this clone was provided by Dr. Wes Warren,
Department of Genetics, Washington University, St. Louis MO. For
additional information about the map position of this sequence, see
http://genome.wustl.edu
SOURCE INFORMATION:
The RPCI-11 human BAC library was made from the blood of one male
donor, as described by Osoegawa,K., Woon,P.Y., Zhao,B., Frengen,E.,
Tateno,M., Catanese,J.J. and de Jong,P.J. (1998) An improved
approach for construction of bacterial artificial chromosome
libraries. Genomics 51:1-8. The clone may be obtained either from
Research Genetics, Inc. (http://www.resgen.com) or Pieter de Jong
and coworkers at http://www.chori.org
VECTOR: pBACe3.6
NEIGHBORING SEQUENCE INFORMATION:
The clone sequenced to the left is AF225899, 2000 bp overlap; the
clone sequenced to the right is RP11-278L16. Actual end of this
clone is at base position 160970 of RP11-175H4.
Data from AC103880 was used to finish the clone, AC010138.
FEATURES Location/Qualifiers
source 1..160970
/organism="Homo sapiens"
/mol_type="genomic DNA"
/db_xref="taxon:9606"
/chromosome="2"
/clone="RP11-175H4"
/clone_lib="RPCI-11"
misc_feature 7244..7513
/note="CpG_island (\%GC=59.6, o/e=0.68, #CpGs=19)"
misc_feature 9260..9524
/note="CpG_island (\%GC=62.3, o/e=0.80, #CpGs=20)"
misc_feature 16039..16425
/note="CpG_island (\%GC=72.9, o/e=0.60, #CpGs=34)"
gene 98262..104434
/gene="CTLA4"
mRNA join(98262..98525,101060..101407,101852..101961,
103182..104434)
/gene="CTLA4"
CDS join(98417..98525,101060..101407,101852..101961,
103182..103286)
/gene="CTLA4"
/note="Homo sapiens cytotoxic T-lymphocyte-associated
protein 4 (CTLA4), mRNA.; H_NH0175H04.1;
This gene was based on gi(21361211)"
/codon_start=1
/product="unknown"
/protein_id="AAX93176.1"
/translation="MACLGFQRHKAQLNLATRTWPCTLLFFLLFIPVFCKAMHVAQPA
VVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNELTFLDDSI
CTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVIDPEPCPDS
DFLLWILAAVSSGLFFYSFLLTAVSLSKMLKKRSPLTTGVYVKMPPTEPECEKQFQPY
FIPIN"
misc_feature 142112..142382
/note="CpG_island (\%GC=60.5, o/e=0.92, #CpGs=23)
Query Match 99.9%; Score 1999; Length 160970;
Best Local Similarity 100.0%;
Matches 1999; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 2 AGAAAGCTTTCCAAATCCTGGTGCCTGGCGTATTCCAATAGTCTTCTTCCCAGTCTTCCT 61
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 96259 AGAAAGCTTTCCAAATCCTGGTGCCTGGCGTATTCCAATAGTCTTCTTCCCAGTCTTCCT 96318
Qy 62 GGTTACATTTCTCCCTGAACCCATCCTCCCCATCCCTAAAATTTCCCCCAAATGTGAACT 121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 96319 GGTTACATTTCTCCCTGAACCCATCCTCCCCATCCCTAAAATTTCCCCCAAATGTGAACT 96378
Qy 122 CAGTCATACCAGTTTGCTCCTTATGTTTCATTGGCCCTTGCTGCTAAGAGCATCCGCTTG 181
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 96379 CAGTCATACCAGTTTGCTCCTTATGTTTCATTGGCCCTTGCTGCTAAGAGCATCCGCTTG 96438
Qy 182 CACCTTCTGCTCATCCCCAGACAAGCTTTGTCCTGTGACCATAATGAACTCTTCATGCCG 241
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 96439 CACCTTCTGCTCATCCCCAGACAAGCTTTGTCCTGTGACCATAATGAACTCTTCATGCCG 96498
Qy 242 TTTCCAACTTTAGCCCATGTTATTCTTCTTGTCTGAATATCCACCCTTTTCTCTGTTCTC 301
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 96499 TTTCCAACTTTAGCCCATGTTATTCTTCTTGTCTGAATATCCACCCTTTTCTCTGTTCTC 96558
Qy 302 AATAATAAGTTCAGGCTTTTCGTCTTCTGAGAAGCCCTTTCTGACTTCCACAGGCTGAAC 361
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 96559 AATAATAAGTTCAGGCTTTTCGTCTTCTGAGAAGCCCTTTCTGACTTCCACAGGCTGAAC 96618
Qy 362 CACTGGCTTCTGCTCCTCTACATAATACTTCAATTCCAGCATTGATCTCACTCTATCATG 421
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 96619 CACTGGCTTCTGCTCCTCTACATAATACTTCAATTCCAGCATTGATCTCACTCTATCATG 96678
Qy 422 ATCATGGGTTTAGCTGTCTGTCCCTGCCACTGCTGTGTGTTCCTCTTGAGGGCAGGAACA 481
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 96679 ATCATGGGTTTAGCTGTCTGTCCCTGCCACTGCTGTGTGTTCCTCTTGAGGGCAGGAACA 96738
Qy 482 TTTGTTTTTCACTTTTTAAAAAACCTCTGTTGCCCAGTCTGGCATTAGGAAGTGCCCATT 541
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 96739 TTTGTTTTTCACTTTTTAAAAAACCTCTGTTGCCCAGTCTGGCATTAGGAAGTGCCCATT 96798
Qy 542 AGGTTGTTATTGCTTGTTGGCGCTTGAGCTGGGGCTTGAAGGTTTCTATAATGTGTAGCA 601
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 96799 AGGTTGTTATTGCTTGTTGGCGCTTGAGCTGGGGCTTGAAGGTTTCTATAATGTGTAGCA 96858
Qy 602 GTGTATAGAAAACAGGCAGGTCAGAAAAGGCTTCTGTGCATCACACCAACATGGCACATG 661
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 96859 GTGTATAGAAAACAGGCAGGTCAGAAAAGGCTTCTGTGCATCACACCAACATGGCACATG 96918
Qy 662 TATACATATGTAACAAATCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATA 721
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 96919 TATACATATGTAACAAATCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATA 96978
Qy 722 ATAATAAAATTTTAAAAAAAAAAAGAAGAGGCTTCCTGGAGGAGATGACAGCTGAGCTAA 781
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 96979 ATAATAAAATTTTAAAAAAAAAAAGAAGAGGCTTCCTGGAGGAGATGACAGCTGAGCTAA 97038
Qy 782 GTCCTGGAGGATGAGAAGGAGTATAAAATAAGATAATAGGAGAAAAAAGGCAGTAGGAAC 841
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97039 GTCCTGGAGGATGAGAAGGAGTATAAAATAAGATAATAGGAGAAAAAAGGCAGTAGGAAC 97098
Qy 842 AGCATGGGTAAAGGTGATGAGGCCTGAAAGAGGCACGTGGAAGGAAAGACAAATGCAGGA 901
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97099 AGCATGGGTAAAGGTGATGAGGCCTGAAAGAGGCACGTGGAAGGAAAGACAAATGCAGGA 97158
Qy 902 AGGGGGAATGGGAGGGAATGCTGGGGTACAGGCCAAAGAGGGAGGCATTTGGTGAGTATT 961
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97159 AGGGGGAATGGGAGGGAATGCTGGGGTACAGGCCAAAGAGGGAGGCATTTGGTGAGTATT 97218
Qy 962 CTGCAGAGTCTCCTCTGCTGTGCTGAGGTGTGGACAATGGGAAACCATGGACGGACTGGA 1021
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97219 CTGCAGAGTCTCCTCTGCTGTGCTGAGGTGTGGACAATGGGAAACCATGGACGGACTGGA 97278
Qy 1022 GTAGGCAAATGTCATATTCCCTGTTACAACTGTCTGTTTGCATGTCAGCCTTCTAGAAGC 1081
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97279 GTAGGCAAATGTCATATTCCCTGTTACAACTGTCTGTTTGCATGTCAGCCTTCTAGAAGC 97338
Qy 1082 CCCTTAAGGTATCAACTATGTTTTTGTTTTGTCATCATTCAATCCTAAGTGCACAGAATT 1141
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97339 CCCTTAAGGTATCAACTATGTTTTTGTTTTGTCATCATTCAATCCTAAGTGCACAGAATT 97398
Qy 1142 CCGGGCATATTACAGGTTCCCCATGAATGTTTCTTTCTTTATTAAAATGTATGAAAACTC 1201
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97399 CCGGGCATATTACAGGTTCCCCATGAATGTTTCTTTCTTTATTAAAATGTATGAAAACTC 97458
Qy 1202 TCCAGATTTAAGGAAGGTCCTCAATGTTTCAAATTCTTTTTGTTAGATCATTGGTCCTGT 1261
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97459 TCCAGATTTAAGGAAGGTCCTCAATGTTTCAAATTCTTTTTGTTAGATCATTGGTCCTGT 97518
Qy 1262 CTACAGCTGTCACAAATTTAAGGACTCTGGTTATATTTAATCTTCACTTTTGAATTTTCT 1321
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97519 CTACAGCTGTCACAAATTTAAGGACTCTGGTTATATTTAATCTTCACTTTTGAATTTTCT 97578
Qy 1322 GCTTGAAAAATTTGTATTAGAAAAAAAAGTCTATCCTTTTATGGACGGCTCTAATCTCTT 1381
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97579 GCTTGAAAAATTTGTATTAGAAAAAAAAGTCTATCCTTTTATGGACGGCTCTAATCTCTT 97638
Qy 1382 GAATCATTTGGGTTGGCTTTTCTTTGGACCTTCTTCAACTCTGTTTTGTCTCTGTTGAGT 1441
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97639 GAATCATTTGGGTTGGCTTTTCTTTGGACCTTCTTCAACTCTGTTTTGTCTCTGTTGAGT 97698
Qy 1442 TAAGGCTTTTAAGAACACCTGAATTCTTTCCTTCTGCAAAACCAGAGGCAGCTTCTTTTC 1501
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97699 TAAGGCTTTTAAGAACACCTGAATTCTTTCCTTCTGCAAAACCAGAGGCAGCTTCTTTTC 97758
Qy 1502 CGCCTATTTTCAGTTTATTTCTTGTGATTTTAGTTTTTTTCTCTTAACCAAATGCTAAAT 1561
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97759 CGCCTATTTTCAGTTTATTTCTTGTGATTTTAGTTTTTTTCTCTTAACCAAATGCTAAAT 97818
Qy 1562 GGATTTAGGAGAAATAAACTTATTTGTAAAGCTGTCAAGGGACCATTAGAAGGATGGTGC 1621
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97819 GGATTTAGGAGAAATAAACTTATTTGTAAAGCTGTCAAGGGACCATTAGAAGGATGGTGC 97878
Qy 1622 TTCACAGATAGAATACAGTTTTTATTAATGATGCCTAGACAAATCCTGCCATTAGCCCAA 1681
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97879 TTCACAGATAGAATACAGTTTTTATTAATGATGCCTAGACAAATCCTGCCATTAGCCCAA 97938
Qy 1682 GGGCTCAGAAAGTTAGCAGCCTAGTAGTTTTGGAGTTGTCAATGAAATGAATTGGACTGG 1741
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97939 GGGCTCAGAAAGTTAGCAGCCTAGTAGTTTTGGAGTTGTCAATGAAATGAATTGGACTGG 97998
Qy 1742 ATGGTTAAGGATGCCCAGAAGATTGAATAAAATTGGGATTTAGGAGGACCCTTGTACTCC 1801
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 97999 ATGGTTAAGGATGCCCAGAAGATTGAATAAAATTGGGATTTAGGAGGACCCTTGTACTCC 98058
Qy 1802 AGGAAATTCTCCAAGTCTCCACTTAGTTATCCAGATCCTCAAAGTGAACATGAAGCTTCA 1861
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 98059 AGGAAATTCTCCAAGTCTCCACTTAGTTATCCAGATCCTCAAAGTGAACATGAAGCTTCA 98118
Qy 1862 GTTTCAAATTGAATACATTTTCCATCCATGGATTGGCTTGTTTTGTTCAGTTGAGTGCTT 1921
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 98119 GTTTCAAATTGAATACATTTTCCATCCATGGATTGGCTTGTTTTGTTCAGTTGAGTGCTT 98178
Qy 1922 GAGGTTGTCTTTTCGACGTAACAGCTAAACCCACGGCTTCCTTTCTCGTAAAACCAAAAC 1981
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 98179 GAGGTTGTCTTTTCGACGTAACAGCTAAACCCACGGCTTCCTTTCTCGTAAAACCAAAAC 98238
Qy 1982 AAAAAGGCTTTCTATTCAA 2000
|||||||||||||||||||
Db 98239 AAAAAGGCTTTCTATTCAA 98257
In addition, data provided by Atlas2 show that CTLA4 (which an artisan would understand is under the control of its own promoter sequence in a natural setting) is expressed in CD3+ cells, including at a ratio of at least 2:1 (see, e.g., data for §Immune Cell Type Expression [RNA]). Portions of those data are presented here:
PNG
media_image2.png
392
1187
media_image2.png
Greyscale
The following sequence alignment demonstrates that a sequence at least 95% identical to SEQ ID NO 8 is found within the human genome:
RESULT 1
AC008608
LOCUS AC008608 160672 bp DNA linear PRI 15-DEC-2001
DEFINITION Homo sapiens chromosome 5 clone CTB-113I20, complete sequence.
ACCESSION AC008608
VERSION AC008608.7
KEYWORDS HTG.
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 160672)
AUTHORS DOE Joint Genome Institute and Stanford Human Genome Center.
TITLE Direct Submission
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 160672)
AUTHORS DOE Joint Genome Institute.
TITLE Direct Submission
JOURNAL Submitted (03-AUG-1999) Production Sequencing Facility, DOE Joint
Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
REFERENCE 3 (bases 1 to 160672)
AUTHORS DOE Joint Genome Institute and Stanford Human Genome Center.
TITLE Direct Submission
JOURNAL Submitted (15-DEC-2001) DOE Joint Genome Institute, 2800 Mitchell
Drive, Walnut Creek, CA 94598, USA
COMMENT On Dec 15, 2001 this sequence version replaced AC008608.6.
Draft Sequence Produced by DOE Joint Genome Institute
www.jgi.doe.gov
Finishing Completed at Stanford Human Genome Center
www-shgc.stanford.edu
Quality: Phrap Quality >=40 99.4\% of Sequence;
Estimated Total Number of Errors is 0.7.
FEATURES Location/Qualifiers
source 1..160672
/organism="Homo sapiens"
/mol_type="genomic DNA"
/db_xref="taxon:9606"
/chromosome="5"
/clone="CTB-113I20
Query Match 99.9%; Score 1999; Length 160672;
Best Local Similarity 100.0%;
Matches 1999; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 2 GAGGCGTGAGCGTCTACAGTGAACCCAGCACAGAAACCTGCTAGGGGAGCTGCTGTTGAC 61
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141447 GAGGCGTGAGCGTCTACAGTGAACCCAGCACAGAAACCTGCTAGGGGAGCTGCTGTTGAC 141506
Qy 62 TGCATCGCGATCCAAAGGACCGGCGTCTTTTGTAGATGCAGGGGCTGAGCCAGGCCAAGC 121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141507 TGCATCGCGATCCAAAGGACCGGCGTCTTTTGTAGATGCAGGGGCTGAGCCAGGCCAAGC 141566
Qy 122 GCGCCGTGGAGGCCCGCGTGGACGCAGACCCGGGTGCCATACAGATGCGCTGGAATCCAG 181
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141567 GCGCCGTGGAGGCCCGCGTGGACGCAGACCCGGGTGCCATACAGATGCGCTGGAATCCAG 141626
Qy 182 GCACTTTCCCGCGCTCCGCAAATCTAGATGTTTCAGCCTGGATCGAGCGAGGGTTAGAGG 241
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141627 GCACTTTCCCGCGCTCCGCAAATCTAGATGTTTCAGCCTGGATCGAGCGAGGGTTAGAGG 141686
Qy 242 GTTAGTCAGGCCAGGGTCAACTTCAGAGTCATGGGCTCCCTAAATGCGACTTCTAGGGTT 301
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141687 GTTAGTCAGGCCAGGGTCAACTTCAGAGTCATGGGCTCCCTAAATGCGACTTCTAGGGTT 141746
Qy 302 GAGTTGCTGTGGACGAGCGACCCATGTCGGAATCCCGCGCCCACGTGGCTGCCCAAAGTT 361
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141747 GAGTTGCTGTGGACGAGCGACCCATGTCGGAATCCCGCGCCCACGTGGCTGCCCAAAGTT 141806
Qy 362 CCGAGTCTCCGGGCTGCAGGTTCTAGTCACGGAACCGAGTTGGGAGAGTCATAGGGGCTG 421
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141807 CCGAGTCTCCGGGCTGCAGGTTCTAGTCACGGAACCGAGTTGGGAGAGTCATAGGGGCTG 141866
Qy 422 GGACTTGGAGGATCGGCTGAGGTCCGGTGCTCTTGGCTGTGTTCGCGGCTCGGAGCCGTC 481
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141867 GGACTTGGAGGATCGGCTGAGGTCCGGTGCTCTTGGCTGTGTTCGCGGCTCGGAGCCGTC 141926
Qy 482 GCCTGACTGAGGGGCCCGTCACAGATGTGTGATGTATAAGCTCTGCACGCAACAGGAGCT 541
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141927 GCCTGACTGAGGGGCCCGTCACAGATGTGTGATGTATAAGCTCTGCACGCAACAGGAGCT 141986
Qy 542 CAATAAATGTGCGAAGGGGGGTATACTTATGTTCGCACTGTATGCAGGCGGCCTAGAAGG 601
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141987 CAATAAATGTGCGAAGGGGGGTATACTTATGTTCGCACTGTATGCAGGCGGCCTAGAAGG 142046
Qy 602 AAGTCCCTGATTGGCACAGGGATGGAGGATGGGGCAAGAGCCGCAACAGCGCCGCGGAGT 661
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142047 AAGTCCCTGATTGGCACAGGGATGGAGGATGGGGCAAGAGCCGCAACAGCGCCGCGGAGT 142106
Qy 662 TCCAACGCTGCCGGTTCCCTGGGGTACGAGCACAGCCTCAAGCAGCCTCAAGCCCTAGGA 721
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142107 TCCAACGCTGCCGGTTCCCTGGGGTACGAGCACAGCCTCAAGCAGCCTCAAGCCCTAGGA 142166
Qy 722 AGCCCCCAGTTCAAAGCACAGGGCGCATTGGAGCCTGGGCACGATACAGTTCACACCACG 781
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142167 AGCCCCCAGTTCAAAGCACAGGGCGCATTGGAGCCTGGGCACGATACAGTTCACACCACG 142226
Qy 782 GCTGCGATGGTAAGCCACGCCCAAGTCCCAAGGGCCTAGGGGACCCCCGCCCTCCACAGC 841
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142227 GCTGCGATGGTAAGCCACGCCCAAGTCCCAAGGGCCTAGGGGACCCCCGCCCTCCACAGC 142286
Qy 842 CGGAGGAGAAACCTGGGCGCAGAAAGCAGGGGGAATATCTGGTTGTAGGTGAGTAAGCGG 901
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142287 CGGAGGAGAAACCTGGGCGCAGAAAGCAGGGGGAATATCTGGTTGTAGGTGAGTAAGCGG 142346
Qy 902 GGTCAGGAGTTCCCGTTAGAGTCTCTGCGTTTCGGGAGAAGGGTGATCATTCCCAGGCTT 961
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142347 GGTCAGGAGTTCCCGTTAGAGTCTCTGCGTTTCGGGAGAAGGGTGATCATTCCCAGGCTT 142406
Qy 962 GTCCGACGTCTCTCTCAGGGTGCGCTCCGGAAGAGCGAGCCCTTTAAGGCTATGCCGAGT 1021
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142407 GTCCGACGTCTCTCTCAGGGTGCGCTCCGGAAGAGCGAGCCCTTTAAGGCTATGCCGAGT 142466
Qy 1022 GGGCGCGTCCCGGCCTCTCCCGGGAGAGGAGAGGCGGGGCGGACCTGTGTCCCGCCCCCG 1081
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142467 GGGCGCGTCCCGGCCTCTCCCGGGAGAGGAGAGGCGGGGCGGACCTGTGTCCCGCCCCCG 142526
Qy 1082 GCCCGGCCCGCCCCCAGTGCCCGCCCCGCCCCCGGCACTCGGCCGGCGGCGCCTTTGATG 1141
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142527 GCCCGGCCCGCCCCCAGTGCCCGCCCCGCCCCCGGCACTCGGCCGGCGGCGCCTTTGATG 142586
Qy 1142 TTCCGACCCGCCAGCTCGCGGAGCCGCTCTGCCCCGCGCCCTAGCCCGCGCCTGCAGCCC 1201
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142587 TTCCGACCCGCCAGCTCGCGGAGCCGCTCTGCCCCGCGCCCTAGCCCGCGCCTGCAGCCC 142646
Qy 1202 GCCCAGGCGGAGTCAGCCCGCGCTCCGCCCGCCGCGATCCGAGCTCGGAGGTTCGGACTC 1261
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142647 GCCCAGGCGGAGTCAGCCCGCGCTCCGCCCGCCGCGATCCGAGCTCGGAGGTTCGGACTC 142706
Qy 1262 CGGGCTCGCCGCCCCCCGGGCCGGCTCCGCGCCCCGCACTCCCGGCGCCCAGCGCCCCGC 1321
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142707 CGGGCTCGCCGCCCCCCGGGCCGGCTCCGCGCCCCGCACTCCCGGCGCCCAGCGCCCCGC 142766
Qy 1322 GCCCCGGCGGGCGGAGCGCACCATGCCGCAGCTGGACTCCGGCGGGGGCGGCGCGGGCGG 1381
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142767 GCCCCGGCGGGCGGAGCGCACCATGCCGCAGCTGGACTCCGGCGGGGGCGGCGCGGGCGG 142826
Qy 1382 CGGCGACGACCTCGGCGCGCCGGACGAGCTGCTGGCCTTCCAGGATGAAGGCGAGGAGCA 1441
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142827 CGGCGACGACCTCGGCGCGCCGGACGAGCTGCTGGCCTTCCAGGATGAAGGCGAGGAGCA 142886
Qy 1442 GGACGACAAGAGCCGCGACAGCGCCGCCGGTCCCGAGCGCGACCTGGCCGAGCTCAAGTC 1501
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142887 GGACGACAAGAGCCGCGACAGCGCCGCCGGTCCCGAGCGCGACCTGGCCGAGCTCAAGTC 142946
Qy 1502 GTCGCTCGTGAACGAGTCCGAGGGCGCGGCCGGCGGCGCAGGGATCCCGGGGGTCCCGGG 1561
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142947 GTCGCTCGTGAACGAGTCCGAGGGCGCGGCCGGCGGCGCAGGGATCCCGGGGGTCCCGGG 143006
Qy 1562 GGCCGGCGCCGGGGCCCGCGGCGAGGCCGAGGTGAGCCCCCGCCGGCGCCGGCTCCTCCC 1621
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143007 GGCCGGCGCCGGGGCCCGCGGCGAGGCCGAGGTGAGCCCCCGCCGGCGCCGGCTCCTCCC 143066
Qy 1622 CCGCGGTCGCCGCGCCGCGCCGCCCCAGTTGCGCGCGGCCCTCGGGGTCTCCAGCGCGCA 1681
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143067 CCGCGGTCGCCGCGCCGCGCCGCCCCAGTTGCGCGCGGCCCTCGGGGTCTCCAGCGCGCA 143126
Qy 1682 GAGCGTCCCTGCCCCGGCGTCGGCCCCGACCCCCGCGGTCCCACCGCCCCTCACTCCCCT 1741
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143127 GAGCGTCCCTGCCCCGGCGTCGGCCCCGACCCCCGCGGTCCCACCGCCCCTCACTCCCCT 143186
Qy 1742 CCGGTTCTCCCTCCAGGCTCTCGGGCGGGAACACGCTGCGCAGAGACTCTTCCCGGACAA 1801
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143187 CCGGTTCTCCCTCCAGGCTCTCGGGCGGGAACACGCTGCGCAGAGACTCTTCCCGGACAA 143246
Qy 1802 ACTTCCAGAGCCCCTGGAGGACGGTGAGTTTCTGCCCGGCCCGGCTTCCCTTCGTCGCGC 1861
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143247 ACTTCCAGAGCCCCTGGAGGACGGTGAGTTTCTGCCCGGCCCGGCTTCCCTTCGTCGCGC 143306
Qy 1862 TCAGGCCCTGGCCTCGGTGGGACGGGGACGCCAAGGACCGCGGGGAGCCGGGTGCCTCCC 1921
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143307 TCAGGCCCTGGCCTCGGTGGGACGGGGACGCCAAGGACCGCGGGGAGCCGGGTGCCTCCC 143366
Qy 1922 CCACCGCAGCTCAGGAGGCGGCAGAACCCAGGGGTGGAGAGTGGGGGGCGGGCTTCCCGG 1981
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143367 CCACCGCAGCTCAGGAGGCGGCAGAACCCAGGGGTGGAGAGTGGGGGGCGGGCTTCCCGG 143426
Qy 1982 GCGCCGCCGGGTCGAGTCA 2000
|||||||||||||||||||
Db 143427 GCGCCGCCGGGTCGAGTCA 143445
NCBI (cited above) indicates that SEQ ID NO 8 has 100% identity to the gene TCF7. Data provided by Atlas2 show that TCF7 (which an artisan would understand is under the control of its own promoter sequence) is expressed in CD3+ cells, including at a ratio of at least 2:1 (see, e.g., data for § Immune Cell Type Expression [RNA]). Portions of those data are presented here:
PNG
media_image3.png
417
1170
media_image3.png
Greyscale
The following sequence alignment demonstrates that a sequence at least 95% identical to SEQ ID NO 14 is found within the human genome:
RESULT 4
BBG54293
(NOTE: this sequence has 8 duplicates in the database searched.
See complete list at the end of this report)
ID BBG54293 standard; DNA; 34927 BP.
XX
AC BBG54293;
XX
DT 17-JUL-2014 (first entry)
XX
DE Human LCK gene sequence, SEQ ID: 452.
XX
KW LCK gene; Lck tyrosine kinase; colorectal tumor; ds; gene expression;
KW prognosis; tumor marker.
XX
OS Homo sapiens.
XX
CC PN WO2014080381-A1.
XX
CC PD 30-MAY-2014.
XX
CC PF 26-NOV-2013; 2013WO-IB060416.
XX
PR 26-NOV-2012; 2012WO-IB056728.
XX
CC PA (EPFL ) ECOLE POLYTECHNIQUE FEDERALE LAUSANNE.
XX
CC PI Gray J, Hanahan D, Lyssiotis C, Sadanandam A;
XX
DR WPI; 2014-K73017/40.
XX
CC PT In-vitro method for prognosing disease-free survival of patient suffering
CC PT from colorectal cancer, involves providing biological sample, measuring
CC PT gene expression level, and classifying based on expression profile.
XX
CC PS Claim 1; SEQ ID NO 452; 126pp; English.
XX
CC The present invention relates to a novel in-vitro method for the
CC prognosis of disease-free survival of a subject suffering from colorectal
CC cancer. The method comprises: providing a biological sample from the
CC subject; measuring the expression level of one or a combination of genes
CC selected from the group of genes listed in table 2; and classifying the
CC biological sample as stem-like, inflammatory, transit amplifying (TA),
CC goblet-like and enterocyte on the basis of the gene expression profile.
CC The invention further includes: in-vitro method for predicting the
CC likelihood that a subject suffering from or suspected of suffering from
CC colorectal cancer and who has undergone surgical resection of colorectal
CC cancer will respond to therapies inhibiting or targeting epidermal growth
CC factor receptor (EGFR) and/or cMET; and an in-vitro method for predicting
CC the likelihood that a subject suffering from colorectal cancer or
CC suspected of suffering from colorectal cancer and who has undergone a
CC surgical resection of colorectal cancer will respond to cytotoxic
CC chemotherapies. The present sequence represents a subtype specific human
CC LCK gene analyzed by prediction analysis of microarray and is used for
CC the prognosis of disease-free survival of a subject suffering from
CC colorectal cancer.
XX
SQ Sequence 34927 BP; 8875 A; 8322 C; 8997 G; 8733 T; 0 U; 0 Other;
Query Match 100.0%; Score 2000; Length 34927;
Best Local Similarity 100.0%;
Matches 2000; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 AAAAATACAAAAGTTAGCCAAGCGTGATGGTGCATGCCTGTAATCCCAACTACTCAGGAG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 20884 AAAAATACAAAAGTTAGCCAAGCGTGATGGTGCATGCCTGTAATCCCAACTACTCAGGAG 20943
Qy 61 GCCGAGGCAGGAGAATTGCTTGAACCTGGGAGGTAGAGGTTGCAGGAAAAAAAAAAAAGG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 20944 GCCGAGGCAGGAGAATTGCTTGAACCTGGGAGGTAGAGGTTGCAGGAAAAAAAAAAAAGG 21003
Qy 121 TAATATTTCAGCTGAGCCTTGAAGGTTGAGTTAGAATTCAGCAGTTGGACAAAAGAGAGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21004 TAATATTTCAGCTGAGCCTTGAAGGTTGAGTTAGAATTCAGCAGTTGGACAAAAGAGAGC 21063
Qy 181 ATGCCGACTGGGTTCGGTGGTGCATGCCTATAATCCTAGCATTTGGGGAGGCCAAGGCAG 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21064 ATGCCGACTGGGTTCGGTGGTGCATGCCTATAATCCTAGCATTTGGGGAGGCCAAGGCAG 21123
Qy 241 GAGGATTGCTTGAGCCCAGGAGTTCGAGATCAGACTGGGCAACATAGTGAGACCTCATCT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21124 GAGGATTGCTTGAGCCCAGGAGTTCGAGATCAGACTGGGCAACATAGTGAGACCTCATCT 21183
Qy 301 CTACAAAAAAATAATCAGCTGGGCATGATGGTGTGCACCTTTAGTCTCAGCTACTGGGGA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21184 CTACAAAAAAATAATCAGCTGGGCATGATGGTGTGCACCTTTAGTCTCAGCTACTGGGGA 21243
Qy 361 GGTTGAGGTGGGAAGATTGCTTGAGCCCAGGAGGTCTAAGGGGATTGCGCCACTGCACTT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21244 GGTTGAGGTGGGAAGATTGCTTGAGCCCAGGAGGTCTAAGGGGATTGCGCCACTGCACTT 21303
Qy 421 CAGCCTGGGAGAGGAAGGGAGACCCTGTCTCAAGAGAGAGAGAGAAAGAGAGAGAGAGAG 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21304 CAGCCTGGGAGAGGAAGGGAGACCCTGTCTCAAGAGAGAGAGAGAAAGAGAGAGAGAGAG 21363
Qy 481 AGAAAGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGCGAGAGAGCGCA 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21364 AGAAAGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGCGAGAGAGCGCA 21423
Qy 541 CGCATTTCAAAGCAGGGAGAACCACAAGTACAAAGGCATTAAGTAAGAAAATAGCATGGG 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21424 CGCATTTCAAAGCAGGGAGAACCACAAGTACAAAGGCATTAAGTAAGAAAATAGCATGGG 21483
Qy 601 GTGTTTGGGAAAGGCAAGAATAGTTCAGAACACAGGCTGTGTGTGTGGGGGTGTGTGGGG 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21484 GTGTTTGGGAAAGGCAAGAATAGTTCAGAACACAGGCTGTGTGTGTGGGGGTGTGTGGGG 21543
Qy 661 GTGCCTGTGTGTGGGTGTTTGTGTGTGTGTGAGTGTGGGTGTGTGGGGGTATCTATGGAG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21544 GTGCCTGTGTGTGGGTGTTTGTGTGTGTGTGAGTGTGGGTGTGTGGGGGTATCTATGGAG 21603
Qy 721 GGGATGCCTGTGTGTGTGTGTAAGGTGAGTGTGTGGATGTGTGCATGGGTGTGGGTGAGT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21604 GGGATGCCTGTGTGTGTGTGTAAGGTGAGTGTGTGGATGTGTGCATGGGTGTGGGTGAGT 21663
Qy 781 GTGTGGAGGTGCCTGTGTGTGTGTATGAATGTGTGTTGGGGAGGGGAGAATGTGTGTGTG 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21664 GTGTGGAGGTGCCTGTGTGTGTGTATGAATGTGTGTTGGGGAGGGGAGAATGTGTGTGTG 21723
Qy 841 TGGGGTGAGTGCGTGTGTGTGGGGGTGAATGCGTGTGTGTGTGTATGTGGGTGTGACTGT 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21724 TGGGGTGAGTGCGTGTGTGTGGGGGTGAATGCGTGTGTGTGTGTATGTGGGTGTGACTGT 21783
Qy 901 GTGGGTGTGTGGACGAGTGTGTGTGTTCCTGGGTGTGGGAGCCTGTGTGTGTAGGGGGAG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21784 GTGGGTGTGTGGACGAGTGTGTGTGTTCCTGGGTGTGGGAGCCTGTGTGTGTAGGGGGAG 21843
Qy 961 TATGTATAGGGTGTGTGCATGAATGTGTGTGTGGGTACGTGTGTGAGAGTGGGTGCCTGT 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21844 TATGTATAGGGTGTGTGCATGAATGTGTGTGTGGGTACGTGTGTGAGAGTGGGTGCCTGT 21903
Qy 1021 GTGTGGGGGGTGAGTGTGTGTGTGGGGGGGCACTTGTGGAGGGTGAGTGTATGTGTTTAC 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21904 GTGTGGGGGGTGAGTGTGTGTGTGGGGGGGCACTTGTGGAGGGTGAGTGTATGTGTTTAC 21963
Qy 1081 TGAGTGTGAGTGTGGGTGCCTGTGTGTGGGAGGGTGAGTCTGTGTGTGAGTGTGTGGGGG 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21964 TGAGTGTGAGTGTGGGTGCCTGTGTGTGGGAGGGTGAGTCTGTGTGTGAGTGTGTGGGGG 22023
Qy 1141 AGTACCTGTGAGGGGTGAGTGTGTGTGTTTATGTGAAAGTGTGTGTGTGTGGATGCCTCT 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22024 AGTACCTGTGAGGGGTGAGTGTGTGTGTTTATGTGAAAGTGTGTGTGTGTGGATGCCTCT 22083
Qy 1201 GTGGAGGTGGGATAGGGGGTGCCTCTGTGTGTGTGTGTGAGAGTGTGTGTGTGTAGGGTG 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22084 GTGGAGGTGGGATAGGGGGTGCCTCTGTGTGTGTGTGTGAGAGTGTGTGTGTGTAGGGTG 22143
Qy 1261 TGTATATGTATAGGGTGTGTGTGAGTGTGTGTGTGTGAGAGAGTGTGTGTGTGGCAGAAT 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22144 TGTATATGTATAGGGTGTGTGTGAGTGTGTGTGTGTGAGAGAGTGTGTGTGTGGCAGAAT 22203
Qy 1321 AGACTGCGGAGGTGGATTTCATCTTGATATGAAAGGTCTGGAATGCATGGTACATTAAAC 1380
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22204 AGACTGCGGAGGTGGATTTCATCTTGATATGAAAGGTCTGGAATGCATGGTACATTAAAC 22263
Qy 1381 TTTGAGGACAGCGCTTTCCAAGCACTCTGAGGAGCAGCCCTAGAGAAGGAGGAGCTGCAG 1440
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22264 TTTGAGGACAGCGCTTTCCAAGCACTCTGAGGAGCAGCCCTAGAGAAGGAGGAGCTGCAG 22323
Qy 1441 GGACTCCGGGGGCTTCAAAGTGAGGGCCCCACTCTGCTTCAGGCAAAACAGGCACACATT 1500
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22324 GGACTCCGGGGGCTTCAAAGTGAGGGCCCCACTCTGCTTCAGGCAAAACAGGCACACATT 22383
Qy 1501 TATCACTTTATCTATGGAGTTCTGCTTGATTTCATCAGACAAAAAATTTCCACTGCTAAA 1560
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22384 TATCACTTTATCTATGGAGTTCTGCTTGATTTCATCAGACAAAAAATTTCCACTGCTAAA 22443
Qy 1561 ACAGGCAAATAAACAAAAAAAAAGTTATGGCCAACAGAGTCACTGGAGGGTTTTCTGCTG 1620
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22444 ACAGGCAAATAAACAAAAAAAAAGTTATGGCCAACAGAGTCACTGGAGGGTTTTCTGCTG 22503
Qy 1621 GGGAGAAGCAAGCCCGTGTTTGAAGGAACCCTGTGAGATGACTGTGGGCTGTGTGAGGGG 1680
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22504 GGGAGAAGCAAGCCCGTGTTTGAAGGAACCCTGTGAGATGACTGTGGGCTGTGTGAGGGG 22563
Qy 1681 AACAGCGGGGGCTTGATGGTGGACTTCGGGAGCAGAAGCCTCTTTCTCAGCCTCCTCAGC 1740
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22564 AACAGCGGGGGCTTGATGGTGGACTTCGGGAGCAGAAGCCTCTTTCTCAGCCTCCTCAGC 22623
Qy 1741 TAGACAGGGGAATTATAATAGGAGGTGTGGCGTGCACACCTCTCCAGTAGGGGAGGGTCT 1800
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22624 TAGACAGGGGAATTATAATAGGAGGTGTGGCGTGCACACCTCTCCAGTAGGGGAGGGTCT 22683
Qy 1801 GATAAGTCAGGTCTCTCCCAGGCTTGGGAAAGTGTGTGTCATCTCTAGGAGGTGGTCCTC 1860
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22684 GATAAGTCAGGTCTCTCCCAGGCTTGGGAAAGTGTGTGTCATCTCTAGGAGGTGGTCCTC 22743
Qy 1861 CCAACACAGGGTACTGGCAGAGGGAGAGGGAGGGGGCAGAGGCAGGAAGTGGGTAACTAG 1920
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22744 CCAACACAGGGTACTGGCAGAGGGAGAGGGAGGGGGCAGAGGCAGGAAGTGGGTAACTAG 22803
Qy 1921 ACTAACAAAGGTGCCTGTGGCGGTTTGCCCATCCCAGGTGGGAGGGTGGGGCTAGGGCTC 1980
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 22804 ACTAACAAAGGTGCCTGTGGCGGTTTGCCCATCCCAGGTGGGAGGGTGGGGCTAGGGCTC 22863
Qy 1981 AGGGGCCGTGTGTGAATTTA 2000
||||||||||||||||||||
Db 22864 AGGGGCCGTGTGTGAATTTA 22883
Data provided by Atlas2 show that LCK (which an artisan would understand is under the control of its own promoter sequence) is expressed in CD3+ cells (see, e.g., data for § Immune Cell Type Expression [RNA]). Portions of those data are presented here:
PNG
media_image4.png
382
1150
media_image4.png
Greyscale
The following sequence alignment demonstrates that a sequence at least 95% identical to SEQ ID NO 15 is found within the human genome:
RESULT 1
AC008608
LOCUS AC008608 160672 bp DNA linear PRI 15-DEC-2001
DEFINITION Homo sapiens chromosome 5 clone CTB-113I20, complete sequence.
ACCESSION AC008608
VERSION AC008608.7
KEYWORDS HTG.
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 160672)
AUTHORS DOE Joint Genome Institute and Stanford Human Genome Center.
TITLE Direct Submission
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 160672)
AUTHORS DOE Joint Genome Institute.
TITLE Direct Submission
JOURNAL Submitted (03-AUG-1999) Production Sequencing Facility, DOE Joint
Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
REFERENCE 3 (bases 1 to 160672)
AUTHORS DOE Joint Genome Institute and Stanford Human Genome Center.
TITLE Direct Submission
JOURNAL Submitted (15-DEC-2001) DOE Joint Genome Institute, 2800 Mitchell
Drive, Walnut Creek, CA 94598, USA
COMMENT On Dec 15, 2001 this sequence version replaced AC008608.6.
Draft Sequence Produced by DOE Joint Genome Institute
www.jgi.doe.gov
Finishing Completed at Stanford Human Genome Center
www-shgc.stanford.edu
Quality: Phrap Quality >=40 99.4\% of Sequence;
Estimated Total Number of Errors is 0.7.
FEATURES Location/Qualifiers
source 1..160672
/organism="Homo sapiens"
/mol_type="genomic DNA"
/db_xref="taxon:9606"
/chromosome="5"
/clone="CTB-113I20
Query Match 99.9%; Score 1999; Length 160672;
Best Local Similarity 100.0%;
Matches 1999; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 2 GAGGCGTGAGCGTCTACAGTGAACCCAGCACAGAAACCTGCTAGGGGAGCTGCTGTTGAC 61
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141447 GAGGCGTGAGCGTCTACAGTGAACCCAGCACAGAAACCTGCTAGGGGAGCTGCTGTTGAC 141506
Qy 62 TGCATCGCGATCCAAAGGACCGGCGTCTTTTGTAGATGCAGGGGCTGAGCCAGGCCAAGC 121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141507 TGCATCGCGATCCAAAGGACCGGCGTCTTTTGTAGATGCAGGGGCTGAGCCAGGCCAAGC 141566
Qy 122 GCGCCGTGGAGGCCCGCGTGGACGCAGACCCGGGTGCCATACAGATGCGCTGGAATCCAG 181
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141567 GCGCCGTGGAGGCCCGCGTGGACGCAGACCCGGGTGCCATACAGATGCGCTGGAATCCAG 141626
Qy 182 GCACTTTCCCGCGCTCCGCAAATCTAGATGTTTCAGCCTGGATCGAGCGAGGGTTAGAGG 241
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141627 GCACTTTCCCGCGCTCCGCAAATCTAGATGTTTCAGCCTGGATCGAGCGAGGGTTAGAGG 141686
Qy 242 GTTAGTCAGGCCAGGGTCAACTTCAGAGTCATGGGCTCCCTAAATGCGACTTCTAGGGTT 301
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141687 GTTAGTCAGGCCAGGGTCAACTTCAGAGTCATGGGCTCCCTAAATGCGACTTCTAGGGTT 141746
Qy 302 GAGTTGCTGTGGACGAGCGACCCATGTCGGAATCCCGCGCCCACGTGGCTGCCCAAAGTT 361
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141747 GAGTTGCTGTGGACGAGCGACCCATGTCGGAATCCCGCGCCCACGTGGCTGCCCAAAGTT 141806
Qy 362 CCGAGTCTCCGGGCTGCAGGTTCTAGTCACGGAACCGAGTTGGGAGAGTCATAGGGGCTG 421
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141807 CCGAGTCTCCGGGCTGCAGGTTCTAGTCACGGAACCGAGTTGGGAGAGTCATAGGGGCTG 141866
Qy 422 GGACTTGGAGGATCGGCTGAGGTCCGGTGCTCTTGGCTGTGTTCGCGGCTCGGAGCCGTC 481
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141867 GGACTTGGAGGATCGGCTGAGGTCCGGTGCTCTTGGCTGTGTTCGCGGCTCGGAGCCGTC 141926
Qy 482 GCCTGACTGAGGGGCCCGTCACAGATGTGTGATGTATAAGCTCTGCACGCAACAGGAGCT 541
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141927 GCCTGACTGAGGGGCCCGTCACAGATGTGTGATGTATAAGCTCTGCACGCAACAGGAGCT 141986
Qy 542 CAATAAATGTGCGAAGGGGGGTATACTTATGTTCGCACTGTATGCAGGCGGCCTAGAAGG 601
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 141987 CAATAAATGTGCGAAGGGGGGTATACTTATGTTCGCACTGTATGCAGGCGGCCTAGAAGG 142046
Qy 602 AAGTCCCTGATTGGCACAGGGATGGAGGATGGGGCAAGAGCCGCAACAGCGCCGCGGAGT 661
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142047 AAGTCCCTGATTGGCACAGGGATGGAGGATGGGGCAAGAGCCGCAACAGCGCCGCGGAGT 142106
Qy 662 TCCAACGCTGCCGGTTCCCTGGGGTACGAGCACAGCCTCAAGCAGCCTCAAGCCCTAGGA 721
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142107 TCCAACGCTGCCGGTTCCCTGGGGTACGAGCACAGCCTCAAGCAGCCTCAAGCCCTAGGA 142166
Qy 722 AGCCCCCAGTTCAAAGCACAGGGCGCATTGGAGCCTGGGCACGATACAGTTCACACCACG 781
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142167 AGCCCCCAGTTCAAAGCACAGGGCGCATTGGAGCCTGGGCACGATACAGTTCACACCACG 142226
Qy 782 GCTGCGATGGTAAGCCACGCCCAAGTCCCAAGGGCCTAGGGGACCCCCGCCCTCCACAGC 841
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142227 GCTGCGATGGTAAGCCACGCCCAAGTCCCAAGGGCCTAGGGGACCCCCGCCCTCCACAGC 142286
Qy 842 CGGAGGAGAAACCTGGGCGCAGAAAGCAGGGGGAATATCTGGTTGTAGGTGAGTAAGCGG 901
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142287 CGGAGGAGAAACCTGGGCGCAGAAAGCAGGGGGAATATCTGGTTGTAGGTGAGTAAGCGG 142346
Qy 902 GGTCAGGAGTTCCCGTTAGAGTCTCTGCGTTTCGGGAGAAGGGTGATCATTCCCAGGCTT 961
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142347 GGTCAGGAGTTCCCGTTAGAGTCTCTGCGTTTCGGGAGAAGGGTGATCATTCCCAGGCTT 142406
Qy 962 GTCCGACGTCTCTCTCAGGGTGCGCTCCGGAAGAGCGAGCCCTTTAAGGCTATGCCGAGT 1021
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142407 GTCCGACGTCTCTCTCAGGGTGCGCTCCGGAAGAGCGAGCCCTTTAAGGCTATGCCGAGT 142466
Qy 1022 GGGCGCGTCCCGGCCTCTCCCGGGAGAGGAGAGGCGGGGCGGACCTGTGTCCCGCCCCCG 1081
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142467 GGGCGCGTCCCGGCCTCTCCCGGGAGAGGAGAGGCGGGGCGGACCTGTGTCCCGCCCCCG 142526
Qy 1082 GCCCGGCCCGCCCCCAGTGCCCGCCCCGCCCCCGGCACTCGGCCGGCGGCGCCTTTGATG 1141
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142527 GCCCGGCCCGCCCCCAGTGCCCGCCCCGCCCCCGGCACTCGGCCGGCGGCGCCTTTGATG 142586
Qy 1142 TTCCGACCCGCCAGCTCGCGGAGCCGCTCTGCCCCGCGCCCTAGCCCGCGCCTGCAGCCC 1201
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142587 TTCCGACCCGCCAGCTCGCGGAGCCGCTCTGCCCCGCGCCCTAGCCCGCGCCTGCAGCCC 142646
Qy 1202 GCCCAGGCGGAGTCAGCCCGCGCTCCGCCCGCCGCGATCCGAGCTCGGAGGTTCGGACTC 1261
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142647 GCCCAGGCGGAGTCAGCCCGCGCTCCGCCCGCCGCGATCCGAGCTCGGAGGTTCGGACTC 142706
Qy 1262 CGGGCTCGCCGCCCCCCGGGCCGGCTCCGCGCCCCGCACTCCCGGCGCCCAGCGCCCCGC 1321
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142707 CGGGCTCGCCGCCCCCCGGGCCGGCTCCGCGCCCCGCACTCCCGGCGCCCAGCGCCCCGC 142766
Qy 1322 GCCCCGGCGGGCGGAGCGCACCATGCCGCAGCTGGACTCCGGCGGGGGCGGCGCGGGCGG 1381
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142767 GCCCCGGCGGGCGGAGCGCACCATGCCGCAGCTGGACTCCGGCGGGGGCGGCGCGGGCGG 142826
Qy 1382 CGGCGACGACCTCGGCGCGCCGGACGAGCTGCTGGCCTTCCAGGATGAAGGCGAGGAGCA 1441
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142827 CGGCGACGACCTCGGCGCGCCGGACGAGCTGCTGGCCTTCCAGGATGAAGGCGAGGAGCA 142886
Qy 1442 GGACGACAAGAGCCGCGACAGCGCCGCCGGTCCCGAGCGCGACCTGGCCGAGCTCAAGTC 1501
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142887 GGACGACAAGAGCCGCGACAGCGCCGCCGGTCCCGAGCGCGACCTGGCCGAGCTCAAGTC 142946
Qy 1502 GTCGCTCGTGAACGAGTCCGAGGGCGCGGCCGGCGGCGCAGGGATCCCGGGGGTCCCGGG 1561
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 142947 GTCGCTCGTGAACGAGTCCGAGGGCGCGGCCGGCGGCGCAGGGATCCCGGGGGTCCCGGG 143006
Qy 1562 GGCCGGCGCCGGGGCCCGCGGCGAGGCCGAGGTGAGCCCCCGCCGGCGCCGGCTCCTCCC 1621
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143007 GGCCGGCGCCGGGGCCCGCGGCGAGGCCGAGGTGAGCCCCCGCCGGCGCCGGCTCCTCCC 143066
Qy 1622 CCGCGGTCGCCGCGCCGCGCCGCCCCAGTTGCGCGCGGCCCTCGGGGTCTCCAGCGCGCA 1681
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143067 CCGCGGTCGCCGCGCCGCGCCGCCCCAGTTGCGCGCGGCCCTCGGGGTCTCCAGCGCGCA 143126
Qy 1682 GAGCGTCCCTGCCCCGGCGTCGGCCCCGACCCCCGCGGTCCCACCGCCCCTCACTCCCCT 1741
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143127 GAGCGTCCCTGCCCCGGCGTCGGCCCCGACCCCCGCGGTCCCACCGCCCCTCACTCCCCT 143186
Qy 1742 CCGGTTCTCCCTCCAGGCTCTCGGGCGGGAACACGCTGCGCAGAGACTCTTCCCGGACAA 1801
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143187 CCGGTTCTCCCTCCAGGCTCTCGGGCGGGAACACGCTGCGCAGAGACTCTTCCCGGACAA 143246
Qy 1802 ACTTCCAGAGCCCCTGGAGGACGGTGAGTTTCTGCCCGGCCCGGCTTCCCTTCGTCGCGC 1861
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143247 ACTTCCAGAGCCCCTGGAGGACGGTGAGTTTCTGCCCGGCCCGGCTTCCCTTCGTCGCGC 143306
Qy 1862 TCAGGCCCTGGCCTCGGTGGGACGGGGACGCCAAGGACCGCGGGGAGCCGGGTGCCTCCC 1921
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143307 TCAGGCCCTGGCCTCGGTGGGACGGGGACGCCAAGGACCGCGGGGAGCCGGGTGCCTCCC 143366
Qy 1922 CCACCGCAGCTCAGGAGGCGGCAGAACCCAGGGGTGGAGAGTGGGGGGCGGGCTTCCCGG 1981
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 143367 CCACCGCAGCTCAGGAGGCGGCAGAACCCAGGGGTGGAGAGTGGGGGGCGGGCTTCCCGG 143426
Qy 1982 GCGCCGCCGGGTCGAGTCA 2000
|||||||||||||||||||
Db 143427 GCGCCGCCGGGTCGAGTCA 143445
NCBI (cited above) indicates that SEQ ID NO 15 has at least 95% identity to the gene ITK. Data provided by Atlas2 show that ITK (which an artisan would understand is under the control of its own promoter sequence) is expressed in CD3+ cells, including at a ratio of at least 2:1 (see, e.g., data for § Immune Cell Type Expression [RNA]). Portions of those data are presented here:
PNG
media_image5.png
381
1142
media_image5.png
Greyscale
The following sequence alignment demonstrates that a sequence at least 95% identical to SEQ ID NO 16 is found within the human genome:
RESULT 1
HSU57613
LOCUS HSU57613 10975 bp DNA linear PRI 10-OCT-2001
DEFINITION Human interleukin-2 receptor alpha chain (IL2RA) gene, promoter
region and exon 1.
ACCESSION U57613 AF243502
VERSION U57613.2
KEYWORDS .
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 4212)
AUTHORS John,S., Robbins,C.M. and Leonard,W.J.
TITLE An IL-2 response element in the human IL-2 receptor alpha chain
promoter is a composite element that binds Stat5, Elf-1, HMG-I(Y)
and a GATA family protein
JOURNAL EMBO J. 15 (20), 5627-5635 (1996)
PUBMED 8896456
REFERENCE 2 (bases 3631 to 10975)
AUTHORS Kim,H.P., Kelly,J. and Leonard,W.J.
TITLE The basis for IL-2-induced IL-2 receptor alpha chain gene
regulation: importance of two widely separated IL-2 response
elements
JOURNAL Immunity 15 (1), 159-172 (2001)
PUBMED 11485747
REFERENCE 3 (bases 1 to 10975)
AUTHORS Kim,H.-P. and Leonard,W.J.
TITLE Direct Submission
JOURNAL Submitted (03-MAY-1996) Lab of Molecular Immunology, NIH/NHLBI, 10
Center Dr., Bldg. 10, Rm. 7N240, Bethesda, MD 20892, USA
REFERENCE 4 (bases 1 to 10975)
AUTHORS Kim,H.-P. and Leonard,W.J.
TITLE Direct Submission
JOURNAL Submitted (03-APR-2001) Lab of Molecular Immunology, NIH/NHLBI,
Bldg. 10, Rm. 7N240, 10 Center Dr., Bethesda, MD 20892, USA
REMARK Sequence update by submitter
COMMENT On Oct 10, 2001 this sequence version replaced U57613.1.
FEATURES Location/Qualifiers
source 1..10975
/organism="Homo sapiens"
/mol_type="genomic DNA"
/db_xref="taxon:9606"
/chromosome="10"
/map="10p15-14"
gene 324..>10975
/gene="IL2RA"
regulatory 324..401
/regulatory_class="enhancer"
/gene="IL2RA"
/note="Positive regulatory region III. A composite site
with one consensus and one non-consensus gamma interferon
activated sequence (GAS motif). Together these motifs
mediate the binding of Stat5A and Stat5B. An Ets binding
site overlaps the consensus motif, whereas a GATA motif
overlaps the non-consensus GAS motif. PRRIII also contains
an Ets binding site downstream of both GAS motifs; this
Ets binding site can bind Elf-1. PRRIII is essential for
IL-2 induced IL-2Ralpha promoter activity in YT cells."
regulatory 3828..3860
/regulatory_class="enhancer"
/gene="IL2RA"
/note="Positive regulatory region 1. This spans an NF-kB
site (GGGGAATCTCCC) and a CArG motif (CCTTTTATGG). An Sp1
site begins within PRRI and extends 3' of PRRI."
regulatory 3967..4040
/regulatory_class="enhancer"
/gene="IL2RA"
/note="Positive regulatory region II, contains an
essential binding site for Elf-1 and multiple sites for
HMG-I(Y). The Elf-1 site is essential for PMA-induced
IL-2Ralpha promoter activity in Jurkat T cells and IL-2
induced IL-2Ralpha promoter activity in YT natural killer
like cells."
prim_transcript 4114..>10975
/gene="IL2RA"
ORIGIN
Query Match 96.2%; Score 1924.2; Length 10975;
Best Local Similarity 99.1%;
Matches 1982; Conservative 0; Mismatches 3; Indels 16; Gaps 4;
Qy 2 CACCCCCAACTTCTTCTCACATCCCTGCATCGTGCCATGCAGCATCAACTGGAAACCTCA 61
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2060 CACCCCCAACTTCTTCTCACATCCCTGCATCGTGCCATGCAGCATCAACTGGAAACCTCA 2119
Qy 62 GCATCAGCAAACGACGACAGAGCGTTCATCCGTAAGGTGAACCAGAAAAGCCAGTTCAAT 121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2120 GCATCAGCAAACGACGACAGAGCGTTCATCCGTAAGGTGAACCAGAAAAGCCAGTTCAAT 2179
Qy 122 GACTTGTTTAACCATGGTCCATCTCAGAACCAAGAGTTGGGCCTCTTATTTACCAGAAAA 181
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2180 GACTTGTTTAACCATGGTCCATCTCAGAACCAAGAGTTGGGCCTCTTATTTACCAGAAAA 2239
Qy 182 ATTGTGGGGGCTTTGTGATATGGCTTTAAAAAAATCTTGTAATTGCCAGGCGTGGTGGCT 241
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2240 ATTGTGGGGGCTTTGTGATATGGCTTTAAAAAAATCTTGTAATTGCCAGGCGTGGTGGCT 2299
Qy 242 CACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGTGAATCGCCTAAGGTCAGGAG 301
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2300 CACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGTGAATCGCCTAAGGTCAGGAG 2359
Qy 302 TTCGAGACCAGCCTGACCAACATGGTGAAACTCCGTCTCTACTAAAAATACAAAAACTAG 361
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2360 TTCGAGACCAGCCTGACCAACATGGTGAAACTCCGTCTCTACTAAAAATACAAAAACTAG 2419
Qy 362 CTGGATGTGGTGACGCGTGCCTGTAATCCTAGCTACTCAGGAGGCTGACGCAGGAGAATC 421
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2420 CTGGATGTGGTGACGCGTGCCTGTAATCCTAGCTACTCAGGAGGCTGACGCAGGAGAATC 2479
Qy 422 ACTTGAACCTGGGAGGCAGAGGTTGCAGTGAGCCAAGATTGTGCCATTGCGCTCC-AAAA 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Db 2480 ACTTGAACCTGGGAGGCAGAGGTTGCAGTGAGCCAAGATTGTGCCATTGCGCTCCAAAAA 2539
Qy 481 AAAAAAAAAAAAAGACATTAACATAAATTTAAATATTTTATAATGACAATCCACATTAAC 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2540 AAAAAAAAAAAAAGACATTAACATAAATTTAAATATTTTATAATGACAATCCACATTAAC 2599
Qy 541 TACTTAAAGCATAAGCTATTTTCCAGGAGAGGCAGCAAGTGCATTCTACTCCCATGCCCA 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2600 TACTTAAAGCATAAGCTATTTTCCAGGAGAGGCAGCAAGTGCATTCTACTCCCATGCCCA 2659
Qy 601 AGAAGAAAGGAGCGTGACTTTGGTGGGAGTACTAGGAGTTTCTACTGGAGCACTTGCCCG 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2660 AGAAGAAAGGAGCGTGACTTTGGTGGGAGTACTAGGAGTTTCTACTGGAGCACTTGCCCG 2719
Qy 661 CAGAGTGAGAAACGTTCCTAGAGAGGAAGTTATACCTGCTGTGGAATTTAAGAGAATCTT 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2720 CAGAGTGAGAAACGTTCCTAGAGAGGAAGTTATACCTGCTGTGGAATTTAAGAGAATCTT 2779
Qy 721 GTCATATTTTGACAAGTTTTTTGAGATGGAAGTCTCACTCTGTCGCCCAGGCTGGAGTGC 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2780 GTCATATTTTGACAAGTTTTTTGAGATGGAAGTCTCACTCTGTCGCCCAGGCTGGAGTGC 2839
Qy 781 AGTGGCGCAATCTCAGCTCACTGCAGCCTGCACCTCCTCGGTTCCAGCTATTCTCTTGTC 840
||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Db 2840 AGTGGCGCAATCTCAGCTCACTGCAGCCTGCACCTCCTCGGCTCCAGCTATTCTCTTGTC 2899
Qy 841 TCAGCCTCCTGAGTAACTGGGATTACAGGCGCCCGCCACTACGCCTGGCTAATTTTTGTA 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2900 TCAGCCTCCTGAGTAACTGGGATTACAGGCGCCCGCCACTACGCCTGGCTAATTTTTGTA 2959
Qy 901 TTTTTAGTAGAAATGGGGTTTTACCATGTTGGCCAGACTGGTCTCAAACTCCCGACCTCA 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2960 TTTTTAGTAGAAATGGGGTTTTACCATGTTGGCCAGACTGGTCTCAAACTCCCGACCTCA 3019
Qy 961 GGTGATCTGCCTGCCTCAGCCTCCCAAAGTGCTGGAATTACAGGCGTGTGCCACTGCGCC 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3020 GGTGATCTGCCTGCCTCAGCCTCCCAAAGTGCTGGAATTACAGGCGTGTGCCACTGCGCC 3079
Qy 1021 TGGCTAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGTAGAGACGGTGGTTTCAC 1080
||||||| |||||||||||||||||||||||||||||||||||||||||
Db 3080 TGGCTAA------------TTTTTTTTTTTTTTTTTTTTTAGTAGAGACGGTGGTTTCAC 3127
Qy 1081 CATGTCATCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCACCTTGGTCTAC 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3128 CATGTCATCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCACCTTGGTCTAC 3187
Qy 1141 CAAAGTGCTCGGATTACAGGCATGAGCCACCAGGCCCAGTCAACGTGATGTGTTTTGGAA 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3188 CAAAGTGCTCGGATTACAGGCATGAGCCACCAGGCCCAGTCAACGTGATGTGTTTTGGAA 3247
Qy 1201 CCCTGAATTCCTTGGCTTGCCCGGAGGGTTTTCTTTTTGTTAATATCTTTGCTTGCTTTC 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3248 CCCTGAATTCCTTGGCTTGCCCGGAGGGTTTTCTTTTTGTTAATATCTTTGCTTGCTTTC 3307
Qy 1261 TAGTATTTAAAAAATTGTGTTTTGCTCTAACTATGCAATGGCTTTAAGTCTTAGACAAAT 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3308 TAGTATTTAAAAAATTGTGTTTTGCTCTAACTATGCAATGGCTTTAAGTCTTAGACAAAT 3367
Qy 1321 TTCCAGGGAGCAAAACACACTCAACC-ATTTCATAATAATCAGAAGAGAGCTCTGATCAA 1379
|||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
Db 3368 TTCCAGGGAGCAAAACACACTCAACCAATTTCATAATAATCAGAAGAGAGCTCTGATCAA 3427
Qy 1380 TAAATAAGCAAGACTGAATTTTACAAAATAATCCAAAGTTTAAAACCAAAGCCCACTTTT 1439
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3428 TAAATAAGCAAGACTGAATTTTACAAAATAATCCAAAGTTTAAAACCAAAGCCCACTTTT 3487
Qy 1440 TGCATGATCCTTTAAGAGAAAGAAATCTGGAAGCAAAACACCTTATAAAATGACAATGCA 1499
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3488 TGCATGATCCTTTAAGAGAAAGAAATCTGGAAGCAAAACACCTTATAAAATGACAATGCA 3547
Qy 1500 CTTTCAGGAGCCCAGGGCACTGTGGTGAAATGATGATGGCTAGTACAGGTTATAAGCCTT 1559
||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||
Db 3548 CTTTCAGGAGCCCAGAGCACTGTGGTGAAATGATGATGGCTACTACAGGTTATAAGCCTT 3607
Qy 1560 GGGGAATTATTTATGAATTCTCAGGATCCTTCAGTTCGCCGCATCCTTCTCCATTATTTG 1619
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3608 GGGGAATTATTTATGAATTCTCAGGATCCTTCAGTTCGCCGCATCCTTCTCCATTATTTG 3667
Qy 1620 AATATTGGAGGCTGCCTGACCAGAATCTTGTCAGGACTTTGCTCCTTCATCCCAGGTGGT 1679
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3668 AATATTGGAGGCTGCCTGACCAGAATCTTGTCAGGACTTTGCTCCTTCATCCCAGGTGGT 3727
Qy 1680 CCCGGCTGACTCCTGAGGACGTTACAGCCCTGAGGGGAGGACTCAGCTTATGAAGTGCTG 1739
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3728 CCCGGCTGACTCCTGAGGACGTTACAGCCCTGAGGGGAGGACTCAGCTTATGAAGTGCTG 3787
Qy 1740 GGTGAGACCACTGCCAAGAAGTGCTTGCTCACCCTACCTTCAACGGCAGGGGAATCTCCC 1799
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3788 GGTGAGACCACTGCCAAGAAGTGCTTGCTCACCCTACCTTCAACGGCAGGGGAATCTCCC 3847
Qy 1800 TCTCCTTTTATGGGCGTAGCTGAAGAAAGGATTCATAAATGAAGTTCAATCCTTCTCATC 1859
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3848 TCTCCTTTTATGGGCGTAGCTGAAGAAAGGATTCATAAATGAAGTTCAATCCTTCTCATC 3907
Qy 1860 AACCCCAGCCCACACCTCCAGCAATTGAACTTGAAAAAAAAAACCTGGTTTGAAAAATTA 1919
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3908 AACCCCAGCCCACACCTCCAGCAATTGAACTTGAAAAAAAAAACCTGGTTTGAAAAATTA 3967
Qy 1920 CCGCAAACTATATTGTCATCAAAAAAAAAAAAAAAAAAAAACACTTCCTATATTTGAGAT 1979
|||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Db 3968 CCGCAAACTATATTGTCATC--AAAAAAAAAAAAAAAAAAACACTTCCTATATTTGAGAT 4025
Qy 1980 GAGAGAAGAGAGTGCTAGGCA 2000
|||||||||||||||||||||
Db 4026 GAGAGAAGAGAGTGCTAGGCA 4046
Data provided by Atlas2 show that IL2RA (which an artisan would understand is under the control of its own promoter sequence) is expressed in CD3+ cells, including at a ratio of at least 2:1 (see, e.g., data for § Immune Cell Type Expression [RNA]). Portions of those data are presented here:
PNG
media_image6.png
400
1183
media_image6.png
Greyscale
Since the information provided above demonstrates sequences having at least 95% identity to SEQ ID NOs 3, 7-8, and 14-16 exist in Nature, such sequences have identical nucleic acids and can be considered equivalent to the naturally occurring nucleic acids. Since those sequences occur in Nature, the claimed invention is directed to a product of Nature, has no markedly different characteristics, and therefore falls within the judicial exception category.
Note that even though the claims recite that the promoter is used to express a transgene, that does not elevate the claimed invention above a product of Nature because the Spec. does not define a transgene in any particular way so a transgene can be literally any gene including the native gene (in which case the claimed invention would have characteristics that are not markedly different from a naturally occurring counterpart) or could be a virus gene inserted (via viral infection) to the reading frame downstream of the promoter encoded by SEQ ID NOs 3, 7-8, and 14-16.
Step 2A Judicial Exception – Prong 2 (Judicial exception is integrated into a practical application): Prong 2 asks whether a claim recites additional elements that integrate the judicial exception into a practical application. A promoter promoting gene expression is a feature inherent to the nucleic acid sequence and its structure and function within a cell (see MPEP 2106.04[c][II][C][2]). None of the claims recites any practical application beyond for use in expression of a transgene. As discussed in the preceding ¶, the Spec. does not define a transgene in any particular way. Therefore, a transgene can be literally any gene including the native gene regulated by the promoter encoded by SEQ ID NOs 3, 7-8, and 14-16. The courts have found that linking the use of a judicial exception to a particular technological environment or field of use do not integrate a judicial exception (see MPEP 2106.04(d)(I)). Therefore, using a promoter sequence to promote expression of a gene is not a practical application beyond how the product of nature operates in its natural environment.
Step 2B Judicial Exception – Significantly More: The “significantly more” analysis determines that a claim is patent eligible if the claims recite additional elements that contribute an “inventive concept”, which requires an additional element in the claim to apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception.
Claims 1-4 recite the promoter is for use in expression of a transgene. The fact that the recited transgene does not have characteristics markedly different from its natural counterpart has been addressed above. As discussed above, a technological environment—and certainly using a naturally-occurring thing for its natural purpose—does not contribute an inventive concept. Claims 1-2 read on at least SEQ ID NO 3 as a natural product without markedly different characteristics; Claims 1-4 read on at least SEQ ID NOs 7-8 and 14-16 as a natural product without markedly different characteristics.
Claim 5 recites the promoter possesses binding sequences for one or more transcription factors. However, the claimed promoters each inherently possess a sequence that comprises binding sequences for one or more transcription factors, including those recited in Claim 5. The Spec. shows (starts on p. 23) the claimed SEQ ID NOs comprise the claimed binding sequences for one or more recited transcription factors. Therefore Claim 5 cannot be considered to contribute an inventive concept.
Claims 6-7 recite the promoter expresses a transgene at a higher level—or the particular higher level of a 2:1 ratio—in a CD3+ cell compared with a CD3- cell. The Atlas data shown above demonstrate that SEQ ID NOs 3, 7-8, and 14-16 are expressed at a higher level (and by the higher level of an at least 2:1 ratio for SEQ ID NOs 3, 7-8 and 15-16) in CD3+ cells vs. in Natural Killer cells which are not CD3+. The reference Pfefferle (et al. 2020 May 11. Deciphering Natural Killer Cell Homeostasis. Front. Immunol. 11:812, “Pfefferle”, of record) teaches (§NK Cell Differentiation and Functional Specialization) CD3 negativity characterizes NK cells. Therefore Claims 6-7 cannot be considered to contribute any inventive concept.
Claims 9 and 17 recite a nucleic acid molecule comprising the promoter sequence of Claim 1 (Claim 9) and a cell comprising the nucleic acid molecule (Claim 17). Since the sequence alignments shown above indicate that sequences having at least 95% identity to SEQ ID NOs 3, 7-8, and 14-16 exist in the human genome, either recited sequence exists on a chromosome which is a kind of nucleic acid molecule. Those chromosomes exist within the context of a cell. Since the natural nucleic acid molecules of the human genome comprise each of the promoter sequences, and those nucleic acid molecules exist within the context of any cell or any isolated cell, Claims 9 and 17 cannot be considered to contribute any inventive concept.
Claim 20 recites a nanoparticle comprising the vector of Claim 9, wherein the nanoparticle (NP) is capable of delivery of the vector into a CD3+ cell. First of all, the art of Billingsley (et al. 2020 Jan. Ionizable Lipid Nanoparticle-Mediated mRNA Delivery for Human CAR T Cell Engineering. Nano Lett. 20[3]:1578-1589, “Billingsley”, of record; see Fig. in §Abstract) and Zhao (and Huang. 2014. Chapter Two – Lipid Nanoparticles for Gene Delivery. Adv. Genetics 88:13-36. Abstract and Snippets only, “Zhao”, of record; see §Introduction; §Cationic Lipids; and §Pharmakokinetics and Biodistribution Profile of LNPs) teach using NP to deliver mRNA and vectors to Tcells is known in the art. Therefore Billingsley and Zhao teach that using a NP to deliver a vector to a Tcell is known. In addition, Claim 20 is broad enough to read on a product of Nature because the art of Hong (et al. 2017. Effects of exosome on the activation of CD4+ T cells in rhesus macaques: a potential application for HIV latency reactivation. Sci. Rep. 7:15611, “Hong”, of record) teaches (§Abstract, §Introduction) exosomes are released and taken up by T-cells and they contain DNA and mRNA. Therefore an artisan would expect that, without presentation of evidence to the contrary, CD3+ cells both release and take up exosomes comprising the claimed sequences. For those reasons Claim 20 cannot be deemed to contribute an inventive concept.
Altogether the limitations of Claims 1-7, 9, 17, and 20 do not recite any meaningful additional limitations, modification(s) or transformation(s) that distinguish the claimed promoter sequences from promoter sequences present in the genome (or an exosome), and therefore do not recite any limitations significantly more than the judicial exception. Therefore, Claims 1-7, 9, 17, and 20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a product of nature and does not meet patent subject matter eligibility requirements.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1-7, 9 and 17 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by International Publication Number WO2008/073303 (published 19 June 2008, “WO303”, of record).
WO303 is drawn to transcriptional regulatory elements of biological pathways, tools, and methods. WO303 discloses (§Abstract) an array of expression constructs, each comprising: a nucleic acid segment operably linked with a reporter sequence in an expression vector such that expression of the reporter sequence is under the transcriptional control of the nucleic acid segment. WO303 discloses (¶142) transgenic expression constructs for gene therapy. An artisan would readily understand the invention of WO303 is for expressing transgenes.
WO303 discloses (¶123) their invention provides transcriptional promoters including at least 1000 or 5000 nt selected from the group consisting of SEQ ID NOs 3837-122716. Therefore WO303 discloses sequences having at least 95% identity to claimed SEQ ID NOs 3, 7-8, and 14-16. Since WO303 discloses sequences having at least 95% identity to the full length of those SEQ ID NOs, it also discloses promoter sequences comprising a fragment of any of those sequences wherein the fragment has 95% identity to nt 1501-2000, 1001-2000, 501-2000 of the claimed SEQ ID NOs. Alignments showing % identity to the full length of the claimed SEQ ID NOs are provided here:
RESULT 2
ATN05849
ID ATN05849 standard; DNA; 6000 BP.
XX
AC ATN05849;
XX
DT 11-DEC-2008 (first entry)
XX
DE Human transcriptional regulatory element SEQ ID NO 3789.
XX
KW gene expression; gene regulation; transcription; DNA library;
KW DNA microarray; ds; pharmacogenetics; mapping; DNA polymorphism.
XX
OS Homo sapiens.
XX
CC PN WO2008073303-A2.
XX
CC PD 19-JUN-2008.
XX
CC PF 06-DEC-2007; 2007WO-US025093.
XX
PR 07-DEC-2006; 2006US-0873737P.
PR 07-DEC-2006; 2006US-0873738P.
PR 07-DEC-2006; 2006US-0873739P.
PR 07-DEC-2006; 2006US-0873853P.
PR 07-DEC-2006; 2006US-0873871P.
PR 07-DEC-2006; 2006US-0873882P.
PR 07-DEC-2006; 2006US-0873883P.
PR 06-JUL-2007; 2007US-0958616P.
XX
CC PA (SWIT-) SWITCHGEAR GENOMICS.
XX
CC PI Aldred SF, Trinklein N;
XX
DR WPI; 2008-H01915/44.
XX
CC PT New library of different expression constructs, useful for personalized
CC PT medicine, pharmacogenomics or correlation of polymorphisms with
CC PT phenotypic traits.
XX
CC PS Claim 10; SEQ ID NO 3789; 59pp; English.
XX
CC The invention relates to a library of different expression constructs.
CC Each member of the library comprises a different nucleic acid segment
CC from a genome, where the segment comprises transcription regulatory
CC sequences operably linked with a heterologous reporter sequence in an
CC expression vector such that expression of the reporter sequence is under
CC transcriptional control of the transcription regulatory sequences, where
CC at least 20\% of the transcription regulatory sequences of the expression
CC constructs in the library are part of a common pathway. The common
CC pathway is oncology, membrane, vascular, neuronal, signaling or nuclear
CC receptor pathway. The common pathway is an oncology pathway. The oncology
CC pathway is hypoxia pathway, DNA-damage pathway, apoptosis pathway, cell
CC cycle pathway or p53 pathway. The regulatory elements are SEQ ID NO: 1-
CC 3836. The common pathway is a membrane pathway. The membrane pathway is
CC transport protein pathways, G-protein coupled receptor pathways, ion
CC channel pathways or cell adhesion protein pathways. The regulatory
CC elements are SEQ ID NO: 3837-12716. The common pathway is a nuclear
CC receptor pathway. The nuclear receptor pathway is glucocorticoid receptor
CC pathway, peroxisome proliferator-activated receptor pathway, estrogen
CC receptor pathway, androgen receptor pathway, cytochrome P450 pathway or
CC transporter pathways. The regulatory elements are SEQ ID NO: 12717-13994.
CC The library of different expression constructs is useful for personalized
CC medicine, pharmacogenomics or correlation of polymorphisms with
CC phenotypic traits. The invention provides a library of different
CC expression constructs for large scale structural and functional
CC characterization of gene expression regulatory elements in a genome of an
CC organism, especially in a human genome that is part of a common pathway.
XX
SQ Sequence 6000 BP; 1786 A; 1408 C; 1298 G; 1508 T; 0 U; 0 Other;
Query Match 99.9%; Score 1998.4; Length 6000;
Best Local Similarity 99.9%;
Matches 1999; Conservative 0; Mismatches 1; Indels 0; Gaps 0;
Qy 1 TTTTCCACTGCCCTTCTCAGCCCCACAGGCCTTCAGGAAGACCCGAACTTCAAGCAAAGC 60 SEQ ID NO 3
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2608 TTTTCCACTGCCCTTCTCAGCCCCACAGGCCTTCAGGAAGACCCGAACTTCAAGCAAAGC 2667 WO303 SEQ #3789
Qy 61 CTTTTTATTTTTCAACACCCACAGCTTCCATTCAACAATCAGAAGTTTTCCACTTTGATC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2668 CTTTTTATTTTTCAACACCCACAGCTTCCATTCAACAATCAGAAGTTTTCCACTTTGATC 2727
Qy 121 AAAGAGGCTGAACAAGAGGGCCAAGGGAGCAGCTGGTTCTCAGCAACTCTGGGCAGACCA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2728 AAAGAGGCTGAACAAGAGGGCCAAGGGAGCAGCTGGTTCTCAGCAACTCTGGGCAGACCA 2787
Qy 181 CAGAGCCCTTGCTACCCACTCACTGTCCGTGCCCACCAGAGGACACAGCCTTCTCCCCAA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2788 CAGAGCCCTTGCTACCCACTCACTGTCCGTGCCCACCAGAGGACACAGCCTTCTCCCCAA 2847
Qy 241 ATCAGCCAGGTACATGCCCCAGAAAACACTGGCTTGCCTCGTTCCCACCTTAATTACCGG 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2848 ATCAGCCAGGTACATGCCCCAGAAAACACTGGCTTGCCTCGTTCCCACCTTAATTACCGG 2907
Qy 301 ACCAAACGAACGTGAACACACTGTTTTCAAAACCAAACTCAATTGGGATCACGGGGGCCT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2908 ACCAAACGAACGTGAACACACTGTTTTCAAAACCAAACTCAATTGGGATCACGGGGGCCT 2967
Qy 361 CGGTTTCCTTGATTGTAAAATGGGTATATCGCCCCCCACTCTATTTAGCCCAAGAAAACA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2968 CGGTTTCCTTGATTGTAAAATGGGTATATCGCCCCCCACTCTATTTAGCCCAAGAAAACA 3027
Qy 421 ATTTATCTCTTGATGTCTCTTTCGTCTCCAGGATCTATGCTTTTACAGACTCACTGGGAG 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3028 ATTTATCTCTTGATGTCTCTTTCGTCTCCAGGATCTATGCTTTTACAGACTCACTGGGAG 3087
Qy 481 GAAATATCCAGACCAAATCCTAAAGCCTGATCTAATTTGGGAGATGCTCAGAAGTTTTGG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3088 GAAATATCCAGACCAAATCCTAAAGCCTGATCTAATTTGGGAGATGCTCAGAAGTTTTGG 3147
Qy 541 TTCTATGCAAGAACAGCAGTGGTAATAATCCAAGCTTGGCTTTAGACACAGGACGTTTCC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3148 TTCTATGCAAGAACAGCAGTGGTAATAATCCAAGCTTGGCTTTAGACACAGGACGTTTCC 3207
Qy 601 TTAGGGGCATCTGGGATCTCTGCTGGCTCAAAGTGATGCGCTGCAGACAAAAAGTGAGCA 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3208 TTAGGGGCATCTGGGATCTCTGCTGGCTCAAAGTGATGCGCTGCAGACAAAAAGTGAGCA 3267
Qy 661 GAAAGGAAAGGAGGTGCTATGCAGAATGAGCTTCTTCCACGGTGATACCAAATGGAGCTT 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3268 GAAAGGAAAGGAGGTGCTATGCAGAATGAGCTTCTTCCACGGTGATACCAAATGGAGCTT 3327
Qy 721 TCAAAGGCCCACATCTGGAGGCAGCAGCTATGCAGTGATTAACATTTTAAACGGTATTTT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3328 TCAAAGGCCCACATCTGGAGGCAGCAGCTATGCAGTGATTAACATTTTAAACGGTATTTT 3387
Qy 781 GAAATGGAGATCATTAGTAACCACAGATGTGATCTGACTCTGTCCCCCAGGTAATCTGTC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3388 GAAATGGAGATCATTAGTAACCACAGATGTGATCTGACTCTGTCCCCCAGGTAATCTGTC 3447
Qy 841 TATTGTATCTAAATTCCAGACTTAGCCCAGTAGACAGCTTGGGATGTTTAACAGGAATTG 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3448 TATTGTATCTAAATTCCAGACTTAGCCCAGTAGACAGCTTGGGATGTTTAACAGGAATTG 3507
Qy 901 TCCAACACCATCCCCAAATCTATTTTTATTCATGGAGTACTCTGACATCATCTCGCTTGG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3508 TCCAACACCATCCCCAAATCTATTTTTATTCATGGAGTACTCTGACATCATCTCGCTTGG 3567
Qy 961 TCTTCCTGATGACTGTAATGCAGATTGGGAACAGAGAAAGCCATAAAGACTTGTATGATG 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3568 TCTTCCTGATGACTGTAATGCAGATTGGGAACAGAGAAAGCCATAAAGACTTGTATGATG 3627
Qy 1021 GCCCAAGGCTAAGAAGGGAAAGGGCTGAGACCACACTTCAGGTTTTAGCTTTCAGGTGCA 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3628 GCCCAAGGCTAAGAAGGGAAAGGGCTGAGACCACACTTCAGGTTTTAGCTTTCAGGTGCA 3687
Qy 1081 GTGAAGATTGAATGACTTAGCACGAGCTTTCAGCCAGGCAGGCTGCAAAGTGCACCCAAG 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3688 GTGAAGATTGAATGACTTAGCACGAGCTTTCAGCCAGGCAGGCTGCAAAGTGCACCCAAG 3747
Qy 1141 TTCTTTCAGTGATCGACACTTGCGACTTAGGTTGAGATAGTTTTCATCCTCCCTGAGCCT 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3748 TTCTTTCAGTGATCGACACTTGCGACTTAGGTTGAGATAGTTTTCATCCTCCCTGAGCCT 3807
Qy 1201 CAGTTTTCCCATCTGTAAAAAATAAACATTGCCTGCCTCGGAGGGTGGAGGTGGAAGTGG 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3808 CAGTTTTCCCATCTGTAAAAAATAAACATTGCCTGCCTCGGAGGGTGGAGGTGGAAGTGG 3867
Qy 1261 AATGAAGCCACATGTAACTCCTAGCGCTGTGCCTGAGACAGTAGAGGTTCAATTATAGTA 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3868 AATGAAGCCACATGTAACTCCTAGCGCTGTGCCTGAGACAGTAGAGGTTCAATTATAGTA 3927
Qy 1321 GTCACATACACACACAACACATACATACACAAGACACAACACACCACACACAACACATAC 1380
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3928 GTCACATACACACACAACACATACATACACAAGACACAACACACCACACACAACACATAC 3987
Qy 1381 ATACACACCACACACAACACTTACATACGCACCACACTCGGCATGCATTGCAGATCACAA 1440
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3988 ATACACACCACACACAACACTTACATACGCACCACACTCGGCATGCATTGCAGATCACAA 4047
Qy 1441 ATGCACACCACACACACACTGCATACATATACCATAGAGAACACACAACACCTACACATA 1500
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4048 ATGCACACCACACACACACTGCATACATATACCATAGAGAACACACAACACCTACACATA 4107
Qy 1501 ACCCCATACCACAAATACACACACACTACATAGTACACCACGCAGAACACACACAGCCCC 1560
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4108 CCCCCATACCACAAATACACACACACTACATAGTACACCACGCAGAACACACACAGCCCC 4167
Qy 1561 CATATTCCACACCACACCATCTCACTGCCAATTCCTTCCCCTCTTCATGAGTTTTACGGC 1620
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4168 CATATTCCACACCACACCATCTCACTGCCAATTCCTTCCCCTCTTCATGAGTTTTACGGC 4227
Qy 1621 AGGTCCAGGTTCATCTGCCAGTTTAACAGATCCCAAAACTTCTGCAGGAGTGTTTGTTCA 1680
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4228 AGGTCCAGGTTCATCTGCCAGTTTAACAGATCCCAAAACTTCTGCAGGAGTGTTTGTTCA 4287
Qy 1681 AAAGATTGATATTTCCAGATTCCTGCTTTCTGACAGTATCTTTGAACCCCAAATTTCATA 1740
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4288 AAAGATTGATATTTCCAGATTCCTGCTTTCTGACAGTATCTTTGAACCCCAAATTTCATA 4347
Qy 1741 CTGCCATGAGCCAGTCCCCCTTTGGAGAAATATCTCCATTTGTGTGCCCTTTTTCCCCCA 1800
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4348 CTGCCATGAGCCAGTCCCCCTTTGGAGAAATATCTCCATTTGTGTGCCCTTTTTCCCCCA 4407
Qy 1801 GGGAACCTGCAGCATGTCCCTTTTTCAGCAGTAGCCTATCAAACCGAACCCTTTGGAGTT 1860
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4408 GGGAACCTGCAGCATGTCCCTTTTTCAGCAGTAGCCTATCAAACCGAACCCTTTGGAGTT 4467
Qy 1861 ATTACACTGCAGTCCGAGGGATCCGGCCTCCCTGAGACCCAGCAAGGACTCATTATCTGG 1920
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4468 ATTACACTGCAGTCCGAGGGATCCGGCCTCCCTGAGACCCAGCAAGGACTCATTATCTGG 4527
Qy 1921 GGAGGTCTTCTGAGCCACAGGCCTCGCTGAAAGAAGGTGCAGCTTCTTGAACAGGAAGGC 1980
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4528 GGAGGTCTTCTGAGCCACAGGCCTCGCTGAAAGAAGGTGCAGCTTCTTGAACAGGAAGGC 4587
Qy 1981 GTTTTGTGGCAGAGTCTAAA 2000
||||||||||||||||||||
Db 4588 GTTTTGTGGCAGAGTCTAAA 4607
RESULT 2
ATN10585
ID ATN10585 standard; DNA; 6000 BP.
XX
AC ATN10585;
XX
DT 11-DEC-2008 (first entry)
XX
DE Human transcriptional regulatory element SEQ ID NO 8525.
XX
KW gene expression; gene regulation; transcription; DNA library;
KW DNA microarray; ds; pharmacogenetics; mapping; DNA polymorphism.
XX
OS Homo sapiens.
XX
CC PN WO2008073303-A2.
XX
CC PD 19-JUN-2008.
XX
CC PF 06-DEC-2007; 2007WO-US025093.
XX
PR 07-DEC-2006; 2006US-0873737P.
PR 07-DEC-2006; 2006US-0873738P.
PR 07-DEC-2006; 2006US-0873739P.
PR 07-DEC-2006; 2006US-0873853P.
PR 07-DEC-2006; 2006US-0873871P.
PR 07-DEC-2006; 2006US-0873882P.
PR 07-DEC-2006; 2006US-0873883P.
PR 06-JUL-2007; 2007US-0958616P.
XX
CC PA (SWIT-) SWITCHGEAR GENOMICS.
XX
CC PI Aldred SF, Trinklein N;
XX
DR WPI; 2008-H01915/44.
XX
CC PT New library of different expression constructs, useful for personalized
CC PT medicine, pharmacogenomics or correlation of polymorphisms with
CC PT phenotypic traits.
XX
CC PS Claim 15; SEQ ID NO 8525; 59pp; English.
XX
CC The invention relates to a library of different expression constructs.
CC Each member of the library comprises a different nucleic acid segment
CC from a genome, where the segment comprises transcription regulatory
CC sequences operably linked with a heterologous reporter sequence in an
CC expression vector such that expression of the reporter sequence is under
CC transcriptional control of the transcription regulatory sequences, where
CC at least 20\% of the transcription regulatory sequences of the expression
CC constructs in the library are part of a common pathway. The common
CC pathway is oncology, membrane, vascular, neuronal, signaling or nuclear
CC receptor pathway. The common pathway is an oncology pathway. The oncology
CC pathway is hypoxia pathway, DNA-damage pathway, apoptosis pathway, cell
CC cycle pathway or p53 pathway. The regulatory elements are SEQ ID NO: 1-
CC 3836. The common pathway is a membrane pathway. The membrane pathway is
CC transport protein pathways, G-protein coupled receptor pathways, ion
CC channel pathways or cell adhesion protein pathways. The regulatory
CC elements are SEQ ID NO: 3837-12716. The common pathway is a nuclear
CC receptor pathway. The nuclear receptor pathway is glucocorticoid receptor
CC pathway, peroxisome proliferator-activated receptor pathway, estrogen
CC receptor pathway, androgen receptor pathway, cytochrome P450 pathway or
CC transporter pathways. The regulatory elements are SEQ ID NO: 12717-13994.
CC The library of different expression constructs is useful for personalized
CC medicine, pharmacogenomics or correlation of polymorphisms with
CC phenotypic traits. The invention provides a library of different
CC expression constructs for large scale structural and functional
CC characterization of gene expression regulatory elements in a genome of an
CC organism, especially in a human genome that is part of a common pathway.
XX
SQ Sequence 6000 BP; 1706 A; 1211 C; 1187 G; 1896 T; 0 U; 0 Other;
Query Match 99.9%; Score 1999; Length 6000;
Best Local Similarity 100.0%;
Matches 1999; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 2 AGAAAGCTTTCCAAATCCTGGTGCCTGGCGTATTCCAATAGTCTTCTTCCCAGTCTTCCT 61 SEQ ID NO 7
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2843 AGAAAGCTTTCCAAATCCTGGTGCCTGGCGTATTCCAATAGTCTTCTTCCCAGTCTTCCT 2902 WO303 #8525
Qy 62 GGTTACATTTCTCCCTGAACCCATCCTCCCCATCCCTAAAATTTCCCCCAAATGTGAACT 121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2903 GGTTACATTTCTCCCTGAACCCATCCTCCCCATCCCTAAAATTTCCCCCAAATGTGAACT 2962
Qy 122 CAGTCATACCAGTTTGCTCCTTATGTTTCATTGGCCCTTGCTGCTAAGAGCATCCGCTTG 181
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2963 CAGTCATACCAGTTTGCTCCTTATGTTTCATTGGCCCTTGCTGCTAAGAGCATCCGCTTG 3022
Qy 182 CACCTTCTGCTCATCCCCAGACAAGCTTTGTCCTGTGACCATAATGAACTCTTCATGCCG 241
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3023 CACCTTCTGCTCATCCCCAGACAAGCTTTGTCCTGTGACCATAATGAACTCTTCATGCCG 3082
Qy 242 TTTCCAACTTTAGCCCATGTTATTCTTCTTGTCTGAATATCCACCCTTTTCTCTGTTCTC 301
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3083 TTTCCAACTTTAGCCCATGTTATTCTTCTTGTCTGAATATCCACCCTTTTCTCTGTTCTC 3142
Qy 302 AATAATAAGTTCAGGCTTTTCGTCTTCTGAGAAGCCCTTTCTGACTTCCACAGGCTGAAC 361
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3143 AATAATAAGTTCAGGCTTTTCGTCTTCTGAGAAGCCCTTTCTGACTTCCACAGGCTGAAC 3202
Qy 362 CACTGGCTTCTGCTCCTCTACATAATACTTCAATTCCAGCATTGATCTCACTCTATCATG 421
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3203 CACTGGCTTCTGCTCCTCTACATAATACTTCAATTCCAGCATTGATCTCACTCTATCATG 3262
Qy 422 ATCATGGGTTTAGCTGTCTGTCCCTGCCACTGCTGTGTGTTCCTCTTGAGGGCAGGAACA 481
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3263 ATCATGGGTTTAGCTGTCTGTCCCTGCCACTGCTGTGTGTTCCTCTTGAGGGCAGGAACA 3322
Qy 482 TTTGTTTTTCACTTTTTAAAAAACCTCTGTTGCCCAGTCTGGCATTAGGAAGTGCCCATT 541
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3323 TTTGTTTTTCACTTTTTAAAAAACCTCTGTTGCCCAGTCTGGCATTAGGAAGTGCCCATT 3382
Qy 542 AGGTTGTTATTGCTTGTTGGCGCTTGAGCTGGGGCTTGAAGGTTTCTATAATGTGTAGCA 601
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3383 AGGTTGTTATTGCTTGTTGGCGCTTGAGCTGGGGCTTGAAGGTTTCTATAATGTGTAGCA 3442
Qy 602 GTGTATAGAAAACAGGCAGGTCAGAAAAGGCTTCTGTGCATCACACCAACATGGCACATG 661
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3443 GTGTATAGAAAACAGGCAGGTCAGAAAAGGCTTCTGTGCATCACACCAACATGGCACATG 3502
Qy 662 TATACATATGTAACAAATCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATA 721
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3503 TATACATATGTAACAAATCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATA 3562
Qy 722 ATAATAAAATTTTAAAAAAAAAAAGAAGAGGCTTCCTGGAGGAGATGACAGCTGAGCTAA 781
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3563 ATAATAAAATTTTAAAAAAAAAAAGAAGAGGCTTCCTGGAGGAGATGACAGCTGAGCTAA 3622
Qy 782 GTCCTGGAGGATGAGAAGGAGTATAAAATAAGATAATAGGAGAAAAAAGGCAGTAGGAAC 841
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3623 GTCCTGGAGGATGAGAAGGAGTATAAAATAAGATAATAGGAGAAAAAAGGCAGTAGGAAC 3682
Qy 842 AGCATGGGTAAAGGTGATGAGGCCTGAAAGAGGCACGTGGAAGGAAAGACAAATGCAGGA 901
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3683 AGCATGGGTAAAGGTGATGAGGCCTGAAAGAGGCACGTGGAAGGAAAGACAAATGCAGGA 3742
Qy 902 AGGGGGAATGGGAGGGAATGCTGGGGTACAGGCCAAAGAGGGAGGCATTTGGTGAGTATT 961
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3743 AGGGGGAATGGGAGGGAATGCTGGGGTACAGGCCAAAGAGGGAGGCATTTGGTGAGTATT 3802
Qy 962 CTGCAGAGTCTCCTCTGCTGTGCTGAGGTGTGGACAATGGGAAACCATGGACGGACTGGA 1021
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3803 CTGCAGAGTCTCCTCTGCTGTGCTGAGGTGTGGACAATGGGAAACCATGGACGGACTGGA 3862
Qy 1022 GTAGGCAAATGTCATATTCCCTGTTACAACTGTCTGTTTGCATGTCAGCCTTCTAGAAGC 1081
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3863 GTAGGCAAATGTCATATTCCCTGTTACAACTGTCTGTTTGCATGTCAGCCTTCTAGAAGC 3922
Qy 1082 CCCTTAAGGTATCAACTATGTTTTTGTTTTGTCATCATTCAATCCTAAGTGCACAGAATT 1141
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3923 CCCTTAAGGTATCAACTATGTTTTTGTTTTGTCATCATTCAATCCTAAGTGCACAGAATT 3982
Qy 1142 CCGGGCATATTACAGGTTCCCCATGAATGTTTCTTTCTTTATTAAAATGTATGAAAACTC 1201
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3983 CCGGGCATATTACAGGTTCCCCATGAATGTTTCTTTCTTTATTAAAATGTATGAAAACTC 4042
Qy 1202 TCCAGATTTAAGGAAGGTCCTCAATGTTTCAAATTCTTTTTGTTAGATCATTGGTCCTGT 1261
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4043 TCCAGATTTAAGGAAGGTCCTCAATGTTTCAAATTCTTTTTGTTAGATCATTGGTCCTGT 4102
Qy 1262 CTACAGCTGTCACAAATTTAAGGACTCTGGTTATATTTAATCTTCACTTTTGAATTTTCT 1321
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4103 CTACAGCTGTCACAAATTTAAGGACTCTGGTTATATTTAATCTTCACTTTTGAATTTTCT 4162
Qy 1322 GCTTGAAAAATTTGTATTAGAAAAAAAAGTCTATCCTTTTATGGACGGCTCTAATCTCTT 1381
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4163 GCTTGAAAAATTTGTATTAGAAAAAAAAGTCTATCCTTTTATGGACGGCTCTAATCTCTT 4222
Qy 1382 GAATCATTTGGGTTGGCTTTTCTTTGGACCTTCTTCAACTCTGTTTTGTCTCTGTTGAGT 1441
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4223 GAATCATTTGGGTTGGCTTTTCTTTGGACCTTCTTCAACTCTGTTTTGTCTCTGTTGAGT 4282
Qy 1442 TAAGGCTTTTAAGAACACCTGAATTCTTTCCTTCTGCAAAACCAGAGGCAGCTTCTTTTC 1501
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4283 TAAGGCTTTTAAGAACACCTGAATTCTTTCCTTCTGCAAAACCAGAGGCAGCTTCTTTTC 4342
Qy 1502 CGCCTATTTTCAGTTTATTTCTTGTGATTTTAGTTTTTTTCTCTTAACCAAATGCTAAAT 1561
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4343 CGCCTATTTTCAGTTTATTTCTTGTGATTTTAGTTTTTTTCTCTTAACCAAATGCTAAAT 4402
Qy 1562 GGATTTAGGAGAAATAAACTTATTTGTAAAGCTGTCAAGGGACCATTAGAAGGATGGTGC 1621
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4403 GGATTTAGGAGAAATAAACTTATTTGTAAAGCTGTCAAGGGACCATTAGAAGGATGGTGC 4462
Qy 1622 TTCACAGATAGAATACAGTTTTTATTAATGATGCCTAGACAAATCCTGCCATTAGCCCAA 1681
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4463 TTCACAGATAGAATACAGTTTTTATTAATGATGCCTAGACAAATCCTGCCATTAGCCCAA 4522
Qy 1682 GGGCTCAGAAAGTTAGCAGCCTAGTAGTTTTGGAGTTGTCAATGAAATGAATTGGACTGG 1741
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4523 GGGCTCAGAAAGTTAGCAGCCTAGTAGTTTTGGAGTTGTCAATGAAATGAATTGGACTGG 4582
Qy 1742 ATGGTTAAGGATGCCCAGAAGATTGAATAAAATTGGGATTTAGGAGGACCCTTGTACTCC 1801
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4583 ATGGTTAAGGATGCCCAGAAGATTGAATAAAATTGGGATTTAGGAGGACCCTTGTACTCC 4642
Qy 1802 AGGAAATTCTCCAAGTCTCCACTTAGTTATCCAGATCCTCAAAGTGAACATGAAGCTTCA 1861
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4643 AGGAAATTCTCCAAGTCTCCACTTAGTTATCCAGATCCTCAAAGTGAACATGAAGCTTCA 4702
Qy 1862 GTTTCAAATTGAATACATTTTCCATCCATGGATTGGCTTGTTTTGTTCAGTTGAGTGCTT 1921
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4703 GTTTCAAATTGAATACATTTTCCATCCATGGATTGGCTTGTTTTGTTCAGTTGAGTGCTT 4762
Qy 1922 GAGGTTGTCTTTTCGACGTAACAGCTAAACCCACGGCTTCCTTTCTCGTAAAACCAAAAC 1981
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4763 GAGGTTGTCTTTTCGACGTAACAGCTAAACCCACGGCTTCCTTTCTCGTAAAACCAAAAC 4822
Qy 1982 AAAAAGGCTTTCTATTCAA 2000
|||||||||||||||||||
Db 4823 AAAAAGGCTTTCTATTCAA 4841
RESULT 2
ATN12803
ID ATN12803 standard; DNA; 6000 BP.
XX
AC ATN12803;
XX
DT 11-DEC-2008 (first entry)
XX
DE Human transcriptional regulatory element SEQ ID NO 10743.
XX
KW gene expression; gene regulation; transcription; DNA library;
KW DNA microarray; ds; pharmacogenetics; mapping; DNA polymorphism.
XX
OS Homo sapiens.
XX
CC PN WO2008073303-A2.
XX
CC PD 19-JUN-2008.
XX
CC PF 06-DEC-2007; 2007WO-US025093.
XX
PR 07-DEC-2006; 2006US-0873737P.
PR 07-DEC-2006; 2006US-0873738P.
PR 07-DEC-2006; 2006US-0873739P.
PR 07-DEC-2006; 2006US-0873853P.
PR 07-DEC-2006; 2006US-0873871P.
PR 07-DEC-2006; 2006US-0873882P.
PR 07-DEC-2006; 2006US-0873883P.
PR 06-JUL-2007; 2007US-0958616P.
XX
CC PA (SWIT-) SWITCHGEAR GENOMICS.
XX
CC PI Aldred SF, Trinklein N;
XX
DR WPI; 2008-H01915/44.
XX
CC PT New library of different expression constructs, useful for personalized
CC PT medicine, pharmacogenomics or correlation of polymorphisms with
CC PT phenotypic traits.
XX
CC PS Claim 15; SEQ ID NO 10743; 59pp; English.
XX
CC The invention relates to a library of different expression constructs.
CC Each member of the library comprises a different nucleic acid segment
CC from a genome, where the segment comprises transcription regulatory
CC sequences operably linked with a heterologous reporter sequence in an
CC expression vector such that expression of the reporter sequence is under
CC transcriptional control of the transcription regulatory sequences, where
CC at least 20\% of the transcription regulatory sequences of the expression
CC constructs in the library are part of a common pathway. The common
CC pathway is oncology, membrane, vascular, neuronal, signaling or nuclear
CC receptor pathway. The common pathway is an oncology pathway. The oncology
CC pathway is hypoxia pathway, DNA-damage pathway, apoptosis pathway, cell
CC cycle pathway or p53 pathway. The regulatory elements are SEQ ID NO: 1-
CC 3836. The common pathway is a membrane pathway. The membrane pathway is
CC transport protein pathways, G-protein coupled receptor pathways, ion
CC channel pathways or cell adhesion protein pathways. The regulatory
CC elements are SEQ ID NO: 3837-12716. The common pathway is a nuclear
CC receptor pathway. The nuclear receptor pathway is glucocorticoid receptor
CC pathway, peroxisome proliferator-activated receptor pathway, estrogen
CC receptor pathway, androgen receptor pathway, cytochrome P450 pathway or
CC transporter pathways. The regulatory elements are SEQ ID NO: 12717-13994.
CC The library of different expression constructs is useful for personalized
CC medicine, pharmacogenomics or correlation of polymorphisms with
CC phenotypic traits. The invention provides a library of different
CC expression constructs for large scale structural and functional
CC characterization of gene expression regulatory elements in a genome of an
CC organism, especially in a human genome that is part of a common pathway.
XX
SQ Sequence 6000 BP; 1270 A; 1793 C; 1722 G; 1215 T; 0 U; 0 Other;
Query Match 99.9%; Score 1999; Length 6000;
Best Local Similarity 100.0%;
Matches 1999; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 2 GAGGCGTGAGCGTCTACAGTGAACCCAGCACAGAAACCTGCTAGGGGAGCTGCTGTTGAC 61 SEQ ID NO 8
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2727 GAGGCGTGAGCGTCTACAGTGAACCCAGCACAGAAACCTGCTAGGGGAGCTGCTGTTGAC 2786 WO303 #10743
Qy 62 TGCATCGCGATCCAAAGGACCGGCGTCTTTTGTAGATGCAGGGGCTGAGCCAGGCCAAGC 121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2787 TGCATCGCGATCCAAAGGACCGGCGTCTTTTGTAGATGCAGGGGCTGAGCCAGGCCAAGC 2846
Qy 122 GCGCCGTGGAGGCCCGCGTGGACGCAGACCCGGGTGCCATACAGATGCGCTGGAATCCAG 181
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2847 GCGCCGTGGAGGCCCGCGTGGACGCAGACCCGGGTGCCATACAGATGCGCTGGAATCCAG 2906
Qy 182 GCACTTTCCCGCGCTCCGCAAATCTAGATGTTTCAGCCTGGATCGAGCGAGGGTTAGAGG 241
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2907 GCACTTTCCCGCGCTCCGCAAATCTAGATGTTTCAGCCTGGATCGAGCGAGGGTTAGAGG 2966
Qy 242 GTTAGTCAGGCCAGGGTCAACTTCAGAGTCATGGGCTCCCTAAATGCGACTTCTAGGGTT 301
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2967 GTTAGTCAGGCCAGGGTCAACTTCAGAGTCATGGGCTCCCTAAATGCGACTTCTAGGGTT 3026
Qy 302 GAGTTGCTGTGGACGAGCGACCCATGTCGGAATCCCGCGCCCACGTGGCTGCCCAAAGTT 361
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3027 GAGTTGCTGTGGACGAGCGACCCATGTCGGAATCCCGCGCCCACGTGGCTGCCCAAAGTT 3086
Qy 362 CCGAGTCTCCGGGCTGCAGGTTCTAGTCACGGAACCGAGTTGGGAGAGTCATAGGGGCTG 421
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3087 CCGAGTCTCCGGGCTGCAGGTTCTAGTCACGGAACCGAGTTGGGAGAGTCATAGGGGCTG 3146
Qy 422 GGACTTGGAGGATCGGCTGAGGTCCGGTGCTCTTGGCTGTGTTCGCGGCTCGGAGCCGTC 481
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3147 GGACTTGGAGGATCGGCTGAGGTCCGGTGCTCTTGGCTGTGTTCGCGGCTCGGAGCCGTC 3206
Qy 482 GCCTGACTGAGGGGCCCGTCACAGATGTGTGATGTATAAGCTCTGCACGCAACAGGAGCT 541
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3207 GCCTGACTGAGGGGCCCGTCACAGATGTGTGATGTATAAGCTCTGCACGCAACAGGAGCT 3266
Qy 542 CAATAAATGTGCGAAGGGGGGTATACTTATGTTCGCACTGTATGCAGGCGGCCTAGAAGG 601
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3267 CAATAAATGTGCGAAGGGGGGTATACTTATGTTCGCACTGTATGCAGGCGGCCTAGAAGG 3326
Qy 602 AAGTCCCTGATTGGCACAGGGATGGAGGATGGGGCAAGAGCCGCAACAGCGCCGCGGAGT 661
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3327 AAGTCCCTGATTGGCACAGGGATGGAGGATGGGGCAAGAGCCGCAACAGCGCCGCGGAGT 3386
Qy 662 TCCAACGCTGCCGGTTCCCTGGGGTACGAGCACAGCCTCAAGCAGCCTCAAGCCCTAGGA 721
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3387 TCCAACGCTGCCGGTTCCCTGGGGTACGAGCACAGCCTCAAGCAGCCTCAAGCCCTAGGA 3446
Qy 722 AGCCCCCAGTTCAAAGCACAGGGCGCATTGGAGCCTGGGCACGATACAGTTCACACCACG 781
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3447 AGCCCCCAGTTCAAAGCACAGGGCGCATTGGAGCCTGGGCACGATACAGTTCACACCACG 3506
Qy 782 GCTGCGATGGTAAGCCACGCCCAAGTCCCAAGGGCCTAGGGGACCCCCGCCCTCCACAGC 841
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3507 GCTGCGATGGTAAGCCACGCCCAAGTCCCAAGGGCCTAGGGGACCCCCGCCCTCCACAGC 3566
Qy 842 CGGAGGAGAAACCTGGGCGCAGAAAGCAGGGGGAATATCTGGTTGTAGGTGAGTAAGCGG 901
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3567 CGGAGGAGAAACCTGGGCGCAGAAAGCAGGGGGAATATCTGGTTGTAGGTGAGTAAGCGG 3626
Qy 902 GGTCAGGAGTTCCCGTTAGAGTCTCTGCGTTTCGGGAGAAGGGTGATCATTCCCAGGCTT 961
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3627 GGTCAGGAGTTCCCGTTAGAGTCTCTGCGTTTCGGGAGAAGGGTGATCATTCCCAGGCTT 3686
Qy 962 GTCCGACGTCTCTCTCAGGGTGCGCTCCGGAAGAGCGAGCCCTTTAAGGCTATGCCGAGT 1021
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3687 GTCCGACGTCTCTCTCAGGGTGCGCTCCGGAAGAGCGAGCCCTTTAAGGCTATGCCGAGT 3746
Qy 1022 GGGCGCGTCCCGGCCTCTCCCGGGAGAGGAGAGGCGGGGCGGACCTGTGTCCCGCCCCCG 1081
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3747 GGGCGCGTCCCGGCCTCTCCCGGGAGAGGAGAGGCGGGGCGGACCTGTGTCCCGCCCCCG 3806
Qy 1082 GCCCGGCCCGCCCCCAGTGCCCGCCCCGCCCCCGGCACTCGGCCGGCGGCGCCTTTGATG 1141
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3807 GCCCGGCCCGCCCCCAGTGCCCGCCCCGCCCCCGGCACTCGGCCGGCGGCGCCTTTGATG 3866
Qy 1142 TTCCGACCCGCCAGCTCGCGGAGCCGCTCTGCCCCGCGCCCTAGCCCGCGCCTGCAGCCC 1201
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3867 TTCCGACCCGCCAGCTCGCGGAGCCGCTCTGCCCCGCGCCCTAGCCCGCGCCTGCAGCCC 3926
Qy 1202 GCCCAGGCGGAGTCAGCCCGCGCTCCGCCCGCCGCGATCCGAGCTCGGAGGTTCGGACTC 1261
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3927 GCCCAGGCGGAGTCAGCCCGCGCTCCGCCCGCCGCGATCCGAGCTCGGAGGTTCGGACTC 3986
Qy 1262 CGGGCTCGCCGCCCCCCGGGCCGGCTCCGCGCCCCGCACTCCCGGCGCCCAGCGCCCCGC 1321
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3987 CGGGCTCGCCGCCCCCCGGGCCGGCTCCGCGCCCCGCACTCCCGGCGCCCAGCGCCCCGC 4046
Qy 1322 GCCCCGGCGGGCGGAGCGCACCATGCCGCAGCTGGACTCCGGCGGGGGCGGCGCGGGCGG 1381
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4047 GCCCCGGCGGGCGGAGCGCACCATGCCGCAGCTGGACTCCGGCGGGGGCGGCGCGGGCGG 4106
Qy 1382 CGGCGACGACCTCGGCGCGCCGGACGAGCTGCTGGCCTTCCAGGATGAAGGCGAGGAGCA 1441
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4107 CGGCGACGACCTCGGCGCGCCGGACGAGCTGCTGGCCTTCCAGGATGAAGGCGAGGAGCA 4166
Qy 1442 GGACGACAAGAGCCGCGACAGCGCCGCCGGTCCCGAGCGCGACCTGGCCGAGCTCAAGTC 1501
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4167 GGACGACAAGAGCCGCGACAGCGCCGCCGGTCCCGAGCGCGACCTGGCCGAGCTCAAGTC 4226
Qy 1502 GTCGCTCGTGAACGAGTCCGAGGGCGCGGCCGGCGGCGCAGGGATCCCGGGGGTCCCGGG 1561
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4227 GTCGCTCGTGAACGAGTCCGAGGGCGCGGCCGGCGGCGCAGGGATCCCGGGGGTCCCGGG 4286
Qy 1562 GGCCGGCGCCGGGGCCCGCGGCGAGGCCGAGGTGAGCCCCCGCCGGCGCCGGCTCCTCCC 1621
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4287 GGCCGGCGCCGGGGCCCGCGGCGAGGCCGAGGTGAGCCCCCGCCGGCGCCGGCTCCTCCC 4346
Qy 1622 CCGCGGTCGCCGCGCCGCGCCGCCCCAGTTGCGCGCGGCCCTCGGGGTCTCCAGCGCGCA 1681
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4347 CCGCGGTCGCCGCGCCGCGCCGCCCCAGTTGCGCGCGGCCCTCGGGGTCTCCAGCGCGCA 4406
Qy 1682 GAGCGTCCCTGCCCCGGCGTCGGCCCCGACCCCCGCGGTCCCACCGCCCCTCACTCCCCT 1741
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4407 GAGCGTCCCTGCCCCGGCGTCGGCCCCGACCCCCGCGGTCCCACCGCCCCTCACTCCCCT 4466
Qy 1742 CCGGTTCTCCCTCCAGGCTCTCGGGCGGGAACACGCTGCGCAGAGACTCTTCCCGGACAA 1801
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4467 CCGGTTCTCCCTCCAGGCTCTCGGGCGGGAACACGCTGCGCAGAGACTCTTCCCGGACAA 4526
Qy 1802 ACTTCCAGAGCCCCTGGAGGACGGTGAGTTTCTGCCCGGCCCGGCTTCCCTTCGTCGCGC 1861
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4527 ACTTCCAGAGCCCCTGGAGGACGGTGAGTTTCTGCCCGGCCCGGCTTCCCTTCGTCGCGC 4586
Qy 1862 TCAGGCCCTGGCCTCGGTGGGACGGGGACGCCAAGGACCGCGGGGAGCCGGGTGCCTCCC 1921
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4587 TCAGGCCCTGGCCTCGGTGGGACGGGGACGCCAAGGACCGCGGGGAGCCGGGTGCCTCCC 4646
Qy 1922 CCACCGCAGCTCAGGAGGCGGCAGAACCCAGGGGTGGAGAGTGGGGGGCGGGCTTCCCGG 1981
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4647 CCACCGCAGCTCAGGAGGCGGCAGAACCCAGGGGTGGAGAGTGGGGGGCGGGCTTCCCGG 4706
Qy 1982 GCGCCGCCGGGTCGAGTCA 2000
|||||||||||||||||||
Db 4707 GCGCCGCCGGGTCGAGTCA 4725
RESULT 2
ATN03552
(NOTE: this sequence has 1 duplicate in the database searched.
See complete list at the end of this report)
ID ATN03552 standard; DNA; 6000 BP.
XX
AC ATN03552;
XX
DT 11-DEC-2008 (first entry)
XX
DE Human transcriptional regulatory element SEQ ID NO 1492.
XX
KW gene expression; gene regulation; transcription; DNA library;
KW DNA microarray; ds; pharmacogenetics; mapping; DNA polymorphism.
XX
OS Homo sapiens.
XX
CC PN WO2008073303-A2.
XX
CC PD 19-JUN-2008.
XX
CC PF 06-DEC-2007; 2007WO-US025093.
XX
PR 07-DEC-2006; 2006US-0873737P.
PR 07-DEC-2006; 2006US-0873738P.
PR 07-DEC-2006; 2006US-0873739P.
PR 07-DEC-2006; 2006US-0873853P.
PR 07-DEC-2006; 2006US-0873871P.
PR 07-DEC-2006; 2006US-0873882P.
PR 07-DEC-2006; 2006US-0873883P.
PR 06-JUL-2007; 2007US-0958616P.
XX
CC PA (SWIT-) SWITCHGEAR GENOMICS.
XX
CC PI Aldred SF, Trinklein N;
XX
DR WPI; 2008-H01915/44.
XX
CC PT New library of different expression constructs, useful for personalized
CC PT medicine, pharmacogenomics or correlation of polymorphisms with
CC PT phenotypic traits.
XX
CC PS Claim 10; SEQ ID NO 1492; 59pp; English.
XX
CC The invention relates to a library of different expression constructs.
CC Each member of the library comprises a different nucleic acid segment
CC from a genome, where the segment comprises transcription regulatory
CC sequences operably linked with a heterologous reporter sequence in an
CC expression vector such that expression of the reporter sequence is under
CC transcriptional control of the transcription regulatory sequences, where
CC at least 20\% of the transcription regulatory sequences of the expression
CC constructs in the library are part of a common pathway. The common
CC pathway is oncology, membrane, vascular, neuronal, signaling or nuclear
CC receptor pathway. The common pathway is an oncology pathway. The oncology
CC pathway is hypoxia pathway, DNA-damage pathway, apoptosis pathway, cell
CC cycle pathway or p53 pathway. The regulatory elements are SEQ ID NO: 1-
CC 3836. The common pathway is a membrane pathway. The membrane pathway is
CC transport protein pathways, G-protein coupled receptor pathways, ion
CC channel pathways or cell adhesion protein pathways. The regulatory
CC elements are SEQ ID NO: 3837-12716. The common pathway is a nuclear
CC receptor pathway. The nuclear receptor pathway is glucocorticoid receptor
CC pathway, peroxisome proliferator-activated receptor pathway, estrogen
CC receptor pathway, androgen receptor pathway, cytochrome P450 pathway or
CC transporter pathways. The regulatory elements are SEQ ID NO: 12717-13994.
CC The library of different expression constructs is useful for personalized
CC medicine, pharmacogenomics or correlation of polymorphisms with
CC phenotypic traits. The invention provides a library of different
CC expression constructs for large scale structural and functional
CC characterization of gene expression regulatory elements in a genome of an
CC organism, especially in a human genome that is part of a common pathway.
XX
SQ Sequence 6000 BP; 1393 A; 1301 C; 1783 G; 1523 T; 0 U; 0 Other;
Query Match 100.0%; Score 2000; Length 6000;
Best Local Similarity 100.0%;
Matches 2000; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 AAAAATACAAAAGTTAGCCAAGCGTGATGGTGCATGCCTGTAATCCCAACTACTCAGGAG 60 SEQ ID NO 14
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2943 AAAAATACAAAAGTTAGCCAAGCGTGATGGTGCATGCCTGTAATCCCAACTACTCAGGAG 3002 WO303 #1492
Qy 61 GCCGAGGCAGGAGAATTGCTTGAACCTGGGAGGTAGAGGTTGCAGGAAAAAAAAAAAAGG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3003 GCCGAGGCAGGAGAATTGCTTGAACCTGGGAGGTAGAGGTTGCAGGAAAAAAAAAAAAGG 3062
Qy 121 TAATATTTCAGCTGAGCCTTGAAGGTTGAGTTAGAATTCAGCAGTTGGACAAAAGAGAGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3063 TAATATTTCAGCTGAGCCTTGAAGGTTGAGTTAGAATTCAGCAGTTGGACAAAAGAGAGC 3122
Qy 181 ATGCCGACTGGGTTCGGTGGTGCATGCCTATAATCCTAGCATTTGGGGAGGCCAAGGCAG 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3123 ATGCCGACTGGGTTCGGTGGTGCATGCCTATAATCCTAGCATTTGGGGAGGCCAAGGCAG 3182
Qy 241 GAGGATTGCTTGAGCCCAGGAGTTCGAGATCAGACTGGGCAACATAGTGAGACCTCATCT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3183 GAGGATTGCTTGAGCCCAGGAGTTCGAGATCAGACTGGGCAACATAGTGAGACCTCATCT 3242
Qy 301 CTACAAAAAAATAATCAGCTGGGCATGATGGTGTGCACCTTTAGTCTCAGCTACTGGGGA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3243 CTACAAAAAAATAATCAGCTGGGCATGATGGTGTGCACCTTTAGTCTCAGCTACTGGGGA 3302
Qy 361 GGTTGAGGTGGGAAGATTGCTTGAGCCCAGGAGGTCTAAGGGGATTGCGCCACTGCACTT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3303 GGTTGAGGTGGGAAGATTGCTTGAGCCCAGGAGGTCTAAGGGGATTGCGCCACTGCACTT 3362
Qy 421 CAGCCTGGGAGAGGAAGGGAGACCCTGTCTCAAGAGAGAGAGAGAAAGAGAGAGAGAGAG 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3363 CAGCCTGGGAGAGGAAGGGAGACCCTGTCTCAAGAGAGAGAGAGAAAGAGAGAGAGAGAG 3422
Qy 481 AGAAAGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGCGAGAGAGCGCA 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3423 AGAAAGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGCGAGAGAGCGCA 3482
Qy 541 CGCATTTCAAAGCAGGGAGAACCACAAGTACAAAGGCATTAAGTAAGAAAATAGCATGGG 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3483 CGCATTTCAAAGCAGGGAGAACCACAAGTACAAAGGCATTAAGTAAGAAAATAGCATGGG 3542
Qy 601 GTGTTTGGGAAAGGCAAGAATAGTTCAGAACACAGGCTGTGTGTGTGGGGGTGTGTGGGG 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3543 GTGTTTGGGAAAGGCAAGAATAGTTCAGAACACAGGCTGTGTGTGTGGGGGTGTGTGGGG 3602
Qy 661 GTGCCTGTGTGTGGGTGTTTGTGTGTGTGTGAGTGTGGGTGTGTGGGGGTATCTATGGAG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3603 GTGCCTGTGTGTGGGTGTTTGTGTGTGTGTGAGTGTGGGTGTGTGGGGGTATCTATGGAG 3662
Qy 721 GGGATGCCTGTGTGTGTGTGTAAGGTGAGTGTGTGGATGTGTGCATGGGTGTGGGTGAGT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3663 GGGATGCCTGTGTGTGTGTGTAAGGTGAGTGTGTGGATGTGTGCATGGGTGTGGGTGAGT 3722
Qy 781 GTGTGGAGGTGCCTGTGTGTGTGTATGAATGTGTGTTGGGGAGGGGAGAATGTGTGTGTG 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3723 GTGTGGAGGTGCCTGTGTGTGTGTATGAATGTGTGTTGGGGAGGGGAGAATGTGTGTGTG 3782
Qy 841 TGGGGTGAGTGCGTGTGTGTGGGGGTGAATGCGTGTGTGTGTGTATGTGGGTGTGACTGT 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3783 TGGGGTGAGTGCGTGTGTGTGGGGGTGAATGCGTGTGTGTGTGTATGTGGGTGTGACTGT 3842
Qy 901 GTGGGTGTGTGGACGAGTGTGTGTGTTCCTGGGTGTGGGAGCCTGTGTGTGTAGGGGGAG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3843 GTGGGTGTGTGGACGAGTGTGTGTGTTCCTGGGTGTGGGAGCCTGTGTGTGTAGGGGGAG 3902
Qy 961 TATGTATAGGGTGTGTGCATGAATGTGTGTGTGGGTACGTGTGTGAGAGTGGGTGCCTGT 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3903 TATGTATAGGGTGTGTGCATGAATGTGTGTGTGGGTACGTGTGTGAGAGTGGGTGCCTGT 3962
Qy 1021 GTGTGGGGGGTGAGTGTGTGTGTGGGGGGGCACTTGTGGAGGGTGAGTGTATGTGTTTAC 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3963 GTGTGGGGGGTGAGTGTGTGTGTGGGGGGGCACTTGTGGAGGGTGAGTGTATGTGTTTAC 4022
Qy 1081 TGAGTGTGAGTGTGGGTGCCTGTGTGTGGGAGGGTGAGTCTGTGTGTGAGTGTGTGGGGG 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4023 TGAGTGTGAGTGTGGGTGCCTGTGTGTGGGAGGGTGAGTCTGTGTGTGAGTGTGTGGGGG 4082
Qy 1141 AGTACCTGTGAGGGGTGAGTGTGTGTGTTTATGTGAAAGTGTGTGTGTGTGGATGCCTCT 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4083 AGTACCTGTGAGGGGTGAGTGTGTGTGTTTATGTGAAAGTGTGTGTGTGTGGATGCCTCT 4142
Qy 1201 GTGGAGGTGGGATAGGGGGTGCCTCTGTGTGTGTGTGTGAGAGTGTGTGTGTGTAGGGTG 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4143 GTGGAGGTGGGATAGGGGGTGCCTCTGTGTGTGTGTGTGAGAGTGTGTGTGTGTAGGGTG 4202
Qy 1261 TGTATATGTATAGGGTGTGTGTGAGTGTGTGTGTGTGAGAGAGTGTGTGTGTGGCAGAAT 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4203 TGTATATGTATAGGGTGTGTGTGAGTGTGTGTGTGTGAGAGAGTGTGTGTGTGGCAGAAT 4262
Qy 1321 AGACTGCGGAGGTGGATTTCATCTTGATATGAAAGGTCTGGAATGCATGGTACATTAAAC 1380
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4263 AGACTGCGGAGGTGGATTTCATCTTGATATGAAAGGTCTGGAATGCATGGTACATTAAAC 4322
Qy 1381 TTTGAGGACAGCGCTTTCCAAGCACTCTGAGGAGCAGCCCTAGAGAAGGAGGAGCTGCAG 1440
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4323 TTTGAGGACAGCGCTTTCCAAGCACTCTGAGGAGCAGCCCTAGAGAAGGAGGAGCTGCAG 4382
Qy 1441 GGACTCCGGGGGCTTCAAAGTGAGGGCCCCACTCTGCTTCAGGCAAAACAGGCACACATT 1500
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4383 GGACTCCGGGGGCTTCAAAGTGAGGGCCCCACTCTGCTTCAGGCAAAACAGGCACACATT 4442
Qy 1501 TATCACTTTATCTATGGAGTTCTGCTTGATTTCATCAGACAAAAAATTTCCACTGCTAAA 1560
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4443 TATCACTTTATCTATGGAGTTCTGCTTGATTTCATCAGACAAAAAATTTCCACTGCTAAA 4502
Qy 1561 ACAGGCAAATAAACAAAAAAAAAGTTATGGCCAACAGAGTCACTGGAGGGTTTTCTGCTG 1620
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4503 ACAGGCAAATAAACAAAAAAAAAGTTATGGCCAACAGAGTCACTGGAGGGTTTTCTGCTG 4562
Qy 1621 GGGAGAAGCAAGCCCGTGTTTGAAGGAACCCTGTGAGATGACTGTGGGCTGTGTGAGGGG 1680
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4563 GGGAGAAGCAAGCCCGTGTTTGAAGGAACCCTGTGAGATGACTGTGGGCTGTGTGAGGGG 4622
Qy 1681 AACAGCGGGGGCTTGATGGTGGACTTCGGGAGCAGAAGCCTCTTTCTCAGCCTCCTCAGC 1740
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4623 AACAGCGGGGGCTTGATGGTGGACTTCGGGAGCAGAAGCCTCTTTCTCAGCCTCCTCAGC 4682
Qy 1741 TAGACAGGGGAATTATAATAGGAGGTGTGGCGTGCACACCTCTCCAGTAGGGGAGGGTCT 1800
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4683 TAGACAGGGGAATTATAATAGGAGGTGTGGCGTGCACACCTCTCCAGTAGGGGAGGGTCT 4742
Qy 1801 GATAAGTCAGGTCTCTCCCAGGCTTGGGAAAGTGTGTGTCATCTCTAGGAGGTGGTCCTC 1860
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4743 GATAAGTCAGGTCTCTCCCAGGCTTGGGAAAGTGTGTGTCATCTCTAGGAGGTGGTCCTC 4802
Qy 1861 CCAACACAGGGTACTGGCAGAGGGAGAGGGAGGGGGCAGAGGCAGGAAGTGGGTAACTAG 1920
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4803 CCAACACAGGGTACTGGCAGAGGGAGAGGGAGGGGGCAGAGGCAGGAAGTGGGTAACTAG 4862
Qy 1921 ACTAACAAAGGTGCCTGTGGCGGTTTGCCCATCCCAGGTGGGAGGGTGGGGCTAGGGCTC 1980
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4863 ACTAACAAAGGTGCCTGTGGCGGTTTGCCCATCCCAGGTGGGAGGGTGGGGCTAGGGCTC 4922
Qy 1981 AGGGGCCGTGTGTGAATTTA 2000
||||||||||||||||||||
Db 4923 AGGGGCCGTGTGTGAATTTA 4942
RESULT 2
ATN12776
ID ATN12776 standard; DNA; 6000 BP.
XX
AC ATN12776;
XX
DT 11-DEC-2008 (first entry)
XX
DE Human transcriptional regulatory element SEQ ID NO 10716.
XX
KW gene expression; gene regulation; transcription; DNA library;
KW DNA microarray; ds; pharmacogenetics; mapping; DNA polymorphism.
XX
OS Homo sapiens.
XX
CC PN WO2008073303-A2.
XX
CC PD 19-JUN-2008.
XX
CC PF 06-DEC-2007; 2007WO-US025093.
XX
PR 07-DEC-2006; 2006US-0873737P.
PR 07-DEC-2006; 2006US-0873738P.
PR 07-DEC-2006; 2006US-0873739P.
PR 07-DEC-2006; 2006US-0873853P.
PR 07-DEC-2006; 2006US-0873871P.
PR 07-DEC-2006; 2006US-0873882P.
PR 07-DEC-2006; 2006US-0873883P.
PR 06-JUL-2007; 2007US-0958616P.
XX
CC PA (SWIT-) SWITCHGEAR GENOMICS.
XX
CC PI Aldred SF, Trinklein N;
XX
DR WPI; 2008-H01915/44.
XX
CC PT New library of different expression constructs, useful for personalized
CC PT medicine, pharmacogenomics or correlation of polymorphisms with
CC PT phenotypic traits.
XX
CC PS Claim 15; SEQ ID NO 10716; 59pp; English.
XX
CC The invention relates to a library of different expression constructs.
CC Each member of the library comprises a different nucleic acid segment
CC from a genome, where the segment comprises transcription regulatory
CC sequences operably linked with a heterologous reporter sequence in an
CC expression vector such that expression of the reporter sequence is under
CC transcriptional control of the transcription regulatory sequences, where
CC at least 20\% of the transcription regulatory sequences of the expression
CC constructs in the library are part of a common pathway. The common
CC pathway is oncology, membrane, vascular, neuronal, signaling or nuclear
CC receptor pathway. The common pathway is an oncology pathway. The oncology
CC pathway is hypoxia pathway, DNA-damage pathway, apoptosis pathway, cell
CC cycle pathway or p53 pathway. The regulatory elements are SEQ ID NO: 1-
CC 3836. The common pathway is a membrane pathway. The membrane pathway is
CC transport protein pathways, G-protein coupled receptor pathways, ion
CC channel pathways or cell adhesion protein pathways. The regulatory
CC elements are SEQ ID NO: 3837-12716. The common pathway is a nuclear
CC receptor pathway. The nuclear receptor pathway is glucocorticoid receptor
CC pathway, peroxisome proliferator-activated receptor pathway, estrogen
CC receptor pathway, androgen receptor pathway, cytochrome P450 pathway or
CC transporter pathways. The regulatory elements are SEQ ID NO: 12717-13994.
CC The library of different expression constructs is useful for personalized
CC medicine, pharmacogenomics or correlation of polymorphisms with
CC phenotypic traits. The invention provides a library of different
CC expression constructs for large scale structural and functional
CC characterization of gene expression regulatory elements in a genome of an
CC organism, especially in a human genome that is part of a common pathway.
XX
SQ Sequence 6000 BP; 1698 A; 1277 C; 1127 G; 1898 T; 0 U; 0 Other;
Query Match 99.9%; Score 1998.4; Length 6000;
Best Local Similarity 99.9%;
Matches 1999; Conservative 0; Mismatches 1; Indels 0; Gaps 0;
Qy 1 TTGGCTCCTATGAAGTGAACTTTTTAAAACCAAAACAAACAAAGGGACTATTTGTTTTTG 60 SEQ ID NO 15
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2955 TTGGCTCCTATGAAGTGAACTTTTTAAAACCAAAACAAACAAAGGGACTATTTGTTTTTG 3014 WO303 #10716
Qy 61 TTTATGTTTTCCTTAAAGTGAGAAAAAAATATTGAGCCTCCTAAGTTTGCATTTAAAAGT 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3015 TTTATGTTTTCCTTAAAGTGAGAAAAAAATATTGAGCCTCCTAAGTTTGCATTTAAAAGT 3074
Qy 121 TGGCAAAGATGAGTCTCAGTTAGTGGGTTTGATGGCTCTATGAGAAAGAGAATAAAATTA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3075 TGGCAAAGATGAGTCTCAGTTAGTGGGTTTGATGGCTCTATGAGAAAGAGAATAAAATTA 3134
Qy 181 CTTACGATGACACTCCATGTAGACTGAGCAAACGAAAGACTCCTAAGTATTGCAACAGCT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3135 CTTACGATGACACTCCATGTAGACTGAGCAAACGAAAGACTCCTAAGTATTGCAACAGCT 3194
Qy 241 ACTGATGATATTTTGTTTTCCCGGATGAGAACACTTTGTGAAGTCTATAACTCTTTTCAT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3195 ACTGATGATATTTTGTTTTCCCGGATGAGAACACTTTGTGAAGTCTATAACTCTTTTCAT 3254
Qy 301 CTGAACCAAGCAGGTGTAAAATGTACTTTCCTCAGAGGAGTTTGTAGTCTAGTTTGAGAA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3255 CTGAACCAAGCAGGTGTAAAATGTACTTTCCTCAGAGGAGTTTGTAGTCTAGTTTGAGAA 3314
Qy 361 GATAGCACTGTATTATCTAGGTTTGCTGGTAGTGACAGAAACCTCAAAATAACTGAGACT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3315 GATAGCACTGTATTATCTAGGTTTGCTGGTAGTGACAGAAACCTCAAAATAACTGAGACT 3374
Qy 421 TAGAAAATAGATATTAAAAAATGTAATCCAGGGCTGGCATGGAAGATCCATGGTCACCAG 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3375 TAGAAAATAGATATTAAAAAATGTAATCCAGGGCTGGCATGGAAGATCCATGGTCACCAG 3434
Qy 481 GGTCCCAGGCTCTTTCTATCTTATACTCCATTGTCCTCAACATTCAATTTCCACCTCATG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3435 GGTCCCAGGCTCTTTCTATCTTATACTCCATTGTCCTCAACATTCAATTTCCACCTCATG 3494
Qy 541 ATACTAGATAGCTGCTTCAGCTCCAACTGTTACCTCAATATTCTAGTCACAAGGCAGGAG 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3495 ATACTAGATAGCTGCTTCAGCTCCAACTGTTACCTCAATATTCTAGTCACAAGGCAGGAG 3554
Qy 601 GAAAAGGGAAAGAAAAGGGGATGACAGATCCCACTAAGGAAATTTCCTAGAAGTTGTGCA 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3555 GAAAAGGGAAAGAAAAGGGGATGACAGATCCCACTAAGGAAATTTCCTAGAAGTTGTGCA 3614
Qy 661 CACGACTTCTGCTACATTCAGTTGACCAGAAGACAGTCATACAACTACACCTAGCTACAA 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3615 CACGACTTCTGCTACATTCAGTTGACCAGAAGACAGTCATACAACTACACCTAGCTACAA 3674
Qy 721 GGGAGGCTAAAATTTGTAGTCTTTATTCTTGCTGGCCAGATGCCCAGATAACTGTCAGGG 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3675 GGGAGGCTAAAATTTGTAGTCTTTATTCTTGCTGGCCAGATGCCCAGATAACTGTCAGGG 3734
Qy 781 ATTCTGTTACTCTAGTAAGAAGGAGAGAGTAGCTATTTGGGAATAGTAGCAATCCCTACC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3735 ATTCTGTTACTCTAGTAAGAAGGAGAGAGTAGCTATTTGGGAATAGTAGCAATCCCTACC 3794
Qy 841 TCAAGCCCATACTCAGAAAAAAAAAATACTATCTTGTTTGGGCAGTGTATTTCCACACAT 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3795 TCAAGCCCATACTCAGAAAAAAAAAATACTATCTTGTTTGGGCAGTGTATTTCCACACAT 3854
Qy 901 ATGTCTTAAGAATCTCAGAATGGGGGAGGTAATTTAAAATATACCAGTACCGTACCCTCC 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3855 ATGTCTTAAGAATCTCAGAATGGGGGAGGTAATTTAAAATATACCAGTACCGTACCCTCC 3914
Qy 961 TGGGTGTCTTGATTATGCTGGGGCATCCAGTATATGAAATAAAATTAGGCTGTTGTCTGG 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3915 TGGGTGTCTTGATTATGCTGGGGCATCCAGTATATGAAATAAAATTAGGCTGTTGTCTGG 3974
Qy 1021 TAATTTACATTTAAAAATAAACATTGGAGAATTTCACTCCTATACAGCAATAATTATTAT 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3975 TAATTTACATTTAAAAATAAACATTGGAGAATTTCACTCCTATACAGCAATAATTATTAT 4034
Qy 1081 TTCATTTATTATTTATCCCTACCCACTACATGCAATATCTGCTTACACTAAAATCTCTTG 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4035 TTCATTTATTATTTATCCCTACCCACTACATGCAATATCTGCTTACACTAAAATCTCTTG 4094
Qy 1141 ATTATTAACATAGTAGAGGTAACTGTCACACATTATACTTCAACTATGTACTAACTCTAA 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4095 ATTATTAACATAGTAGAGGTAACTGTCACACATTATACTTCAACTATGTACTAACTCTAA 4154
Qy 1201 GGTGACATGTATGACTAGCACCTACCATTCATAAGATGTATGGGATTCAGTCCTCCAAAG 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4155 GGTGACATGTATGACTAGCACCTACCATTCATAAGATGTATGGGATTCAGTCCTCCAAAG 4214
Qy 1261 GACCCTCACAAGGAAGCTAAGGATCAGAGAAGTCATGGCTTGCTCAAAGAGAAACAGCAT 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4215 GACCCTCACAAGGAAGCTAAGGATCAGAGAAGTCATGGCTTGCTCAAAGAGAAACAGCAT 4274
Qy 1321 AGTAAGTGACAGAGCTGGGAATCCAACACAAGTTTGTCTGTTTTCAAAGCCCACATATAC 1380
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4275 AGTAAGTGACAGAGCTGGGAATCCAACACAAGTTTGTCTGTTTTCAAAGCCCACATATAC 4334
Qy 1381 TTTGTTTATTATGCCATTCTGAAGGATTCACTTATTTTTCACTCTTCCACAAAACGTCAG 1440
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4335 TTTGTTTATTATGCCATTCTGAAGGATTCACTTATTTTTCACTCTTCCACAAAACGTCAG 4394
Qy 1441 GACAGAAAGGCAGTCATCTATATGTAGCATTGAGAAATTTCTATGGGCTTTAATTTAAAT 1500
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4395 GACAGAAAGGCAGTCATCTATATGTAGCATTGAGAAATTTCTATGGGCTTTAATTTAAAT 4454
Qy 1501 CTTAAAAACTAATAAACTTCAGCAACATATTTCTTCACTTTAATGTGTGAGGGTTTTGTG 1560
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4455 CTTAAAAACTAATAAACTTCAGCAACATATTTCTTCACTTTAATGTGTGAGGGTTTTGTG 4514
Qy 1561 CTCATTACCTCTTTTAATTGTCCAACCCAATTTGGTGATGATCCATTCAACAAATTTTTC 1620
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4515 CTCATTACCTCTTTTAATTGTCCAACCCAATTTGGTGATGATCCATTCAACAAATTTTTC 4574
Qy 1621 TTGAACATCTGTTTTATGTGTCAGGTACTGTGATGGTTGCTGAGTATATCATGGTAAGCA 1680
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4575 TTGAACATCTGTTTTATGTGTCAGGTACTGTGATGGTTGCTGAGTATATCATGGTAAGCA 4634
Qy 1681 AAACCACACATTGTCCTTACCCCTTGTGCTACATGATTTAACTGCTGGATGGATTAAACC 1740
|||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Db 4635 AAACCACACATTGTCCTTACTCCTTGTGCTACATGATTTAACTGCTGGATGGATTAAACC 4694
Qy 1741 AGGAACTATAAAGATTAAACTGTAATCCTTACCACAATTTTGAGTTTACAGTTTTTCAAA 1800
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4695 AGGAACTATAAAGATTAAACTGTAATCCTTACCACAATTTTGAGTTTACAGTTTTTCAAA 4754
Qy 1801 TATCATTTCAAGCCATTAGCAAAGGCTGTATGTATTTTTTACATATGCCTCCTCGTTTTG 1860
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4755 TATCATTTCAAGCCATTAGCAAAGGCTGTATGTATTTTTTACATATGCCTCCTCGTTTTG 4814
Qy 1861 TGAATTTTGAAAGGATGTGGTTTCGGCCTTTGACATCAGAGGAGAAGCTCAGCTATGTTG 1920
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4815 TGAATTTTGAAAGGATGTGGTTTCGGCCTTTGACATCAGAGGAGAAGCTCAGCTATGTTG 4874
Qy 1921 GCTGAACGTTGATAGAAAGATAACGTTGAAGGCAAGTTGCCCTTGAGCAGCTCTCTGAAG 1980
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4875 GCTGAACGTTGATAGAAAGATAACGTTGAAGGCAAGTTGCCCTTGAGCAGCTCTCTGAAG 4934
Qy 1981 ATCAACTGCCTCCACATTGC 2000
||||||||||||||||||||
Db 4935 ATCAACTGCCTCCACATTGC 4954
RESULT 2
ATN03632
(NOTE: this sequence has 1 duplicate in the database searched.
See complete list at the end of this report)
ID ATN03632 standard; DNA; 6000 BP.
XX
AC ATN03632;
XX
DT 11-DEC-2008 (first entry)
XX
DE Human transcriptional regulatory element SEQ ID NO 1572.
XX
KW gene expression; gene regulation; transcription; DNA library;
KW DNA microarray; ds; pharmacogenetics; mapping; DNA polymorphism.
XX
OS Homo sapiens.
XX
CC PN WO2008073303-A2.
XX
CC PD 19-JUN-2008.
XX
CC PF 06-DEC-2007; 2007WO-US025093.
XX
PR 07-DEC-2006; 2006US-0873737P.
PR 07-DEC-2006; 2006US-0873738P.
PR 07-DEC-2006; 2006US-0873739P.
PR 07-DEC-2006; 2006US-0873853P.
PR 07-DEC-2006; 2006US-0873871P.
PR 07-DEC-2006; 2006US-0873882P.
PR 07-DEC-2006; 2006US-0873883P.
PR 06-JUL-2007; 2007US-0958616P.
XX
CC PA (SWIT-) SWITCHGEAR GENOMICS.
XX
CC PI Aldred SF, Trinklein N;
XX
DR WPI; 2008-H01915/44.
XX
CC PT New library of different expression constructs, useful for personalized
CC PT medicine, pharmacogenomics or correlation of polymorphisms with
CC PT phenotypic traits.
XX
CC PS Claim 10; SEQ ID NO 1572; 59pp; English.
XX
CC The invention relates to a library of different expression constructs.
CC Each member of the library comprises a different nucleic acid segment
CC from a genome, where the segment comprises transcription regulatory
CC sequences operably linked with a heterologous reporter sequence in an
CC expression vector such that expression of the reporter sequence is under
CC transcriptional control of the transcription regulatory sequences, where
CC at least 20\% of the transcription regulatory sequences of the expression
CC constructs in the library are part of a common pathway. The common
CC pathway is oncology, membrane, vascular, neuronal, signaling or nuclear
CC receptor pathway. The common pathway is an oncology pathway. The oncology
CC pathway is hypoxia pathway, DNA-damage pathway, apoptosis pathway, cell
CC cycle pathway or p53 pathway. The regulatory elements are SEQ ID NO: 1-
CC 3836. The common pathway is a membrane pathway. The membrane pathway is
CC transport protein pathways, G-protein coupled receptor pathways, ion
CC channel pathways or cell adhesion protein pathways. The regulatory
CC elements are SEQ ID NO: 3837-12716. The common pathway is a nuclear
CC receptor pathway. The nuclear receptor pathway is glucocorticoid receptor
CC pathway, peroxisome proliferator-activated receptor pathway, estrogen
CC receptor pathway, androgen receptor pathway, cytochrome P450 pathway or
CC transporter pathways. The regulatory elements are SEQ ID NO: 12717-13994.
CC The library of different expression constructs is useful for personalized
CC medicine, pharmacogenomics or correlation of polymorphisms with
CC phenotypic traits. The invention provides a library of different
CC expression constructs for large scale structural and functional
CC characterization of gene expression regulatory elements in a genome of an
CC organism, especially in a human genome that is part of a common pathway.
XX
SQ Sequence 6000 BP; 1691 A; 1415 C; 1270 G; 1624 T; 0 U; 0 Other;
Query Match 99.9%; Score 1999; Length 6000;
Best Local Similarity 100.0%;
Matches 1999; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 2 CACCCCCAACTTCTTCTCACATCCCTGCATCGTGCCATGCAGCATCAACTGGAAACCTCA 61 SEQ ID NO 16
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2928 CACCCCCAACTTCTTCTCACATCCCTGCATCGTGCCATGCAGCATCAACTGGAAACCTCA 2987 WO303 #1572
Qy 62 GCATCAGCAAACGACGACAGAGCGTTCATCCGTAAGGTGAACCAGAAAAGCCAGTTCAAT 121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2988 GCATCAGCAAACGACGACAGAGCGTTCATCCGTAAGGTGAACCAGAAAAGCCAGTTCAAT 3047
Qy 122 GACTTGTTTAACCATGGTCCATCTCAGAACCAAGAGTTGGGCCTCTTATTTACCAGAAAA 181
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3048 GACTTGTTTAACCATGGTCCATCTCAGAACCAAGAGTTGGGCCTCTTATTTACCAGAAAA 3107
Qy 182 ATTGTGGGGGCTTTGTGATATGGCTTTAAAAAAATCTTGTAATTGCCAGGCGTGGTGGCT 241
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3108 ATTGTGGGGGCTTTGTGATATGGCTTTAAAAAAATCTTGTAATTGCCAGGCGTGGTGGCT 3167
Qy 242 CACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGTGAATCGCCTAAGGTCAGGAG 301
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3168 CACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGTGAATCGCCTAAGGTCAGGAG 3227
Qy 302 TTCGAGACCAGCCTGACCAACATGGTGAAACTCCGTCTCTACTAAAAATACAAAAACTAG 361
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3228 TTCGAGACCAGCCTGACCAACATGGTGAAACTCCGTCTCTACTAAAAATACAAAAACTAG 3287
Qy 362 CTGGATGTGGTGACGCGTGCCTGTAATCCTAGCTACTCAGGAGGCTGACGCAGGAGAATC 421
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3288 CTGGATGTGGTGACGCGTGCCTGTAATCCTAGCTACTCAGGAGGCTGACGCAGGAGAATC 3347
Qy 422 ACTTGAACCTGGGAGGCAGAGGTTGCAGTGAGCCAAGATTGTGCCATTGCGCTCCAAAAA 481
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3348 ACTTGAACCTGGGAGGCAGAGGTTGCAGTGAGCCAAGATTGTGCCATTGCGCTCCAAAAA 3407
Qy 482 AAAAAAAAAAAAGACATTAACATAAATTTAAATATTTTATAATGACAATCCACATTAACT 541
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3408 AAAAAAAAAAAAGACATTAACATAAATTTAAATATTTTATAATGACAATCCACATTAACT 3467
Qy 542 ACTTAAAGCATAAGCTATTTTCCAGGAGAGGCAGCAAGTGCATTCTACTCCCATGCCCAA 601
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3468 ACTTAAAGCATAAGCTATTTTCCAGGAGAGGCAGCAAGTGCATTCTACTCCCATGCCCAA 3527
Qy 602 GAAGAAAGGAGCGTGACTTTGGTGGGAGTACTAGGAGTTTCTACTGGAGCACTTGCCCGC 661
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3528 GAAGAAAGGAGCGTGACTTTGGTGGGAGTACTAGGAGTTTCTACTGGAGCACTTGCCCGC 3587
Qy 662 AGAGTGAGAAACGTTCCTAGAGAGGAAGTTATACCTGCTGTGGAATTTAAGAGAATCTTG 721
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3588 AGAGTGAGAAACGTTCCTAGAGAGGAAGTTATACCTGCTGTGGAATTTAAGAGAATCTTG 3647
Qy 722 TCATATTTTGACAAGTTTTTTGAGATGGAAGTCTCACTCTGTCGCCCAGGCTGGAGTGCA 781
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3648 TCATATTTTGACAAGTTTTTTGAGATGGAAGTCTCACTCTGTCGCCCAGGCTGGAGTGCA 3707
Qy 782 GTGGCGCAATCTCAGCTCACTGCAGCCTGCACCTCCTCGGTTCCAGCTATTCTCTTGTCT 841
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3708 GTGGCGCAATCTCAGCTCACTGCAGCCTGCACCTCCTCGGTTCCAGCTATTCTCTTGTCT 3767
Qy 842 CAGCCTCCTGAGTAACTGGGATTACAGGCGCCCGCCACTACGCCTGGCTAATTTTTGTAT 901
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3768 CAGCCTCCTGAGTAACTGGGATTACAGGCGCCCGCCACTACGCCTGGCTAATTTTTGTAT 3827
Qy 902 TTTTAGTAGAAATGGGGTTTTACCATGTTGGCCAGACTGGTCTCAAACTCCCGACCTCAG 961
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3828 TTTTAGTAGAAATGGGGTTTTACCATGTTGGCCAGACTGGTCTCAAACTCCCGACCTCAG 3887
Qy 962 GTGATCTGCCTGCCTCAGCCTCCCAAAGTGCTGGAATTACAGGCGTGTGCCACTGCGCCT 1021
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3888 GTGATCTGCCTGCCTCAGCCTCCCAAAGTGCTGGAATTACAGGCGTGTGCCACTGCGCCT 3947
Qy 1022 GGCTAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGTAGAGACGGTGGTTTCACC 1081
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3948 GGCTAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGTAGAGACGGTGGTTTCACC 4007
Qy 1082 ATGTCATCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCACCTTGGTCTACC 1141
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4008 ATGTCATCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCACCTTGGTCTACC 4067
Qy 1142 AAAGTGCTCGGATTACAGGCATGAGCCACCAGGCCCAGTCAACGTGATGTGTTTTGGAAC 1201
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4068 AAAGTGCTCGGATTACAGGCATGAGCCACCAGGCCCAGTCAACGTGATGTGTTTTGGAAC 4127
Qy 1202 CCTGAATTCCTTGGCTTGCCCGGAGGGTTTTCTTTTTGTTAATATCTTTGCTTGCTTTCT 1261
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4128 CCTGAATTCCTTGGCTTGCCCGGAGGGTTTTCTTTTTGTTAATATCTTTGCTTGCTTTCT 4187
Qy 1262 AGTATTTAAAAAATTGTGTTTTGCTCTAACTATGCAATGGCTTTAAGTCTTAGACAAATT 1321
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4188 AGTATTTAAAAAATTGTGTTTTGCTCTAACTATGCAATGGCTTTAAGTCTTAGACAAATT 4247
Qy 1322 TCCAGGGAGCAAAACACACTCAACCATTTCATAATAATCAGAAGAGAGCTCTGATCAATA 1381
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4248 TCCAGGGAGCAAAACACACTCAACCATTTCATAATAATCAGAAGAGAGCTCTGATCAATA 4307
Qy 1382 AATAAGCAAGACTGAATTTTACAAAATAATCCAAAGTTTAAAACCAAAGCCCACTTTTTG 1441
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4308 AATAAGCAAGACTGAATTTTACAAAATAATCCAAAGTTTAAAACCAAAGCCCACTTTTTG 4367
Qy 1442 CATGATCCTTTAAGAGAAAGAAATCTGGAAGCAAAACACCTTATAAAATGACAATGCACT 1501
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4368 CATGATCCTTTAAGAGAAAGAAATCTGGAAGCAAAACACCTTATAAAATGACAATGCACT 4427
Qy 1502 TTCAGGAGCCCAGGGCACTGTGGTGAAATGATGATGGCTAGTACAGGTTATAAGCCTTGG 1561
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4428 TTCAGGAGCCCAGGGCACTGTGGTGAAATGATGATGGCTAGTACAGGTTATAAGCCTTGG 4487
Qy 1562 GGAATTATTTATGAATTCTCAGGATCCTTCAGTTCGCCGCATCCTTCTCCATTATTTGAA 1621
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4488 GGAATTATTTATGAATTCTCAGGATCCTTCAGTTCGCCGCATCCTTCTCCATTATTTGAA 4547
Qy 1622 TATTGGAGGCTGCCTGACCAGAATCTTGTCAGGACTTTGCTCCTTCATCCCAGGTGGTCC 1681
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4548 TATTGGAGGCTGCCTGACCAGAATCTTGTCAGGACTTTGCTCCTTCATCCCAGGTGGTCC 4607
Qy 1682 CGGCTGACTCCTGAGGACGTTACAGCCCTGAGGGGAGGACTCAGCTTATGAAGTGCTGGG 1741
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4608 CGGCTGACTCCTGAGGACGTTACAGCCCTGAGGGGAGGACTCAGCTTATGAAGTGCTGGG 4667
Qy 1742 TGAGACCACTGCCAAGAAGTGCTTGCTCACCCTACCTTCAACGGCAGGGGAATCTCCCTC 1801
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4668 TGAGACCACTGCCAAGAAGTGCTTGCTCACCCTACCTTCAACGGCAGGGGAATCTCCCTC 4727
Qy 1802 TCCTTTTATGGGCGTAGCTGAAGAAAGGATTCATAAATGAAGTTCAATCCTTCTCATCAA 1861
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4728 TCCTTTTATGGGCGTAGCTGAAGAAAGGATTCATAAATGAAGTTCAATCCTTCTCATCAA 4787
Qy 1862 CCCCAGCCCACACCTCCAGCAATTGAACTTGAAAAAAAAAACCTGGTTTGAAAAATTACC 1921
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4788 CCCCAGCCCACACCTCCAGCAATTGAACTTGAAAAAAAAAACCTGGTTTGAAAAATTACC 4847
Qy 1922 GCAAACTATATTGTCATCAAAAAAAAAAAAAAAAAAAAACACTTCCTATATTTGAGATGA 1981
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4848 GCAAACTATATTGTCATCAAAAAAAAAAAAAAAAAAAAACACTTCCTATATTTGAGATGA 4907
Qy 1982 GAGAAGAGAGTGCTAGGCA 2000
|||||||||||||||||||
Db 4908 GAGAAGAGAGTGCTAGGCA 4926
Therefore WO303 anticipates Claims 1-4.
Regarding Claims 5-7, those claims merely describe structural characteristics of SEQ ID NOs 3, 7-8, and 14-16 and outcomes of the structural characteristics. Those structural features and outcomes are inherently part of SEQ ID NOs 3, 7-8, and 14-16 due to their physical structures. Therefore WO303 anticipates Claims 5-7.
Regarding Claim 9, WO303 discloses (¶6, ¶157) expression vectors comprising the claimed sequences. Regarding Claim 17, WO303 discloses (¶16, ¶157, ¶171-173) delivering the expression construct or vector to a cell so it is expressed in the host cell, and making recombinant cells comprising the expression vectors. That is the same thing as cells comprising the vector. Therefore WO303 anticipates Claims 9 and 17.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1-7, 9, 17, and 20 are rejected under 35 U.S.C. 103 as being unpatentable over International Publication Number WO 2008/073303 (published 19 June 2008, “WO303”) as applied to Claims 1-7, 9, and 17 in the 102 rejection above, and further in view of Smith (et al. 2017. In situ programming of leukaemia-specific T cells using synthetic DNA nanocarriers. Nature Nanotechnol. 12:813-820, “Smith”). All references of record.
The teachings of WO303 as applicable to Claim(s) 1-7, 9 and 17 have been described in the 102 rejection above.
WO303 discloses sequences comprising nts 1501-2000, 1001-2000, 501-2000 of SEQ ID NOs 3, 7-8, and 14-16, a sequence having at least 95% identity with SEQ ID NOs 3, 7-8, and 14-16, and the entirety of SEQ ID NO 14. Those WO303 sequences have the same physical structures as the claimed sequences, so they inherently possess the features as the claimed sequences.
WO303 does not disclose a nanoparticle (NP) comprising the vector of Claim 9, wherein the NP is capable of delivery of the vector into a CD3+ cell (i.e., Claim 20).
However, Smith, drawn to programming of leukemia-specific T-cells, teaches (§Abstract) using nanoparticles to efficiently introduce CAR genes into Tcell nuclei. Smith teaches (same §) their technology is easy to manufacture and store which reduces cost.
Therefore, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the vectors, including (¶157) DNA vectors and (¶169) plasmid DNA of WO303 with the NP comprising DNA of Smith for the benefit of efficiently introducing the gene into T-cell nuclei. One would have been motivated to do so with a reasonable expectation of success because Smith teaches (§Abstract) DNA-carrying nanoparticles can efficiently introduce leukaemia-targeting CAR genes into T-cell nuclei, thereby bringing about long-term disease remission. These polymer nanoparticles are easy to manufacture in a stable form, which simplifies storage and reduces cost and because WO303 teaches (¶7-8) their transcription regulatory sequences are part of a common pathway related to oncology. Therefore the limitations of Claims 1-7, 9, 17, and 20 would have been obvious in view of WO303 and Smith.
Response to Arguments
Applicant's arguments filed 27 April 2026 have been fully considered but they are not persuasive. Arguments are addressed below. Arguments that are no longer relevant are not addressed.
Objections to Spec.
Applicant has capitalized words in the Spec. but hasn’t amended it so terms are appropriately accompanied by ® or TM symbols.
Objection to Claim 17
Claim 17 is objected to for a minor grammatical error.
112(a) Written Description
The rejections due to lack of adequate written description (WD) are maintained. Although Applicant has narrowed the claims from requiring 90% to requiring 95% identity, that still allows for 5%, or a total of 100 nt, to be different from the claimed SEQ ID NOs or fragments of SEQ ID NOs. Applicant hasn’t described or pointed to where the Spec. describes what nts form the structure that is required for the functions of: promoter activity, expressing the transgene at a higher level in CD3+ cells compared to CD3- cells, what sequence(s) comprise the promoter sequence of Claim 1 aside from the entirety of recited SEQ ID NOs, or what sequence(s) are required for delivering the vector into a CD3+ cell.
Applicant’s arguments state (p. 8 §112a) they are entitled to some breadth as otherwise it would be trivial to design around the claims, but that is not persuasive because they haven’t disclosed what structure(s) are responsible for the claimed functions, and they are claiming entire genera of compounds without disclosing what is actually required or demonstrating possession of a representative number of compounds within the genera.
Therefore the WD rejections are maintained.
101
The 101 rejection is applied to the examined species for the same reason the 101 was applied to the previously elected species that are now canceled. Applicant has stated that the claims are amended so they no longer read on a product of nature but the 101 rejection explains that is not the case. Therefore the 101 rejection is applied as necessitated by claim amendments.
To overcome these rejections Applicant should amend the claims so they no longer read on products of Nature.
102 and 103 rejections
The claims have been amended to recite species other than those previously rejected for art purposes, and the claims are examined with respect to the species SEQ ID NOs 3, 7-8, and 14-16.
Applicant’s arguments with respect to the 102 and 103 rejections have been considered but are moot because the new grounds of rejection do not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
The newly applied rejections explain why 102 and 103 rejections over the newly examined are appropriate. Since Applicant hasn’t argued against any of the newly applied rejections (necessitated by cancellation of previously-examined species), the new 102 and 103 rejections are appropriate.
To overcome these rejections Applicant should amend the claims to recite characteristics that differentiate the claimed invention from the prior art.
Conclusion
No claim is allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. A preliminary search indicates:
United States Patent Application Publication No.: US 2007/0161031 (published 12 July 2007) discloses sequences at least 95% identical to claimed SEQ ID NOs 4-5, 7-10, 12, 14-16, and
English translation of Japan Patent Document JP2003116558 (published 22 April 2003) discloses a sequence at least 95% identical to claimed SEQ ID NO 6.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RUTHIE S ARIETI whose telephone number is (571)272-1293. The examiner can normally be reached M-Th 8:30AM-4PM, alternate Fridays 8:30AM-4PM (ET).
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Ram R Shukla can be reached at (571)272-0735. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
RUTHIE S ARIETI
Examiner (Ruth.Arieti@uspto.gov)
Art Unit 1635
/RUTH SOPHIA ARIETI/Examiner, Art Unit 1635
/NANCY J LEITH/Primary Examiner, Art Unit 1636
Prosecution Insights