LOCUS       NM_012476               1161 bp    mRNA    linear   PRI 03-OCT-2024
DEFINITION  Homo sapiens ventral anterior homeobox 2 (VAX2), mRNA.
ACCESSION   NM_012476
VERSION     NM_012476.3
KEYWORDS    RefSeq; MANE Select.
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 1161)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   2  (bases 1 to 1161)
  AUTHORS   Alfano,G., Waseem,N.H., Webster,A.R. and Bhattacharya,S.S.
  TITLE     Identification and characterization of the VAX2 p.Leu139Arg
            variant: possible involvement of VAX2 in cone dystrophy
  JOURNAL   Ophthalmic Genet 39 (4), 539-543 (2018)
   PUBMED   29947570
  REMARK    GeneRIF: This study raises the interesting possibility for
            evaluating VAX2 as a candidate gene for cone dystrophy.
REFERENCE   3  (bases 1 to 1161)
  AUTHORS   Yin,Y., Morgunova,E., Jolma,A., Kaasinen,E., Sahu,B.,
            Khund-Sayeed,S., Das,P.K., Kivioja,T., Dave,K., Zhong,F.,
            Nitta,K.R., Taipale,M., Popov,A., Ginno,P.A., Domcke,S., Yan,J.,
            Schubeler,D., Vinson,C. and Taipale,J.
  TITLE     Impact of cytosine methylation on DNA binding specificities of
            human transcription factors
  JOURNAL   Science 356 (6337) (2017)
   PUBMED   28473536
REFERENCE   4  (bases 1 to 1161)
  AUTHORS   Kitchen,M.O., Bryan,R.T., Emes,R.D., Glossop,J.R., Luscombe,C.,
            Cheng,K.K., Zeegers,M.P., James,N.D., Devall,A.J., Mein,C.A.,
            Gommersall,L., Fryer,A.A. and Farrell,W.E.
  TITLE     Quantitative genome-wide methylation analysis of high-grade
            non-muscle invasive bladder cancer
  JOURNAL   Epigenetics 11 (3), 237-246 (2016)
   PUBMED   26929985
  REMARK    GeneRIF: Although inappropriate promoter methylation was not
            invariantly associated with reduced transcript expression, a
            significant association was apparent for the ARHGEF4, PON3, STAT5a,
            and VAX2 gene transcripts (P<0.05). Herein, we present the first
            genome-wide DNA methylation analysis in a unique HG-NMIBC cohort,
            showing extensive and discrete methylation changes relative to
            normal bladder and low-intermediate-grade tumor
REFERENCE   5  (bases 1 to 1161)
  AUTHORS   Navarini,A.A., Simpson,M.A., Weale,M., Knight,J., Carlavan,I.,
            Reiniche,P., Burden,D.A., Layton,A., Bataille,V., Allen,M.,
            Pleass,R., Pink,A., Creamer,D., English,J., Munn,S., Walton,S.,
            Willis,C., Deret,S., Voegel,J.J., Spector,T., Smith,C.H.,
            Trembath,R.C. and Barker,J.N.
  CONSRTM   Acne Genetic Study Group
  TITLE     Genome-wide association study identifies three novel susceptibility
            loci for severe Acne vulgaris
  JOURNAL   Nat Commun 5, 4020 (2014)
   PUBMED   24927181
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1161)
  AUTHORS   Talmud,P.J., Drenos,F., Shah,S., Shah,T., Palmen,J., Verzilli,C.,
            Gaunt,T.R., Pallas,J., Lovering,R., Li,K., Casas,J.P., Sofat,R.,
            Kumari,M., Rodriguez,S., Johnson,T., Newhouse,S.J., Dominiczak,A.,
            Samani,N.J., Caulfield,M., Sever,P., Stanton,A., Shields,D.C.,
            Padmanabhan,S., Melander,O., Hastie,C., Delles,C., Ebrahim,S.,
            Marmot,M.G., Smith,G.D., Lawlor,D.A., Munroe,P.B., Day,I.N.,
            Kivimaki,M., Whittaker,J., Humphries,S.E. and Hingorani,A.D.
  CONSRTM   ASCOT investigators; NORDIL investigators; BRIGHT Consortium
  TITLE     Gene-centric association signals for lipids and apolipoproteins
            identified via the HumanCVD BeadChip
  JOURNAL   Am J Hum Genet 85 (5), 628-642 (2009)
   PUBMED   19913121
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   7  (bases 1 to 1161)
  AUTHORS   Vaquerizas,J.M., Kummerfeld,S.K., Teichmann,S.A. and Luscombe,N.M.
  TITLE     A census of human transcription factors: function, expression and
            evolution
  JOURNAL   Nat Rev Genet 10 (4), 252-263 (2009)
   PUBMED   19274049
  REMARK    Review article
REFERENCE   8  (bases 1 to 1161)
  AUTHORS   Holland,P.W., Booth,H.A. and Bruford,E.A.
  TITLE     Classification and nomenclature of all human homeobox genes
  JOURNAL   BMC Biol 5, 47 (2007)
   PUBMED   17963489
  REMARK    Publication Status: Online-Only
REFERENCE   9  (bases 1 to 1161)
  AUTHORS   Beaty,T.H., Hetmanski,J.B., Fallin,M.D., Park,J.W., Sull,J.W.,
            McIntosh,I., Liang,K.Y., Vanderkolk,C.A., Redett,R.J.,
            Boyadjiev,S.A., Jabs,E.W., Chong,S.S., Cheah,F.S., Wu-Chou,Y.H.,
            Chen,P.K., Chiu,Y.F., Yeow,V., Ng,I.S., Cheng,J., Huang,S., Ye,X.,
            Wang,H., Ingersoll,R. and Scott,A.F.
  TITLE     Analysis of candidate genes on chromosome 2 in oral cleft
            case-parent trios from three populations
  JOURNAL   Hum Genet 120 (4), 501-518 (2006)
   PUBMED   16953426
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   10 (bases 1 to 1161)
  AUTHORS   Barbieri,A.M., Lupo,G., Bulfone,A., Andreazzoli,M., Mariani,M.,
            Fougerousse,F., Consalez,G.G., Borsani,G., Beckmann,J.S.,
            Barsacchi,G., Ballabio,A. and Banfi,S.
  TITLE     A homeobox gene, vax2, controls the patterning of the eye
            dorsoventral axis
  JOURNAL   Proc Natl Acad Sci U S A 96 (19), 10729-10734 (1999)
   PUBMED   10485894
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC007040.2 and Y17791.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_012476.2.
            
            Summary: This gene encodes a homeobox protein and is almost
            exclusively expressed in the ventral portion of the retina during
            development. In mouse studies, this gene was found to be required
            for the correct formation of the optic fissure and other aspects of
            retinal development. [provided by RefSeq, Sep 2008].
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: Y17791.1, SRR3476690.1009352.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2142853, SAMEA2145743
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000234392.3/ ENSP00000234392.2
            RefSeq Select criteria :: based on conservation, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-14                AC007040.2         48748-48761
            15-979              Y17791.1           1-965
            980-1161            Y17791.1           967-1148
FEATURES             Location/Qualifiers
     source          1..1161
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2p13.3"
     gene            1..1161
                     /gene="VAX2"
                     /gene_synonym="DRES93"
                     /note="ventral anterior homeobox 2"
                     /db_xref="GeneID:25806"
                     /db_xref="HGNC:HGNC:12661"
                     /db_xref="MIM:604295"
     exon            1..293
                     /gene="VAX2"
                     /gene_synonym="DRES93"
                     /inference="alignment:Splign:2.1.0"
     CDS             47..919
                     /gene="VAX2"
                     /gene_synonym="DRES93"
                     /codon_start=1
                     /product="ventral anterior homeobox 2"
                     /protein_id="NP_036608.1"
                     /db_xref="CCDS:CCDS1911.1"
                     /db_xref="GeneID:25806"
                     /db_xref="HGNC:HGNC:12661"
                     /db_xref="MIM:604295"
                     /translation="MGDGGAERDRGPARRAESGGGGGRCGDRSGAGDLRADGGGHSPT
                     EVAGTSASSPAGSRESGADSDGQPGPGEADHCRRILVRDAKGTIREIVLPKGLDLDRP
                     KRTRTSFTAEQLYRLEMEFQRCQYVVGRERTELARQLNLSETQVKVWFQNRRTKQKKD
                     QSRDLEKRASSSASEAFATSNILRLLEQGRLLSVPRAPSLLALTPSLPGLPASHRGTS
                     LGDPRNSSPRLNPLSSASASPPLPPPLPAVCFSSAPLLDLPAGYELGSSAFEPYSWLE
                     RKVGSASSCKKANT"
     exon            294..481
                     /gene="VAX2"
                     /gene_synonym="DRES93"
                     /inference="alignment:Splign:2.1.0"
     exon            482..1161
                     /gene="VAX2"
                     /gene_synonym="DRES93"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1131..1136
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VAX2"
                     /gene_synonym="DRES93"
                     /note="hexamer: AATAAA"
     polyA_site      1161
                     /gene="VAX2"
                     /gene_synonym="DRES93"
                     /note="major polyA site"
ORIGIN      
        1 agcgtaggct ggctccgccg tagaggggtt ggcagtggcg gtcagcatgg gcgatggggg
       61 cgccgagcgc gaccggggcc ccgcgcgccg ggcggagtct ggtggcggcg gtgggcgctg
      121 cggagaccgc agcggagcgg gggacttgcg agctgatggc ggtggccaca gcccaacgga
      181 ggtggccggg acctcagcct ccagtcccgc aggctccagg gagagtggag ccgacagcga
      241 cgggcagccc gggcccggcg aggcagacca ctgccgccgc atactggtgc gagatgccaa
      301 agggacaatt cgggaaattg tcctgcctaa gggcctggac ctggaccggc ccaagcggac
      361 acgtacatcc ttcactgccg agcagctgta ccgcctggag atggagttcc agcgctgcca
      421 gtatgtggtg ggccgcgagc gcactgagct ggcccgccag ctgaacctct ccgagaccca
      481 ggtgaaggtc tggttccaga accgccgcac caagcagaag aaagaccaga gcagagacct
      541 ggagaagcgg gcgtcctcct cagcctccga ggcctttgcc acctccaaca ttctgcggct
      601 gctggagcag ggccggctgc tctctgtgcc cagggcccct agcctcctgg cgctgacccc
      661 tagcctgcca ggcctacctg ccagccacag gggcacctcc ttaggtgacc ccaggaactc
      721 ctccccacgc ctcaacccgc tgtcctcggc ctcagcgtcc cccccactgc cgccccctct
      781 gccagctgtc tgcttttcct cggccccgct cctggatctg cctgccggct acgaactggg
      841 ttcctcggcc ttcgagccat acagctggct agaacggaaa gtgggcagcg ccagcagctg
      901 caagaaagct aacacttaag actcccaccc tgtgacactg agtcccgagc acagcacctt
      961 cccagtctcc tgtgccccag cggacagcac tgagcaggcc ccggagagga ggggctgcag
     1021 ccacacactc ttccccacct gccccccagc tcagagactc gtgaccaaat ggccttggtc
     1081 ccgcagcttg tgtgcgtgag tgcagtgtga gtgtgtgtgt ctctcactga aataaaagga
     1141 aaacaatgac aagaagggaa a
//
