LOCUS       NM_001112704            1937 bp    mRNA    linear   PRI 10-OCT-2024
DEFINITION  Homo sapiens ventral anterior homeobox 1 (VAX1), transcript variant
            1, mRNA.
ACCESSION   NM_001112704
VERSION     NM_001112704.2
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 1937)
  AUTHORS   Feng,H., Wei,B., Xie,X., Li,P. and Shen,X.
  TITLE     The potential up-regulation risk of 3' UTR SNP (rs10787760 G > A)
            for the VAX1 gene is associated with NSCLP in the northwest Chinese
            population
  JOURNAL   Gene 922, 148458 (2024)
   PUBMED   38608796
  REMARK    GeneRIF: The potential up-regulation risk of 3' UTR SNP (rs10787760
            G > A) for the VAX1 gene is associated with NSCLP in the northwest
            Chinese population.
REFERENCE   2  (bases 1 to 1937)
  AUTHORS   You,Y., Shi,J., Shi,B. and Jia,Z.
  TITLE     Target sequencing reveals the association between variants in VAX1
            and NSCL/P in Chinese population
  JOURNAL   Oral Dis 29 (5), 2130-2138 (2023)
   PUBMED   35419918
  REMARK    GeneRIF: Target sequencing reveals the association between variants
            in VAX1 and NSCL/P in Chinese population.
REFERENCE   3  (bases 1 to 1937)
  AUTHORS   Slavec,L., Karas Kuzelicki,N., Locatelli,I. and Gersak,K.
  TITLE     Genetic markers for non-syndromic orofacial clefts in populations
            of European ancestry: a meta-analysis
  JOURNAL   Sci Rep 12 (1), 1214 (2022)
   PUBMED   35075162
  REMARK    GeneRIF: Genetic markers for non-syndromic orofacial clefts in
            populations of European ancestry: a meta-analysis.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1937)
  AUTHORS   Wang,Q., Sun,S., Song,Q., Hu,H., An,J. and Liu,J.
  TITLE     The risk of nonsyndromic cleft lip with or without cleft palate and
            Vax1 rs7078160 polymorphisms in southern Han Chinese
  JOURNAL   Braz J Otorhinolaryngol 87 (6), 718-722 (2021)
   PUBMED   33132092
  REMARK    GeneRIF: The risk of nonsyndromic cleft lip with or without cleft
            palate and Vax1 rs7078160 polymorphisms in southern Han Chinese.
REFERENCE   5  (bases 1 to 1937)
  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   6  (bases 1 to 1937)
  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   7  (bases 1 to 1937)
  AUTHORS   Deloukas,P., Earthrowl,M.E., Grafham,D.V., Rubenfield,M.,
            French,L., Steward,C.A., Sims,S.K., Jones,M.C., Searle,S.,
            Scott,C., Howe,K., Hunt,S.E., Andrews,T.D., Gilbert,J.G.,
            Swarbreck,D., Ashurst,J.L., Taylor,A., Battles,J., Bird,C.P.,
            Ainscough,R., Almeida,J.P., Ashwell,R.I., Ambrose,K.D.,
            Babbage,A.K., Bagguley,C.L., Bailey,J., Banerjee,R., Bates,K.,
            Beasley,H., Bray-Allen,S., Brown,A.J., Brown,J.Y., Burford,D.C.,
            Burrill,W., Burton,J., Cahill,P., Camire,D., Carter,N.P.,
            Chapman,J.C., Clark,S.Y., Clarke,G., Clee,C.M., Clegg,S., Corby,N.,
            Coulson,A., Dhami,P., Dutta,I., Dunn,M., Faulkner,L., Frankish,A.,
            Frankland,J.A., Garner,P., Garnett,J., Gribble,S., Griffiths,C.,
            Grocock,R., Gustafson,E., Hammond,S., Harley,J.L., Hart,E.,
            Heath,P.D., Ho,T.P., Hopkins,B., Horne,J., Howden,P.J., Huckle,E.,
            Hynds,C., Johnson,C., Johnson,D., Kana,A., Kay,M., Kimberley,A.M.,
            Kershaw,J.K., Kokkinaki,M., Laird,G.K., Lawlor,S., Lee,H.M.,
            Leongamornlert,D.A., Laird,G., Lloyd,C., Lloyd,D.M., Loveland,J.,
            Lovell,J., McLaren,S., McLay,K.E., McMurray,A.,
            Mashreghi-Mohammadi,M., Matthews,L., Milne,S., Nickerson,T.,
            Nguyen,M., Overton-Larty,E., Palmer,S.A., Pearce,A.V., Peck,A.I.,
            Pelan,S., Phillimore,B., Porter,K., Rice,C.M., Rogosin,A.,
            Ross,M.T., Sarafidou,T., Sehra,H.K., Shownkeen,R., Skuce,C.D.,
            Smith,M., Standring,L., Sycamore,N., Tester,J., Thorpe,A.,
            Torcasso,W., Tracey,A., Tromans,A., Tsolas,J., Wall,M., Walsh,J.,
            Wang,H., Weinstock,K., West,A.P., Willey,D.L., Whitehead,S.L.,
            Wilming,L., Wray,P.W., Young,L., Chen,Y., Lovering,R.C.,
            Moschonas,N.K., Siebert,R., Fechtel,K., Bentley,D., Durbin,R.,
            Hubbard,T., Doucette-Stamm,L., Beck,S., Smith,D.R. and Rogers,J.
  TITLE     The DNA sequence and comparative analysis of human chromosome 10
  JOURNAL   Nature 429 (6990), 375-381 (2004)
   PUBMED   15164054
REFERENCE   8  (bases 1 to 1937)
  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
REFERENCE   9  (bases 1 to 1937)
  AUTHORS   Hallonet,M., Hollemann,T., Wehr,R., Jenkins,N.A., Copeland,N.G.,
            Pieler,T. and Gruss,P.
  TITLE     Vax1 is a novel homeobox-containing gene expressed in the
            developing anterior ventral forebrain
  JOURNAL   Development 125 (14), 2599-2610 (1998)
   PUBMED   9636075
REFERENCE   10 (bases 1 to 1937)
  AUTHORS   Bardakjian,T., Weiss,A. and Schneider,A.
  TITLE     Microphthalmia/Anophthalmia/Coloboma Spectrum - RETIRED CHAPTER,
            FOR HISTORICAL REFERENCE ONLY
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301552
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK127095.1 and AL731557.7.
            This sequence is a reference standard in the RefSeqGene project.
            
            On May 17, 2019 this sequence version replaced NM_001112704.1.
            
            Summary: This gene encodes a homeo-domain containing protein from a
            class of homeobox transcription factors which are conserved in
            vertebrates. Genes of this family are involved in the regulation of
            body development and morphogenesis. The most conserved genes,
            called HOX genes are found in special gene clusters. This gene
            belongs to the VAX subfamily and lies in the vicinity of the EMX
            homeobox gene family. Another member of VAX family is located on
            chromosome 2. The encoded protein may play an important role in the
            development of anterior ventral forebrain and visual system.
            Multiple transcript variants encoding different isoforms have been
            found for this gene. [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) encodes the longer isoform
            (a).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data because no single transcript was available
            for the full length of the gene. The extent of this transcript is
            supported by orthologous data.
            
            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##
            RNAseq introns :: single sample supports all introns SAMEA2145743,
                              SAMEA2148093 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000369206.6/ ENSP00000358207.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-149               AK127095.1         32-180
            150-170             AL731557.7         35785-35805         c
            171-643             AK127095.1         199-671
            644-1937            AL731557.7         30974-32267         c
FEATURES             Location/Qualifiers
     source          1..1937
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="10"
                     /map="10q25.3"
     gene            1..1937
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /note="ventral anterior homeobox 1"
                     /db_xref="GeneID:11023"
                     /db_xref="HGNC:HGNC:12660"
                     /db_xref="MIM:604294"
     exon            1..455
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /inference="alignment:Splign:2.1.0"
     CDS             215..1219
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /note="isoform a is encoded by transcript variant 1"
                     /codon_start=1
                     /product="ventral anterior homeobox 1 isoform a"
                     /protein_id="NP_001106175.1"
                     /db_xref="CCDS:CCDS44483.1"
                     /db_xref="GeneID:11023"
                     /db_xref="HGNC:HGNC:12660"
                     /db_xref="MIM:604294"
                     /translation="MFGKPDKMDVRCHSDAEAARVSKNAHKESRESKGAEGNLPAAFL
                     KEPQGAFSASGAAEDCNKSKSNSAADPDYCRRILVRDAKGSIREIILPKGLDLDRPKR
                     TRTSFTAEQLYRLEMEFQRCQYVVGRERTELARQLNLSETQVKVWFQNRRTKQKKDQG
                     KDSELRSVVSETAATCSVLRLLEQGRLLSPPGLPALLPPCATGALGSALRGPSLPALG
                     AGAAAGSAAAAAAAAPGPAGAASPHPPAVGGAPGPGPAGPGGLHAGAPAAGHSLFSLP
                     VPSLLGSVASRLSSAPLTMAGSLAGNLQELSARYLSSSAFEPYSRTNNKEGAEKKALD
                     "
     exon            456..643
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /inference="alignment:Splign:2.1.0"
     exon            644..1937
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1911..1916
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /note="hexamer: AATAAA"
     polyA_site      1937
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /note="major polyA site"
ORIGIN      
        1 actctcccgt cgccgctgac ccgcgcgcgg ccgccgaagc ctccccgcgg ggacattcat
       61 tcttgcccct tgcctgtcgc cgggccgggc gtacgggccg cgttgtcggg ggttttgtcc
      121 cctttttcct cttttttttt tccttctccg cccccccccc tttttttttt ttttgctttt
      181 tttttccttt ctgtttttgt tgttgttctt gcctatgttc gggaaaccag acaaaatgga
      241 cgttcgatgc cactcggacg ccgaggctgc ccgggtctcg aagaacgcgc acaaggagag
      301 tcgggagagc aagggcgcgg aggggaacct cccagccgcc ttcctcaagg agccgcaggg
      361 cgccttctca gcgtcgggcg ctgctgagga ttgtaacaaa agtaaatcca attccgcagc
      421 ggacccggat tactgccgcc ggatcctggt ccgagatgcc aaggggtcca tccgagagat
      481 catcctgccc aagggcctgg acttggaccg gcctaagagg acgcgcacgt ccttcaccgc
      541 ggagcagctc tatcggctgg agatggagtt ccagcgctgc cagtacgtgg tgggccgcga
      601 gaggaccgag ctcgcccggc agcttaacct ctccgagacc caggtgaagg tctggttcca
      661 gaaccggcgc accaagcaga agaaggacca gggcaaggac tcggagctac gctcggtggt
      721 gtcggagacc gcggccacgt gcagcgtgct acggctgctg gagcagggcc gcctgttgtc
      781 gccgcccggc ctgcctgcgc tgctgccgcc ttgcgccacg ggcgctctcg gctcagcgct
      841 gcgcgggccc agcttgccgg ccctgggcgc gggcgccgct gcaggctcgg ccgccgcagc
      901 cgccgccgcc gccccgggcc cagcgggcgc tgcatccccg cacccgccgg ctgtgggcgg
      961 tgctccaggt cccgggcccg ccgggccggg gggattgcac gcaggcgccc cggccgcggg
     1021 ccacagcctc ttcagcctgc cggtgccctc gctgctcggc tccgtcgcca gccgcctgtc
     1081 ctccgccccg ttaacaatgg ctggttcgct agctgggaat ttgcaagaac tctccgcccg
     1141 atatctgagc tcctcggcct tcgagcctta ctcccggacc aacaataaag aaggggccga
     1201 gaaaaaagcg ctggactgat tttaagtgtt tccctgtatt tatatttata gtatctattg
     1261 tggtgatatt tatggactca cgcgcattag gtgcccagag ctcctgcgct gggctcctgg
     1321 ctcccaccag gcctctgaca gctctccttt cccactagac tctgctacca atttcatctc
     1381 attcgggcta tttttttttt ctactacctt tcctctgaga ttcctcccca acccccaact
     1441 tccttctgaa tccaggagcg atccaaagaa ttgggaaaaa tgcccgagtt agtcaacctg
     1501 atgccctgac cccgtgccca gcccaggagg gaaaagactg gttctaactc caaagcacag
     1561 gacgtttgct ctagatccgc ggctgctgcg gctgctgccg ctgccgacta ttcctaggaa
     1621 tatttgaaag aggaaaactg cgcgcagacc ccaggggctt ccaggtttct ttagaccaaa
     1681 aaaggaggac gttccttcct cttgccaggg aaaccagggc ttgtgggagc ccctgggccc
     1741 cgctttgcgg acctctcggg atagtcggta cacaacacag cttcctggcg ggcaaatcct
     1801 gcggtttttc tcccctttag ggcaactcca atcacaacca cccccgaccc caggaaacag
     1861 taacaaacgt cgtagtaggc aacgacactg ataaatttga tctaatcagc aataaaagca
     1921 attgctacgt aaaacca
//
