GGRNA | NM_199131.2

LOCUS       NM_199131               4494 bp    mRNA    linear   PRI 24-JUN-2013
DEFINITION  Homo sapiens ventral anterior homeobox 1 (VAX1), transcript variant
            2, mRNA.
ACCESSION   NM_199131
VERSION     NM_199131.2  GI:162951871
KEYWORDS    RefSeq.
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 4494)
  AUTHORS   Nasser,E., Mangold,E., Tradowsky,D.C., Fier,H., Becker,J.,
            Boehmer,A.C., Herberz,R., Fricker,N., Barth,S., Wahle,P., Nowak,S.,
            Reutter,H., Reich,R.H., Lauster,C., Braumann,B., Kreusch,T.,
            Hemprich,A., Potzsch,B., Hoffmann,P., Kramer,F.J., Knapp,M.,
            Lange,C., Nothen,M.M. and Ludwig,K.U.
  TITLE     Resequencing of VAX1 in patients with nonsyndromic cleft lip with
            or without cleft palate
  JOURNAL   Birth Defects Res. Part A Clin. Mol. Teratol. 94 (11), 925-933
            (2012)
   PUBMED   23081944
  REMARK    GeneRIF: The data do not support the hypothesis that highly
            penetrant rare variants in VAX1 are a cause of nonsyndromic cleft
            lip with or without cleft palate.
REFERENCE   2  (bases 1 to 4494)
  AUTHORS   Slavotinek,A.M., Chao,R., Vacik,T., Yahyavi,M., Abouzeid,H.,
            Bardakjian,T., Schneider,A., Shaw,G., Sherr,E.H., Lemke,G.,
            Youssef,M. and Schorderet,D.F.
  TITLE     VAX1 mutation associated with microphthalmia, corpus callosum
            agenesis, and orofacial clefting: the first description of a VAX1
            phenotype in humans
  JOURNAL   Hum. Mutat. 33 (2), 364-368 (2012)
   PUBMED   22095910
  REMARK    GeneRIF: This is the first description of a patient with a VAX1
            mutation and establishes VAX1 as a new causative gene for
            anophthalmia/microphthalmia (A/M) in humans.
REFERENCE   3  (bases 1 to 4494)
  AUTHORS   Mangold,E., Ludwig,K.U., Birnbaum,S., Baluardo,C., Ferrian,M.,
            Herms,S., Reutter,H., de Assis,N.A., Chawa,T.A., Mattheisen,M.,
            Steffens,M., Barth,S., Kluck,N., Paul,A., Becker,J., Lauster,C.,
            Schmidt,G., Braumann,B., Scheer,M., Reich,R.H., Hemprich,A.,
            Potzsch,S., Blaumeiser,B., Moebus,S., Krawczak,M., Schreiber,S.,
            Meitinger,T., Wichmann,H.E., Steegers-Theunissen,R.P., Kramer,F.J.,
            Cichon,S., Propping,P., Wienker,T.F., Knapp,M., Rubini,M.,
            Mossey,P.A., Hoffmann,P. and Nothen,M.M.
  TITLE     Genome-wide association study identifies two susceptibility loci
            for nonsyndromic cleft lip with or without cleft palate
  JOURNAL   Nat. Genet. 42 (1), 24-26 (2010)
   PUBMED   20023658
REFERENCE   4  (bases 1 to 4494)
  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   5  (bases 1 to 4494)
  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   6  (bases 1 to 4494)
  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   7  (bases 1 to 4494)
  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
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK127095.1 and AL731557.7.
            On Dec 18, 2007 this sequence version replaced gi:40217621.
            
            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 (2) differs in the 3' coding
            region and UTR compared to variant 1. The resulting isoform (b) has
            a shorter C-terminus compared to 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.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK127095.1, BC101694.1 [ECO:0000332]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-180               AK127095.1         1-180
            181-201             AL731557.7         35785-35805         c
            202-1186            AK127095.1         199-1183
            1187-4494           AL731557.7         26205-29512         c
FEATURES             Location/Qualifiers
     source          1..4494
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="10"
                     /map="10q26.1"
     gene            1..4494
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /note="ventral anterior homeobox 1"
                     /db_xref="GeneID:11023"
                     /db_xref="HGNC:12660"
                     /db_xref="HPRD:16052"
                     /db_xref="MIM:604294"
     exon            1..486
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /inference="alignment:Splign:1.39.8"
     variation       19
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:199797327"
     variation       44
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:200595272"
     misc_feature    48..50
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /note="upstream in-frame stop codon"
     variation       53
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:201928731"
     variation       139
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:200079110"
     variation       158
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:201020967"
     STS             217..836
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /db_xref="UniSTS:485875"
     CDS             246..806
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /note="isoform b is encoded by transcript variant 2"
                     /codon_start=1
                     /product="ventral anterior homeobox 1 isoform b"
                     /protein_id="NP_954582.1"
                     /db_xref="GI:40217622"
                     /db_xref="CCDS:CCDS7597.1"
                     /db_xref="GeneID:11023"
                     /db_xref="HGNC:12660"
                     /db_xref="HPRD:16052"
                     /db_xref="MIM:604294"
                     /translation="

MFGKPDKMDVRCHSDAEAARVSKNAHKESRESKGAEGNLPAAFLKEPQGAFSASGAAEDCNKSKSNSAADPDYCRRILVRDAKGSIREIILPKGLDLDRPKRTRTSFTAEQLYRLEMEFQRCQYVVGRERTELARQLNLSETQANSEENNERFKRGIKKQKKKRKKEPANDESRRGDSGGRGWQPL

"
     misc_feature    546..>674
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /note="Homeodomain;  DNA binding domains involved in the
                     transcriptional regulation of key eukaryotic developmental
                     processes; may bind to DNA as monomers or as homo- and/or
                     heterodimers, in a sequence-specific manner; Region:
                     homeodomain; cd00086"
                     /db_xref="CDD:28970"
     misc_feature    order(546..560,564..566,615..617,633..635,672..674)
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:28970"
     exon            487..674
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /inference="alignment:Splign:1.39.8"
     variation       520
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:201160236"
     exon            675..712
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /inference="alignment:Splign:1.39.8"
     exon            713..4494
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /inference="alignment:Splign:1.39.8"
     STS             3883..4450
                     /gene="VAX1"
                     /gene_synonym="MCOPS11"
                     /standard_name="VAX1__5061"
                     /db_xref="UniSTS:463347"
ORIGIN

accagactggccgcctctcggcgagcgcgccactctcccgtcgccgctgacccgcgcgcggccgccgaagcctccccgcggggacattcattcttgccccttgcctgtcgccgggccgggcgtacgggccgcgttgtcgggggttttgtcccctttttcctcttttttttttccttctccgccccccccccttttttttttttttgctttttttttcctttctgtttttgttgttgttcttgcctatgttcgggaaaccagacaaaatggacgttcgatgccactcggacgccgaggctgcccgggtctcgaagaacgcgcacaaggagagtcgggagagcaagggcgcggaggggaacctcccagccgccttcctcaaggagccgcagggcgccttctcagcgtcgggcgctgctgaggattgtaacaaaagtaaatccaattccgcagcggacccggattactgccgccggatcctggtccgagatgccaaggggtccatccgagagatcatcctgcccaagggcctggacttggaccggcctaagaggacgcgcacgtccttcaccgcggagcagctctatcggctggagatggagttccagcgctgccagtacgtggtgggccgcgagaggaccgagctcgcccggcagcttaacctctccgagacccaggcaaatagtgaagaaaataatgaacgattcaaacgcgggataaaaaaacaaaagaagaaaaggaagaaagagccagcaaatgatgagtctcggcgtggggactccgggggcagagggtggcagcccctatagtgcggggccctgcgactggtaccgtgagcgcctgggatgaggtttgggcggatttcgggtttccggagaggcagagacgcctggctacgacgatttgttccacttccttgagtgtttcgctctcgatttctctatctgtccctctgaggtcggcccctcagaccctcctccttaatttcccactgcgtaattcttagtttatttaggaactcatctctgggcactataaagtctctgcctcctaatgctaggtttctagagtcttccagctgcatcttcatgccggcagcattttggattttgtgcaatcatgggcccagaataggcaaggttttattttcttctgacttagaatataagtctcgccatcgtcaaagagaaactttgaaggagcaggagactgaaatcgatattaattcctgcaaagagacctcctcaccctggtgcttatgcggtggtgacgggtgtagacgttgcaaacaaatcttgggaagcgaggagggccggggaggacacttccggacacgctcttctaaagcgtgtgcagcacggggcgaagtccgcgctgcgggggcagcggccccggctccttcttgtagcgcctgcacacctgggtgttgcagggacccgcagctcccgtgcggcaccggccctagccaggccttactgcccctactcgtgtactgtgcctgaagctgaagttggaggcatccaaaataaggcggggcacagtgtgggcggcggagtccctgagccttgagctccgctttttgctgagatcacagcagccgcccacagacagttcacttttatttctcaaagttgctgcagatccctcagcttggcttctcttggctcttcccctccctgtccgcctctccttactttctcttgcttgaaactgcttttccttttctactcttttcttccgcgctcctgtcccgtaaacgcctgcgcttcctttaaggagttctctctctgtggtgtgggctcccctctcgttccccctgtctccctcctccattacttcttccttccaggtctctctctctcttttggttttctggtttttttctcctgctcaaggggtcccaaaggccaaggcagtgggtggctctcgctgcagcttcaaggctggtggctgggaccctccaggggtgagaaggaagggagaaggtggcataactttttggaacaaaagaaaacacaaaatcctagcttgggattcccaacaaattcagcctcctctcccaggggcctcagcctgggaagtcaccaagcagatccctccttccagcttcctgctctttctcctttttgctttcttacccctgaaagagggaaggacaagtcacctcataacttctgctctcacctcccttccctccctggctttgggaagagctgctgagctctttgcctgccactcagggagtgcaattgttcttaaagagcctcttctgcatagaaaaagaattgcaattttaatttaaaaacatttatagaaaattcatttaattttagtgactatcttcttttccctccttccccaagggcctccagtaagctgccttggtccctggaggcttctggcttccaactggagactcacaggccttggaggaggaggcaggtaccctctatgccaatagctgggcctgcctggggaaaggtggaaggagaaacagctgcaggaggggggagctgaaaggaatctgatgctcaggcctgcacaaagcaaccgccaaattgtttcagagcagaaaagaaaaagggagaaaacctcttagcaaagccctgtgagtttgggggtcaggttcaagaaagatgtgggaagtcacttggagagctaaacgggacacatgctcctatccacacttgcagttggtctaaccttcagccagaatgtattcataagtagcatttggcaaccctttatagtttacaaatagcattttacatacaccattctactattcctcatggtggctttgggaggtccagctccgttttaaagactcacacaggactgaagcaaataacttgctcaaagccacatagctgctcagaacccaagattgtaagctccccctagggccagaggcctctttctttcagtttttttctttcgtccccctttgacccctctttccttcttccctttctcccctccttcctcctttccttctttttgtgcccacagtgtctggatcatggtacctgaattctttagcctatttgcacccacatctgctaatgtccatatctagccatctattacaccagctgctgaggatttacttggtgccctcatcaagaagtttgaatttctccctccttcctttttttttcctgccactgtcccaactctttccctctacgtctctctagaatgacatctttaaaccccttacactctttggtcttacacatccttaaaaatgattatttataaattgaattataatatccatgaggtaaacactcatagggtaaagtacacaaagcttaactatacaagttgatgatttacacacacacacacacacacacacacacaccccttcttgaatggctccaaggatacccttttaacttcttcccttcagccacataagccatatgatgacacacagtgtctttctcctgtttgaaaagaaattgtgtcatattggtgtgctgttcttgcatagaaagccttttttaagaagtctttttaagatttcttgaaggattttagaaatcatatatctcttctaaccccctgaaatcctgagtttaagtggcttgattaaatggctgatcaaaacttaaaaacacactaggtcaatgtttttcaagatacaactgaggaccagctgcttcagaatcatctggggactggctaaaattccaggttcctaagccctagtcccatctgatgaatcagaaactaggttggggcttaggaacgtgcattttaaacacttttccaaagtgattcttatccagactaatatttgagaagtactgtattaaatggcaaactcccaaaacactgcagcctcctgcatctggcccagggcctggcatttggtaggaatacaatgaatgtttgttaaacaaattaatccacagtttctgacacagtttagaatttcttggaccacattatgctattgtaatttaacaccatttctacgtcgggaaatctttacatttcagtctttttcattttcatggaggtttcattttaatggagcaggagagaaaagagagatctactttggtggtttctcaggtctcagggaaggtcttttataaactcaatggggaccaccttcctggagaggctgctcccttacagacctggtagtttggggaaaggaggaggagagcccttcaggtttgctgaaaagcattcagatgcacacccttcttggttggaactgaaagcttctgtttgaagagacatgagttctggaaggagcaaggccaccaggtccagagaacctggcatgcaatggacatggaagctgaaaattacttgggtattctctgatttctagctaatatgaaaataattttctttctagaaacacatttgcctatcttcttaccctgaaacagaaaataaatattgtgctttatgtggtagtgttgtacccattcttaaaaataaatcacatcatatatatgtgtaaaatat

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