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2024-03-28 18:21:14, GGRNA : RefSeq release 60 (20130726)

LOCUS       NM_006897               1640 bp    mRNA    linear   PRI 05-MAY-2013
DEFINITION  Homo sapiens homeobox C9 (HOXC9), mRNA.
ACCESSION   NM_006897
VERSION     NM_006897.1  GI:24497546
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 1640)
  AUTHORS   Sun,L., Cheng,L., Li,C., Gao,B., Wang,B., Wang,J., Wang,X.,
            Huang,T., Li,H. and Ma,X.
  TITLE     Homeobox C9 is not potentially related to congenital heart disease
            in Chinese patients
  JOURNAL   Genet Test Mol Biomarkers 16 (5), 439-441 (2012)
   PUBMED   22106857
  REMARK    GeneRIF: We did not find any potential pathological mutations in
            the Hoxc9 gene among Chinese patients with congenital heart
            disease.
REFERENCE   2  (bases 1 to 1640)
  AUTHORS   Mao,L., Ding,J., Zha,Y., Yang,L., McCarthy,B.A., King,W., Cui,H.
            and Ding,H.F.
  TITLE     HOXC9 links cell-cycle exit and neuronal differentiation and is a
            prognostic marker in neuroblastoma
  JOURNAL   Cancer Res. 71 (12), 4314-4324 (2011)
   PUBMED   21507931
  REMARK    GeneRIF: HOXC9 links cell-cycle exit and neuronal differentiation
            and is a prognostic marker in neuroblastoma.
REFERENCE   3  (bases 1 to 1640)
  AUTHORS   Stoll,S.J., Bartsch,S., Augustin,H.G. and Kroll,J.
  TITLE     The transcription factor HOXC9 regulates endothelial cell
            quiescence and vascular morphogenesis in zebrafish via inhibition
            of interleukin 8
  JOURNAL   Circ. Res. 108 (11), 1367-1377 (2011)
   PUBMED   21493894
  REMARK    GeneRIF: The data identify HOXC9 as an endothelial cell active
            transcriptional repressor promoting the resting, antiangiogenic
            endothelial cell phenotype in an interleukin 8-dependent manner
REFERENCE   4  (bases 1 to 1640)
  AUTHORS   Lin,Q., Geng,J., Ma,K., Yu,J., Sun,J., Shen,Z., Bao,G., Chen,Y.,
            Zhang,H., He,Y., Luo,X., Feng,X. and Zhu,J.
  TITLE     RASSF1A, APC, ESR1, ABCB1 and HOXC9, but not p16INK4A, DAPK1, PTEN
            and MT1G genes were frequently methylated in the stage I non-small
            cell lung cancer in China
  JOURNAL   J. Cancer Res. Clin. Oncol. 135 (12), 1675-1684 (2009)
   PUBMED   19506903
  REMARK    GeneRIF: Methylated state of this set of genes may be more specific
            to the late rather than the early stage of NSCLC.
            Erratum:[J Cancer Res Clin Oncol. 2010 Jan;136(1):171]
REFERENCE   5  (bases 1 to 1640)
  AUTHORS   Olejnik-Schmidt,A.K., Schmidt,M.T., Kedzia,W. and
            Gozdzicka-Jozefiak,A.
  TITLE     Search for cellular partners of human papillomavirus type 16 E2
            protein
  JOURNAL   Arch. Virol. 153 (5), 983-990 (2008)
   PUBMED   18305892
REFERENCE   6  (bases 1 to 1640)
  AUTHORS   Miano,J.M., Firulli,A.B., Olson,E.N., Hara,P., Giachelli,C.M. and
            Schwartz,S.M.
  TITLE     Restricted expression of homeobox genes distinguishes fetal from
            adult human smooth muscle cells
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 93 (2), 900-905 (1996)
   PUBMED   8570656
REFERENCE   7  (bases 1 to 1640)
  AUTHORS   Redline,R.W., Hudock,P., MacFee,M. and Patterson,P.
  TITLE     Expression of AbdB-type homeobox genes in human tumors
  JOURNAL   Lab. Invest. 71 (5), 663-670 (1994)
   PUBMED   7967520
REFERENCE   8  (bases 1 to 1640)
  AUTHORS   Acampora,D., D'Esposito,M., Faiella,A., Pannese,M., Migliaccio,E.,
            Morelli,F., Stornaiuolo,A., Nigro,V., Simeone,A. and Boncinelli,E.
  TITLE     The human HOX gene family
  JOURNAL   Nucleic Acids Res. 17 (24), 10385-10402 (1989)
   PUBMED   2574852
REFERENCE   9  (bases 1 to 1640)
  AUTHORS   Boncinelli,E., Acampora,D., Pannese,M., D'Esposito,M., Somma,R.,
            Gaudino,G., Stornaiuolo,A., Cafiero,M., Faiella,A. and Simeone,A.
  TITLE     Organization of human class I homeobox genes
  JOURNAL   Genome 31 (2), 745-756 (1989)
   PUBMED   2576652
REFERENCE   10 (bases 1 to 1640)
  AUTHORS   Rabin,M., Ferguson-Smith,A., Hart,C.P. and Ruddle,F.H.
  TITLE     Cognate homeo-box loci mapped on homologous human and mouse
            chromosomes
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 83 (23), 9104-9108 (1986)
   PUBMED   2878432
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AY014301.1, BC032769.1,
            BC053894.1, AC012531.11 and AK000445.1.
            
            Summary: This gene belongs to the homeobox family of genes. The
            homeobox genes encode a highly conserved family of transcription
            factors that play an important role in morphogenesis in all
            multicellular organisms. Mammals possess four similar homeobox gene
            clusters, HOXA, HOXB, HOXC and HOXD, which are located on different
            chromosomes and consist of 9 to 11 genes arranged in tandem. This
            gene is one of several homeobox HOXC genes located in a cluster on
            chromosome 12. [provided by RefSeq, Jul 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 :: AK000445.1, BC021265.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           ERS025084, ERS025085 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-98                AY014301.1         1-98
            99-1012             BC032769.1         12-925
            1013-1391           BC053894.1         987-1365
            1392-1401           AC012531.11        140791-140800
            1402-1640           AK000445.1         1323-1561
FEATURES             Location/Qualifiers
     source          1..1640
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12q13.3"
     gene            1..1640
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /note="homeobox C9"
                     /db_xref="GeneID:3225"
                     /db_xref="HGNC:5130"
                     /db_xref="HPRD:00857"
                     /db_xref="MIM:142971"
     exon            1..634
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /inference="alignment:Splign:1.39.8"
     variation       61
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:373004521"
     variation       62
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:201653133"
     variation       66
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:368017100"
     variation       78
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:373971996"
     misc_feature    82..84
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /note="upstream in-frame stop codon"
     CDS             97..879
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /note="homeo box C9; homeobox protein Hox-3B"
                     /codon_start=1
                     /product="homeobox protein Hox-C9"
                     /protein_id="NP_008828.1"
                     /db_xref="GI:24497547"
                     /db_xref="CCDS:CCDS8869.1"
                     /db_xref="GeneID:3225"
                     /db_xref="HGNC:5130"
                     /db_xref="HPRD:00857"
                     /db_xref="MIM:142971"
                     /translation="
MSATGPISNYYVDSLISHDNEDLLASRFPATGAHPAAARPSGLVPDCSDFPSCSFAPKPAVFSTSWAPVPSQSSVVYHPYGPQPHLGADTRYMRTWLEPLSGAVSFPSFPAGGRHYALKPDAYPGRRADCGPGEGRSYPDYMYGSPGELRDRAPQTLPSPEADALAGSKHKEEKADLDPSNPVANWIHARSTRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMNKEKTDKEQS
"
     misc_feature    97..633
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /note="Hox9 activation region; Region: Hox9_act;
                     pfam04617"
                     /db_xref="CDD:191048"
     misc_feature    673..819
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /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(673..687,691..693,742..744,760..762,799..801,
                     805..810,817..819)
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:28970"
     misc_feature    order(679..681,688..690,808..810,817..819)
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:28970"
     variation       116
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:145111102"
     variation       148
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:370526047"
     variation       208
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:374992460"
     variation       219
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:138926361"
     variation       273
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:35784648"
     variation       305
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:199572863"
     variation       318
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:34136736"
     variation       323
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:138167268"
     variation       336
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:376785654"
     variation       339
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:149559141"
     variation       392
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:371710144"
     variation       398
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:200358721"
     variation       408
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:34079606"
     variation       461
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:11829948"
     variation       582
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:145061695"
     variation       591
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:7137528"
     STS             597..711
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /standard_name="MARC_44775-44776:1100041323:1"
                     /db_xref="UniSTS:471623"
     variation       621
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:2241820"
     exon            635..1542
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /inference="alignment:Splign:1.39.8"
     variation       647
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:370925185"
     variation       683
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:374611200"
     variation       693
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:200142062"
     variation       696
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:202198578"
     variation       708
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:201717585"
     variation       740
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:201378386"
     variation       741
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:199706649"
     variation       760
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:144189376"
     variation       783
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:370297998"
     variation       789
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:200241065"
     STS             844..1139
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /standard_name="Hoxc9"
                     /db_xref="UniSTS:468838"
     STS             868..1054
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /standard_name="RH68776"
                     /db_xref="UniSTS:66349"
     variation       969
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:144848510"
     STS             995..1144
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /standard_name="SGC35159"
                     /db_xref="UniSTS:34723"
     variation       1043
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:140162011"
     variation       1045
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:189249574"
     variation       1057
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:181553076"
     variation       1091
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:1047374"
     variation       1143
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:374995195"
     variation       1144
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:374038445"
     variation       1182
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:367720016"
     variation       1219
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:116659696"
     variation       1227..1228
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace=""
                     /replace="t"
                     /db_xref="dbSNP:145733208"
     variation       1227
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:185824205"
     variation       1271
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:369710269"
     variation       1304
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:116741952"
     variation       1318..1319
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace=""
                     /replace="ac"
                     /db_xref="dbSNP:139550932"
     variation       1318
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace=""
                     /replace="ca"
                     /db_xref="dbSNP:72033532"
     variation       1323
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:374134582"
     variation       1392
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:1867297"
     variation       1396
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:147255161"
     variation       1411
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:376777337"
     variation       1412
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:373812925"
     polyA_site      1542
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /experiment="experimental evidence, no additional details
                     recorded"
ORIGIN      
tggaaaaataattacctgacttgattgttctgtgagcagataaaaagtacatatacagttcatacaataatcttatgtatgtaaaaccccgttacgatgtcggcgacggggcccatcagtaactattacgtggactcgctcatctctcacgacaatgaagacctcctagcgtccaggtttccggccaccggggctcatcccgccgccgccagacccagcggtttggtgccggactgtagcgattttccgtcctgtagcttcgcgcccaagccggcagtgttcagcacgtcgtgggcgcccgtgccctctcagtcgtccgtggtatatcacccgtacggcccccagccccacctcggcgccgacacgcgctacatgcggacttggctcgagccgctgtccggcgccgtctccttccccagcttcccggccgggggccgtcactacgccctcaagccggacgcctaccccgggcgccgcgcggactgcggcccaggggagggccgcagctacccggactacatgtacggctcgcccggggagctgcgcgaccgcgccccgcagacactgccctcgcccgaggcggacgcgctcgccggcagcaagcacaaagaggagaaggccgacctggaccccagcaaccccgtggccaactggattcacgcccgctccacgaggaagaagcgctgcccctacaccaagtaccagacgctggaactggagaaggagtttctcttcaatatgtatttaaccagggaccgtcggtatgaggtggcccgggttctcaatctcaccgagcggcaggtcaaaatctggtttcagaatcgaaggatgaagatgaaaaagatgaataaagagaaaaccgacaaggagcagtcctaaaccctacccagcctgctgcctcagcacagccaagggaaaaacaaaaaccccacaaaataccccaacacaggcgggggagagacgaaaaagaaaaggaaagagcaagatagacaaaagccaatcagcttaaaaagaaaaacaaggaaggggaaaagaaaactcttgcgatttgggagggttcagtgttgagatattggtgttttagagttagttctacccagcgaggaggaggcggggagagaaactgcgttctctttccccagcgcaaccgaaataaatgacacatacaaatgtgatttttttcctcctttcttcagagaagccagtacttgaatcgctatatttctatttttttttccctgtatcgtatttggtccaggtcatccctccccgggcctggggcgctctgcgtgcagattttgtacaaaaaaaaaaaagacacacacacatacatgataatgattcccagcccaggagctgaggggtgagggctggggaccatgccgcgggctaggtcgggcccgtgcaggccggcgccttgggctgtacatagtgttccctctcatccccagggttcgtccccagcgtccgtcctgtaacgtgcttctgtttgttatggtagaacagccctgtgttaatatattgaagtcacttaaccagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
//

Annotations:

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:3225 -> Molecular function: GO:0003700 [sequence-specific DNA binding transcription factor activity] evidence: IEA
            GeneID:3225 -> Molecular function: GO:0043565 [sequence-specific DNA binding] evidence: IEA
            GeneID:3225 -> Biological process: GO:0006351 [transcription, DNA-dependent] evidence: IEA
            GeneID:3225 -> Biological process: GO:0009952 [anterior/posterior pattern specification] evidence: IEA
            GeneID:3225 -> Biological process: GO:0048704 [embryonic skeletal system morphogenesis] evidence: IEA
            GeneID:3225 -> Cellular component: GO:0005634 [nucleus] evidence: IEA

by @meso_cacase at DBCLS
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