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2025-05-09 19:31:44, GGRNA : RefSeq release 60 (20130726)
LOCUS NM_018953 1613 bp mRNA linear PRI 17-APR-2013 DEFINITION Homo sapiens homeobox C5 (HOXC5), transcript variant 1, mRNA. ACCESSION NM_018953 VERSION NM_018953.2 GI:24497541 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 1613) AUTHORS Estrada,K., Styrkarsdottir,U., Evangelou,E., Hsu,Y.H., Duncan,E.L., Ntzani,E.E., Oei,L., Albagha,O.M., Amin,N., Kemp,J.P., Koller,D.L., Li,G., Liu,C.T., Minster,R.L., Moayyeri,A., Vandenput,L., Willner,D., Xiao,S.M., Yerges-Armstrong,L.M., Zheng,H.F., Alonso,N., Eriksson,J., Kammerer,C.M., Kaptoge,S.K., Leo,P.J., Thorleifsson,G., Wilson,S.G., Wilson,J.F., Aalto,V., Alen,M., Aragaki,A.K., Aspelund,T., Center,J.R., Dailiana,Z., Duggan,D.J., Garcia,M., Garcia-Giralt,N., Giroux,S., Hallmans,G., Hocking,L.J., Husted,L.B., Jameson,K.A., Khusainova,R., Kim,G.S., Kooperberg,C., Koromila,T., Kruk,M., Laaksonen,M., Lacroix,A.Z., Lee,S.H., Leung,P.C., Lewis,J.R., Masi,L., Mencej-Bedrac,S., Nguyen,T.V., Nogues,X., Patel,M.S., Prezelj,J., Rose,L.M., Scollen,S., Siggeirsdottir,K., Smith,A.V., Svensson,O., Trompet,S., Trummer,O., van Schoor,N.M., Woo,J., Zhu,K., Balcells,S., Brandi,M.L., Buckley,B.M., Cheng,S., Christiansen,C., Cooper,C., Dedoussis,G., Ford,I., Frost,M., Goltzman,D., Gonzalez-Macias,J., Kahonen,M., Karlsson,M., Khusnutdinova,E., Koh,J.M., Kollia,P., Langdahl,B.L., Leslie,W.D., Lips,P., Ljunggren,O., Lorenc,R.S., Marc,J., Mellstrom,D., Obermayer-Pietsch,B., Olmos,J.M., Pettersson-Kymmer,U., Reid,D.M., Riancho,J.A., Ridker,P.M., Rousseau,F., Slagboom,P.E., Tang,N.L., Urreizti,R., Van Hul,W., Viikari,J., Zarrabeitia,M.T., Aulchenko,Y.S., Castano-Betancourt,M., Grundberg,E., Herrera,L., Ingvarsson,T., Johannsdottir,H., Kwan,T., Li,R., Luben,R., Medina-Gomez,C., Palsson,S.T., Reppe,S., Rotter,J.I., Sigurdsson,G., van Meurs,J.B., Verlaan,D., Williams,F.M., Wood,A.R., Zhou,Y., Gautvik,K.M., Pastinen,T., Raychaudhuri,S., Cauley,J.A., Chasman,D.I., Clark,G.R., Cummings,S.R., Danoy,P., Dennison,E.M., Eastell,R., Eisman,J.A., Gudnason,V., Hofman,A., Jackson,R.D., Jones,G., Jukema,J.W., Khaw,K.T., Lehtimaki,T., Liu,Y., Lorentzon,M., McCloskey,E., Mitchell,B.D., Nandakumar,K., Nicholson,G.C., Oostra,B.A., Peacock,M., Pols,H.A., Prince,R.L., Raitakari,O., Reid,I.R., Robbins,J., Sambrook,P.N., Sham,P.C., Shuldiner,A.R., Tylavsky,F.A., van Duijn,C.M., Wareham,N.J., Cupples,L.A., Econs,M.J., Evans,D.M., Harris,T.B., Kung,A.W., Psaty,B.M., Reeve,J., Spector,T.D., Streeten,E.A., Zillikens,M.C., Thorsteinsdottir,U., Ohlsson,C., Karasik,D., Richards,J.B., Brown,M.A., Stefansson,K., Uitterlinden,A.G., Ralston,S.H., Ioannidis,J.P., Kiel,D.P. and Rivadeneira,F. TITLE Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture JOURNAL Nat. Genet. 44 (5), 491-501 (2012) PUBMED 22504420 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 1613) AUTHORS Gong,L.G., Qiu,G.R., Jiang,H., Xu,X.Y., Zhu,H.Y. and Sun,K.L. TITLE Analysis of single nucleotide polymorphisms and haplotypes in HOXC gene cluster within susceptible region 12q13 of simple congenital heart disease JOURNAL Zhonghua Yi Xue Yi Chuan Xue Za Zhi 22 (5), 497-501 (2005) PUBMED 16215934 REMARK GeneRIF: The A17860G located in 3'flanking sequence of HOXC5 gene is associated with simple congenital heart disease; the haplotype of 3 SNPs may be linked with the susceptible gene of simple CHD. GeneRIF: Observational study of gene-disease association. (HuGE Navigator) REFERENCE 3 (bases 1 to 1613) AUTHORS Kosaki,K., Kosaki,R., Suzuki,T., Yoshihashi,H., Takahashi,T., Sasaki,K., Tomita,M., McGinnis,W. and Matsuo,N. TITLE Complete mutation analysis panel of the 39 human HOX genes JOURNAL Teratology 65 (2), 50-62 (2002) PUBMED 11857506 REFERENCE 4 (bases 1 to 1613) AUTHORS Apiou,F., Flagiello,D., Cillo,C., Malfoy,B., Poupon,M.F. and Dutrillaux,B. TITLE Fine mapping of human HOX gene clusters JOURNAL Cytogenet. Cell Genet. 73 (1-2), 114-115 (1996) PUBMED 8646877 REFERENCE 5 (bases 1 to 1613) AUTHORS Guazzi,S., Lonigro,R., Pintonello,L., Boncinelli,E., Di Lauro,R. and Mavilio,F. TITLE The thyroid transcription factor-1 gene is a candidate target for regulation by Hox proteins JOURNAL EMBO J. 13 (14), 3339-3347 (1994) PUBMED 7913891 REFERENCE 6 (bases 1 to 1613) AUTHORS Arcioni,L., Simeone,A., Guazzi,S., Zappavigna,V., Boncinelli,E. and Mavilio,F. TITLE The upstream region of the human homeobox gene HOX3D is a target for regulation by retinoic acid and HOX homeoproteins JOURNAL EMBO J. 11 (1), 265-277 (1992) PUBMED 1346761 REFERENCE 7 (bases 1 to 1613) 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 8 (bases 1 to 1613) 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 9 (bases 1 to 1613) AUTHORS Simeone,A., Pannese,M., Acampora,D., D'Esposito,M. and Boncinelli,E. TITLE At least three human homeoboxes on chromosome 12 belong to the same transcription unit JOURNAL Nucleic Acids Res. 16 (12), 5379-5390 (1988) PUBMED 2898768 REFERENCE 10 (bases 1 to 1613) 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 X61755.1. This sequence is a reference standard in the RefSeqGene project. On Nov 3, 2002 this sequence version replaced gi:11321637. 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, HOXC5, is one of several homeobox HOXC genes located in a cluster on chromosome 12. Three genes, HOXC5, HOXC4 and HOXC6, share a 5' non-coding exon. Transcripts may include the shared exon spliced to the gene-specific exons, or they may include only the gene-specific exons. Two alternatively spliced variants have been described for HOXC5. The transcript variant which includes the shared exon apparently doesn't encode a protein. The protein-coding transcript variant contains gene-specific exons only. [provided by RefSeq, Jul 2008]. Transcript Variant: This variant (1) represents the shorter transcript and is protein coding. ##Evidence-Data-START## Transcript exon combination :: CN309383.1, CN309384.1 [ECO:0000332] RNAseq introns :: single sample supports all introns ERS025084, ERS025085 [ECO:0000348] ##Evidence-Data-END## COMPLETENESS: full length. FEATURES Location/Qualifiers source 1..1613 /organism="Homo sapiens" /mol_type="mRNA" /db_xref="taxon:9606" /chromosome="12" /map="12q13.3" gene 1..1613 /gene="HOXC5" /gene_synonym="CP11; HOX3; HOX3D" /note="homeobox C5" /db_xref="GeneID:3222" /db_xref="HGNC:5127" /db_xref="HPRD:00859" /db_xref="MIM:142973" exon 1..529 /gene="HOXC5" /gene_synonym="CP11; HOX3; HOX3D" /inference="alignment:Splign:1.39.8" misc_feature 34..36 /gene="HOXC5" /gene_synonym="CP11; HOX3; HOX3D" /note="upstream in-frame stop codon" variation 72 /gene="HOXC5" /gene_synonym="CP11; HOX3; HOX3D" /replace="c" /replace="t" /db_xref="dbSNP:373282368" CDS 76..744 /gene="HOXC5" /gene_synonym="CP11; HOX3; HOX3D" /note="homeo box C5; homeobox protein CP11; homeobox protein Hox-3D" /codon_start=1 /product="homeobox protein Hox-C5" /protein_id="NP_061826.1" /db_xref="GI:11321638" /db_xref="CCDS:CCDS8872.1" /db_xref="GeneID:3222" /db_xref="HGNC:5127" /db_xref="HPRD:00859" /db_xref="MIM:142973" /translation="
MSSYVANSFYKQSPNIPAYNMQTCGNYGSASEVQASRYCYGGLDLSITFPPPAPSNSLHGVDMAANPRAHPDRPACSAAAAPGHAPGRDEAAPLNPGMYSQKAARPALEERAKSSGEIKEEQAQTGQPAGLSQPPAPPQIYPWMTKLHMSHETDGKRSRTSYTRYQTLELEKEFHFNRYLTRRRRIEIANNLCLNERQIKIWFQNRRMKWKKDSKMKSKEAL
"
misc_feature 493..510
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/experiment="experimental evidence, no additional details
recorded"
/note="propagated from UniProtKB/Swiss-Prot (Q00444.1);
Region: Antp-type hexapeptide"
misc_feature 541..696
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/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(541..555,559..561,610..612,628..630,667..669,
673..678,685..690,694..696)
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/note="DNA binding site [nucleotide binding]"
/db_xref="CDD:28970"
misc_feature order(547..549,556..558,676..678,685..690)
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/note="specific DNA base contacts [nucleotide binding];
other site"
/db_xref="CDD:28970"
variation 81
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:201414819"
variation 108
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="g"
/db_xref="dbSNP:35606176"
variation 161
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:200385207"
variation 167
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:199703080"
variation 207
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:151147734"
variation 221
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:200351551"
variation 255
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="g"
/replace="t"
/db_xref="dbSNP:139064806"
variation 277
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:200703154"
variation 280
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="g"
/db_xref="dbSNP:369572312"
variation 312
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="g"
/db_xref="dbSNP:34720266"
variation 317
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:2071448"
variation 341
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="g"
/db_xref="dbSNP:146874223"
variation 383
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="c"
/db_xref="dbSNP:373127865"
variation 393
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="g"
/db_xref="dbSNP:376224435"
variation 416
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="g"
/db_xref="dbSNP:200190925"
variation 449
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:140687506"
variation 481
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="g"
/db_xref="dbSNP:201107649"
STS 497..578
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/standard_name="Hoxc5"
/db_xref="UniSTS:536662"
variation 529
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="g"
/db_xref="dbSNP:202063227"
exon 530..1613
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/inference="alignment:Splign:1.39.8"
variation 533
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="g"
/db_xref="dbSNP:145794998"
variation 537
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="g"
/db_xref="dbSNP:145300322"
variation 545
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="g"
/db_xref="dbSNP:149168463"
variation 561
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:376228055"
variation 589
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="t"
/db_xref="dbSNP:376926310"
variation 622
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="c"
/db_xref="dbSNP:370344965"
variation 735
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="g"
/db_xref="dbSNP:143274247"
variation 781
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="g"
/db_xref="dbSNP:371365110"
variation 832
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="g"
/db_xref="dbSNP:113264704"
variation 839
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="g"
/db_xref="dbSNP:4016778"
variation 972
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:58994757"
variation 1000
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:2071450"
variation 1111
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:149895718"
variation 1151
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="g"
/replace="t"
/db_xref="dbSNP:373936762"
variation 1168
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:61921796"
variation 1215
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="g"
/db_xref="dbSNP:61921797"
variation 1272
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="c"
/db_xref="dbSNP:145357528"
STS 1326..1427
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/standard_name="D12S1961"
/db_xref="UniSTS:9524"
variation 1337..1339
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace=""
/replace="aca"
/db_xref="dbSNP:377514653"
variation 1351
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:191530738"
variation 1384
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="c"
/db_xref="dbSNP:184371311"
variation 1445
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:188058463"
variation 1457
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="c"
/replace="t"
/db_xref="dbSNP:140104713"
variation 1473
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="g"
/db_xref="dbSNP:192290087"
variation 1506
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/replace="a"
/replace="t"
/db_xref="dbSNP:185833901"
polyA_signal 1591..1596
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
polyA_site 1613
/gene="HOXC5"
/gene_synonym="CP11; HOX3; HOX3D"
/experiment="experimental evidence, no additional details
recorded"
ORIGIN
acccctcaacttcaaagagtcacaaatcacccttaatcaaaaagggtgcagaaatttttttgggccctccccgccatgagctcctacgtagccaattcattctataagcagagccccaatatccctgcctataacatgcaaacttgtgggaactatggatcggcctcagaggtgcaggcatccaggtactgctacggcggattggacttaagcatcactttcccaccgcctgcgccttccaactctctccacggggtagacatggctgccaacccccgggctcaccccgaccgccccgcctgcagcgccgcggccgctccgggacacgctccgggcagagacgaagcggctcctctgaaccccgggatgtacagtcagaaggcggctcgcccggcgctggaggagcgagctaagagcagtggggagatcaaagaggagcaggcgcagacagggcagcccgccggactgagccagccaccggccccgccacagatttacccgtggatgaccaaactgcacatgagccacgagacggacggcaagcggtcccgaaccagttacacgcgctaccagactctggaactcgagaaagaattccactttaaccgctacctcactcgccgcaggcgcatagagatcgccaacaacttgtgtctcaatgagagacagatcaagatctggttccagaaccgcaggatgaagtggaagaaagattccaaaatgaaaagcaaagaggctctttagaggcagcgggggaggcccgcagagcgcgcccctagccggttcctgtccctgcgcctttccttttcgcctttcctctctatatttcgggtcgggggcaggtgctggagcactgggctcccgggccccacagacaaaagcgcttttccttggcattccgcatccctaccgacccagggttcccgcggggctgtcggcgctgccccatctcccctcagctcggctcagctcggtacccggggcccagggcaagctccgcaggacttccccggagggctgcggcgtacaggctggcgcagaacgaaccttggcctgggccgtatctccggctcccagcctcagcgcggccctcccgagttaaggtgggcccggcccgcgccacaggaccctcgccggaccctctaacctcgccctctcctttgttcccggctggacgggttagacagccaaaggctggcgagagtctggccctagactcggggtgcttccttgtagcgactaaactagattttcacttatgaatgatttgcatatgaaaggagagcatcggcctagggcccccacagttgctctatgctttccaaaccttatctccacaacctcttccccccaaaacccgggaacctccccagcctgcgcctgctgcatgccctctcaggccggcagccccagcctgctagctagctcaactagtggggtttcctggcactggaccccagcaagtggtcctagaggccctttgctgtcccatagtccctgccacgaatttctgtgccctcctgacccattgctgttgtccaactatttattgactctgggtccttcctgaaactatattttgtcatatcaaataaagagagaacaggactaaa
//
ANNOTATIONS from NCBI Entrez Gene (20130726):
GeneID:3222 -> Molecular function: GO:0003700 [sequence-specific DNA binding transcription factor activity] evidence: IEA
GeneID:3222 -> Molecular function: GO:0043565 [sequence-specific DNA binding] evidence: IEA
GeneID:3222 -> Biological process: GO:0006351 [transcription, DNA-dependent] evidence: IEA
GeneID:3222 -> Biological process: GO:0006357 [regulation of transcription from RNA polymerase II promoter] evidence: TAS
GeneID:3222 -> Biological process: GO:0009952 [anterior/posterior pattern specification] evidence: IEA
GeneID:3222 -> Biological process: GO:0048706 [embryonic skeletal system development] evidence: IEA
GeneID:3222 -> Cellular component: GO:0005634 [nucleus] evidence: IDA
GeneID:3222 -> Cellular component: GO:0005730 [nucleolus] evidence: IDA
GeneID:3222 -> Cellular component: GO:0030054 [cell junction] evidence: IDA
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@meso_cacase at
DBCLS
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