2025-05-09 19:25:04, GGRNA : RefSeq release 60 (20130726)
LOCUS NM_014621 1298 bp mRNA linear PRI 17-APR-2013 DEFINITION Homo sapiens homeobox D4 (HOXD4), mRNA. ACCESSION NM_014621 VERSION NM_014621.2 GI:23397671 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 1298) AUTHORS Zhang,H., He,J.W., Gao,G., Yue,H., Yu,J.B., Hu,W.W., Gu,J.M., Hu,Y.Q., Li,M., Fu,W.Z., Liu,Y.J. and Zhang,Z.L. TITLE Polymorphisms in the HOXD4 gene are not associated with peak bone mineral density in Chinese nuclear families JOURNAL Acta Pharmacol. Sin. 31 (8), 977-983 (2010) PUBMED 20686522 REMARK GeneRIF: The results suggest that genetic polymorphisms in HOXD4 may not be a major contributor to the observed variability in peak BMD in the lumbar spine and the hip in Chinese men and women GeneRIF: Observational study of gene-disease association. (HuGE Navigator) REFERENCE 2 (bases 1 to 1298) AUTHORS Ester,A.R., Weymouth,K.S., Burt,A., Wise,C.A., Scott,A., Gurnett,C.A., Dobbs,M.B., Blanton,S.H. and Hecht,J.T. TITLE Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot JOURNAL Am. J. Med. Genet. A 149A (12), 2745-2752 (2009) PUBMED 19938081 REMARK GeneRIF: Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator) REFERENCE 3 (bases 1 to 1298) AUTHORS Yerges,L.M., Klei,L., Cauley,J.A., Roeder,K., Kammerer,C.M., Moffett,S.P., Ensrud,K.E., Nestlerode,C.S., Marshall,L.M., Hoffman,A.R., Lewis,C., Lang,T.F., Barrett-Connor,E., Ferrell,R.E., Orwoll,E.S. and Zmuda,J.M. CONSRTM MrOS Research Group TITLE High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men JOURNAL J. Bone Miner. Res. 24 (12), 2039-2049 (2009) PUBMED 19453261 REMARK GeneRIF: Observational study of gene-disease association. (HuGE Navigator) REFERENCE 4 (bases 1 to 1298) AUTHORS Tan,Y., Zhang,B., Wu,T., Skogerbo,G., Zhu,X., Guo,X., He,S. and Chen,R. TITLE Transcriptional inhibiton of Hoxd4 expression by miRNA-10a in human breast cancer cells JOURNAL BMC Mol. Biol. 10, 12 (2009) PUBMED 19232136 REMARK GeneRIF: microRNA-10a (miR-10a) targets a homologous DNA region in the promoter region of the hoxd4 gene and represses its expression at the transcriptional level Publication Status: Online-Only REFERENCE 5 (bases 1 to 1298) AUTHORS van Scherpenzeel Thim,V., Remacle,S., Picard,J., Cornu,G., Gofflot,F., Rezsohazy,R. and Verellen-Dumoulin,C. TITLE Mutation analysis of the HOX paralogous 4-13 genes in children with acute lymphoid malignancies: identification of a novel germline mutation of HOXD4 leading to a partial loss-of-function JOURNAL Hum. Mutat. 25 (4), 384-395 (2005) PUBMED 15776434 REMARK GeneRIF: Observational study of gene-disease association. (HuGE Navigator) REFERENCE 6 (bases 1 to 1298) AUTHORS Scott,M.P. TITLE Vertebrate homeobox gene nomenclature JOURNAL Cell 71 (4), 551-553 (1992) PUBMED 1358459 REFERENCE 7 (bases 1 to 1298) AUTHORS Cianetti,L., Di Cristofaro,A., Zappavigna,V., Bottero,L., Boccoli,G., Testa,U., Russo,G., Boncinelli,E. and Peschle,C. TITLE Molecular mechanisms underlying the expression of the human HOX-5.1 gene JOURNAL Nucleic Acids Res. 18 (15), 4361-4368 (1990) PUBMED 1975093 REFERENCE 8 (bases 1 to 1298) AUTHORS McAlpine,P.J. and Shows,T.B. TITLE Nomenclature for human homeobox genes JOURNAL Genomics 7 (3), 460 (1990) PUBMED 1973146 REFERENCE 9 (bases 1 to 1298) 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 1298) AUTHORS Mavilio,F., Simeone,A., Giampaolo,A., Faiella,A., Zappavigna,V., Acampora,D., Poiana,G., Russo,G., Peschle,C. and Boncinelli,E. TITLE Differential and stage-related expression in embryonic tissues of a new human homoeobox gene JOURNAL Nature 324 (6098), 664-668 (1986) PUBMED 2879245 COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from X04706.1. This sequence is a reference standard in the RefSeqGene project. On Oct 1, 2002 this sequence version replaced gi:11024701. 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, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located at 2q31-2q37 chromosome regions. Deletions that removed the entire HOXD gene cluster or 5' end of this cluster have been associated with severe limb and genital abnormalities. The protein encoded by this gene may play a role in determining positional values in developing limb buds. Alternatively spliced variants have been described but their full length nature has not been determined. [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 :: X04706.1, AK313885.1 [ECO:0000332] RNAseq introns :: single sample supports all introns ERS025081, ERS025083 [ECO:0000348] ##Evidence-Data-END## COMPLETENESS: complete on the 3' end. FEATURES Location/Qualifiers source 1..1298 /organism="Homo sapiens" /mol_type="mRNA" /db_xref="taxon:9606" /chromosome="2" /map="2q31.1" gene 1..1298 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /note="homeobox D4" /db_xref="GeneID:3233" /db_xref="HGNC:5138" /db_xref="HPRD:00864" /db_xref="MIM:142981" exon 1..682 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /inference="alignment:Splign:1.39.8" variation 103 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:144430144" misc_feature 169..171 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /note="upstream in-frame stop codon" STS 181..1104 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /standard_name="UniSTS:480790" /db_xref="UniSTS:480790" variation 182 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:16863572" STS 203..1043 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /db_xref="UniSTS:482013" variation 238 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:372977271" variation 239 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="t" /db_xref="dbSNP:181916447" CDS 250..1017 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /note="Hox-4.2, mouse, homolog of homeo box X; homeobox protein Hox-4B; homeobox protein HHO.C13; homeobox protein Hox-5.1" /codon_start=1 /product="homeobox protein Hox-D4" /protein_id="NP_055436.2" /db_xref="GI:23397672" /db_xref="CCDS:CCDS2269.1" /db_xref="GeneID:3233" /db_xref="HGNC:5138" /db_xref="HPRD:00864" /db_xref="MIM:142981" /translation="
MVMSSYMVNSKYVDPKFPPCEEYLQGGYLGEQGADYYGGGAQGADFQPPGLYPRPDFGEQPFGGSGPGPGSALPARGHGQEPGGPGGHYAAPGEPCPAPPAPPPAPLPGARAYSQSDPKQPPSGTALKQPAVVYPWMKKVHVNSVNPNYTGGEPKRSRTAYTRQQVLELEKEFHFNRYLTRRRRIEIAHTLCLSERQIKIWFQNRRMKWKKDHKLPNTKGRSSSSSSSSSCSSSVAPSQHLQPMAKDHHTDLTTL
" misc_feature 646..663 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /experiment="experimental evidence, no additional details recorded" /note="propagated from UniProtKB/Swiss-Prot (P09016.3); Region: Antp-type hexapeptide" misc_feature 712..888 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /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(712..726,730..732,781..783,799..801,838..840, 844..849,856..861,865..873,877..882) /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /note="DNA binding site [nucleotide binding]" /db_xref="CDD:28970" misc_feature order(718..720,727..729,847..849,856..861,868..870) /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /note="specific DNA base contacts [nucleotide binding]; other site" /db_xref="CDD:28970" variation 263 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="g" /db_xref="dbSNP:141531995" variation 306 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:376860683" variation 313 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:150414482" variation 340 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="g" /db_xref="dbSNP:187203814" variation 347 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:149156170" variation 362 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:200815560" variation 366 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:374205432" variation 379 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:138948127" variation 384 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:78015126" variation 391 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:377617802" variation 409 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:370038228" variation 414 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:373841832" variation 491 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="t" /db_xref="dbSNP:104893636" variation 523 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="c" /db_xref="dbSNP:376322574" variation 560 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="c" /db_xref="dbSNP:370375150" variation 597 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="g" /db_xref="dbSNP:373583360" variation 616 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:34727427" variation 652 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="c" /db_xref="dbSNP:149263765" variation 673 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:375984352" exon 683..1298 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /inference="alignment:Splign:1.39.8" variation 687 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="c" /db_xref="dbSNP:201185478" variation 692 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:369822828" variation 693 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="c" /db_xref="dbSNP:200241025" variation 740 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:372805006" variation 762 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:199697693" variation 779 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="g" /db_xref="dbSNP:139645088" variation 780 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:147639954" variation 830 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:201536867" variation 858 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:142229749" variation 867 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:115586056" variation 891 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="g" /db_xref="dbSNP:369450962" variation 912 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:372512362" variation 927 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:202044839" variation 945 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:377042003" variation 963 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:371037366" variation 981 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="g" /db_xref="dbSNP:373439656" variation 998 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:374609255" variation 1002 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:367930048" STS 1012..1235 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /standard_name="STS-X17360" /db_xref="UniSTS:77133" variation 1047 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="g" /db_xref="dbSNP:369247267" variation 1050 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:371995881" variation 1056 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="g" /replace="t" /db_xref="dbSNP:377123607" variation 1081 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="a" /replace="c" /db_xref="dbSNP:143890106" variation 1195 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:1063656" variation 1218 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /replace="c" /replace="t" /db_xref="dbSNP:1063657" polyA_signal 1283..1288 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" polyA_site 1298 /gene="HOXD4" /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B" /experiment="experimental evidence, no additional details recorded" ORIGIN
cattaatatctggcaggggctctcaaatgtgccatagcaagctacttgattacacgtatgttatttagttaaatttgtgaaaattatgagatgctcaccaacccggtgataaacttgctccctcgccattggctggcctggtcacatggctgcccaactttattcagttgacagcaagtaggagggccctatggaaggagaaaaaaagacaacacgagaaaaattagtattttctaccttctgaaattaatggtcatgagttcgtatatggtgaactccaagtatgtggaccccaagttccctccgtgcgaggagtatttgcagggcggctacctaggcgagcagggcgccgactactacggcggcggcgcgcagggcgcagacttccagcccccggggctctacccacggcccgacttcggtgagcagcctttcggaggcagcggccccgggcctggctcggcgctgcctgcgcggggtcacggacaagagccaggcggccccggcggtcactacgccgctccaggagagccttgcccagctcccccggcgcctccgccggcgcccctgcctggcgcccgggcctacagtcagtccgaccccaagcagccgccctccgggacggcactcaagcagccggccgtggtctacccctggatgaagaaggtgcacgtgaattcggtgaaccccaactacaccggtggggaacccaagcggtcccgaacggcctacacccggcagcaagtcctagaactggaaaaagaatttcattttaacaggtatctgacaaggcgccgtcggattgaaatcgctcacaccctgtgtctgtcggagcgccagatcaagatctggttccagaaccggaggatgaagtggaaaaaagatcataagctgcccaacactaaaggcaggtcatcgtcctcatcttcctcctcatcttgctcctcctcagtcgcccccagccagcatttacagccgatggccaaagaccaccacacggacctgacgaccttatagaagtggggaccctgggcccatctctccctgcgcaccaggctgagccgaagctgcgggggcaggccgggcctgctgtcacctcgctgggctctaaggtactgtggggtggacctgggacaagcaggccgccctcggactaggttagcatcctgcccgagggcagccccctccctagagcgggatggggatgggagggggggcgggattctctctctaagtatattatatggcaggagctactgagaacataaaatcttggcgagtcattaaacttatgaaaa
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ANNOTATIONS from NCBI Entrez Gene (20130726): GeneID:3233 -> Molecular function: GO:0003700 [sequence-specific DNA binding transcription factor activity] evidence: NAS GeneID:3233 -> Molecular function: GO:0043565 [sequence-specific DNA binding] evidence: IEA GeneID:3233 -> Biological process: GO:0006351 [transcription, DNA-dependent] evidence: IEA GeneID:3233 -> Biological process: GO:0006355 [regulation of transcription, DNA-dependent] evidence: NAS GeneID:3233 -> Biological process: GO:0007275 [multicellular organismal development] evidence: NAS GeneID:3233 -> Cellular component: GO:0005634 [nucleus] evidence: NAS
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