LOCUS       NM_001199747            1624 bp    mRNA    linear   PRI 17-APR-2013
DEFINITION  Homo sapiens homeobox D8 (HOXD8), transcript variant 3, mRNA.
ACCESSION   NM_001199747
VERSION     NM_001199747.1  GI:315075270
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 1624)
  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   2  (bases 1 to 1624)
  AUTHORS   Harada,K., Yamazaki,T., Iwata,C., Yoshimatsu,Y., Sase,H.,
            Mishima,K., Morishita,Y., Hirashima,M., Oike,Y., Suda,T., Miura,N.,
            Watabe,T. and Miyazono,K.
  TITLE     Identification of targets of Prox1 during in vitro vascular
            differentiation from embryonic stem cells: functional roles of
            HoxD8 in lymphangiogenesis
  JOURNAL   J. Cell. Sci. 122 (PT 21), 3923-3930 (2009)
   PUBMED   19825936
  REMARK    GeneRIF: Prox1 and HoxD8 play important roles in the maturation and
            maintenance of lymphatic vessels.
REFERENCE   3  (bases 1 to 1624)
  AUTHORS   Goodman,F.R.
  TITLE     Limb malformations and the human HOX genes
  JOURNAL   Am. J. Med. Genet. 112 (3), 256-265 (2002)
   PUBMED   12357469
  REMARK    Review article
REFERENCE   4  (bases 1 to 1624)
  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   5  (bases 1 to 1624)
  AUTHORS   Limongi,M.Z., Pelliccia,F., Gaddini,L. and Rocchi,A.
  TITLE     Clustering of two fragile sites and seven homeobox genes in human
            chromosome region 2q31-->q32.1
  JOURNAL   Cytogenet. Cell Genet. 90 (1-2), 151-153 (2000)
   PUBMED   11060466
REFERENCE   6  (bases 1 to 1624)
  AUTHORS   Manohar,C.F., Salwen,H.R., Furtado,M.R. and Cohn,S.L.
  TITLE     Up-regulation of HOXC6, HOXD1, and HOXD8 homeobox gene expression
            in human neuroblastoma cells following chemical induction of
            differentiation
  JOURNAL   Tumour Biol. 17 (1), 34-47 (1996)
   PUBMED   7501971
REFERENCE   7  (bases 1 to 1624)
  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   8  (bases 1 to 1624)
  AUTHORS   Rosen,D.R. and Brown,R.H. Jr.
  TITLE     Dinucleotide repeat polymorphism in the HOX4E locus
  JOURNAL   Hum. Mol. Genet. 2 (5), 617 (1993)
   PUBMED   8100165
REFERENCE   9  (bases 1 to 1624)
  AUTHORS   Redline,R.W., Williams,A.J., Patterson,P. and Collins,T.
  TITLE     Human HOX4E: a gene strongly expressed in the adult male and female
            urogenital tracts
  JOURNAL   Genomics 13 (2), 425-430 (1992)
   PUBMED   1351871
REFERENCE   10 (bases 1 to 1624)
  AUTHORS   Oliver,G., Sidell,N., Fiske,W., Heinzmann,C., Mohandas,T.,
            Sparkes,R.S. and De Robertis,E.M.
  TITLE     Complementary homeo protein gradients in developing limb buds
  JOURNAL   Genes Dev. 3 (5), 641-650 (1989)
   PUBMED   2568311
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC009336.13, BQ429720.1 and
            AW140108.1.
            
            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, located on different
            chromosomes, consisting of 9 to 11 genes arranged in tandem. This
            gene is one of several homeobox HOXD genes located in a cluster on
            chromosome 2. Deletions that remove the entire HOXD gene cluster or
            the 5' end of this cluster have been associated with severe limb
            and genital abnormalities. In addition to effects during
            embryogenesis, this particular gene may also play a role in adult
            urogenital tract function. Alternate splicing results in multiple
            transcript variants.[provided by RefSeq, Dec 2010].
            
            Transcript Variant: This variant (3) differs in the 5' UTR, lacks a
            portion of the 5' coding region, and initiates translation at a
            downstream start codon, compared to variant 1. The encoded isoform
            (3) has a distinct N-terminus and is shorter than isoform 1.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: AL520835.3, BQ429720.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           ERS025081, ERS025084 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-53                AC009336.13        113683-113735
            54-124              BQ429720.1         4-74
            125-125             AC009336.13        114828-114828
            126-774             BQ429720.1         76-724
            775-1150            AC009336.13        115851-116226
            1151-1624           AW140108.1         1-474               c
FEATURES             Location/Qualifiers
     source          1..1624
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q31.1"
     gene            1..1624
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /note="homeobox D8"
                     /db_xref="GeneID:3234"
                     /db_xref="HGNC:5139"
                     /db_xref="MIM:142985"
     exon            1..81
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /inference="alignment:Splign:1.39.8"
     exon            82..229
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /inference="alignment:Splign:1.39.8"
     variation       117
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:147014120"
     variation       133
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:374010247"
     variation       144
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:377728786"
     variation       165
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:3765049"
     variation       177
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:148123943"
     variation       192
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:138972805"
     CDS             205..525
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /note="isoform 3 is encoded by transcript variant 3; homeo
                     box D8; homeobox protein 5.4; homeo box 4E; homeobox
                     protein Hox-D8; Hox-4.5; homeobox protein Hox-4E; homeobox
                     protein Hox-5.4"
                     /codon_start=1
                     /product="homeobox protein Hox-D8 isoform 3"
                     /protein_id="NP_001186676.1"
                     /db_xref="GI:315075271"
                     /db_xref="CCDS:CCDS56149.1"
                     /db_xref="GeneID:3234"
                     /db_xref="HGNC:5139"
                     /db_xref="MIM:142985"
                     /translation="

MFPWMRPQAAPGRRRGRQTYSRFQTLELEKEFLFNPYLTRKRRIEVSHALALTERQVKIWFQNRRMKWKKENNKDKFPVSRQEVKDGETKKEAQELEEDRAEGLTN

"
     misc_feature    259..420
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /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(259..261,379..381,388..393,400..402)
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:28970"
     misc_feature    order(262..264,313..315,331..333,370..372,376..381,
                     388..393,397..405,409..414)
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:28970"
     variation       212
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:142220242"
     variation       219
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:371171284"
     STS             229..354
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /standard_name="RH18089"
                     /db_xref="UniSTS:47553"
     exon            230..1608
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /inference="alignment:Splign:1.39.8"
     variation       244
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:199871239"
     variation       322
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:375411869"
     variation       334
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:139078975"
     variation       337
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:199631106"
     variation       377
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:200630630"
     variation       385
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:201900185"
     variation       394
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:201072995"
     variation       428
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:143950622"
     variation       459
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:371256205"
     variation       460
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:147814791"
     variation       463
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:113257910"
     variation       466
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:201690967"
     variation       477
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:375876165"
     STS             513..1054
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /standard_name="HOXD8_4104"
                     /db_xref="UniSTS:462900"
     variation       519
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:191736932"
     variation       521
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:75818878"
     variation       544
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:184720506"
     variation       582
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:145623178"
     variation       692
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:138242849"
     variation       749
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:189097507"
     variation       761
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:149532657"
     variation       817
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:181506551"
     variation       935
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace=""
                     /replace="a"
                     /db_xref="dbSNP:201637028"
     variation       973
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:144187682"
     STS             1019..1182
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /standard_name="SHGC-52388"
                     /db_xref="UniSTS:64729"
     polyA_signal    1238..1243
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
     polyA_site      1264
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
     variation       1372
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:111760092"
     variation       1460
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:112559843"
     variation       1539
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:148663631"
     polyA_signal    1587..1592
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
     variation       1599
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:190277759"
     polyA_site      1608
                     /gene="HOXD8"
                     /gene_synonym="HOX4; HOX4E; HOX5.4"
ORIGIN      

cgcgcggatccctccgcggggctcctcgtccccgtcacgctgactttccgtgcagtgctgtggtgcgaaaatgcctcgccgagacagccgatttttacgacccagcaagaggccgagctggtacaatatcctgactgtaaatcgtccagtggtaatattggcgaggacccagaccacttaaatcagagctcgtctccttctcaaatgtttccgtggatgagaccacaagcagctcctggtagacgaagaggaagacaaacctacagtcgcttccaaactctagagttggaaaaggaatttctttttaacccctatctgaccaggaaaagaagaatcgaggtttcccacgccctagccctcaccgagagacaggtaaaaatctggttccagaacaggagaatgaaatggaaaaaggaaaacaacaaggacaaatttcccgtttcccggcaggaggtgaaggacggggaaacgaaaaaggaagcccaagagctggaggaagacagagccgaaggcctgacaaattaacttctacctttaaaatttaccacagactattaaaactaataatcaccatatgctgtggacaccacctattttctttgttggaaaggaccttacctgtgtttcaagctaccttcatgtcactgctcttgaggttttctgtgctttgagagggatttgggtgtttaaaaaagtttctagtatcacatagaagctgtccttgagctgtcctatggaagggtaatttgatactgaccttgtagctatatttttataatggtttttaatgtctgagctagtgatttgcctcaacaacgtaaacttcctaatgattagcacttaataattgcatataaaatgctttattaattaaacaagtgcacttgaacattttaatatttgtggtgagtaaattaaaaggagtttattaattaaaaaaaattatgtctgcagaatactttatattatttgattacaatgtattatttatggattttttattctttcctttataatgaatagttcgggtgcgttttgtttactcctaaaaggtttctttgcgtattttctaaatgtaatatctcggggaaaatattagaaaagcacgtattagctgaagaatgtaacttgtagtccagctctgcagcttccttaaacttaagaaaaagattgggccagtgacaagaatttaaagacaatgtccaagttgacaattatttttctatagtccatacaaattaaataatctggcaactctggcaaatcgccttgtaaaatgcgtctcattttttaacttgctttcgttttgaaccgcccttgtaatcgcctgaaatcgctagttctttatgcggtggctgccgctgtgttccgttattttcagtaggtgtcatatttatttgtattgcctttgttctgttcgccgctggttttaaaccagcttgctgtgtgcatctcagacgtcggttggtacgtcctccgctgttcttcaggaaagcgatagcctcacctatttgaaacaagccctgagaggaaacgcagaaaaacctgagtgtaaacaactccggaatgtcgctagctccttagtaaataaatgaatctctttctggaaaaaaaaaaaaaaaaa

//

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:3234 -> Molecular function: GO:0003700 [sequence-specific DNA binding transcription factor activity] evidence: NAS
            GeneID:3234 -> Molecular function: GO:0043565 [sequence-specific DNA binding] evidence: IEA
            GeneID:3234 -> Biological process: GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] evidence: IEA
            GeneID:3234 -> Biological process: GO:0006351 [transcription, DNA-dependent] evidence: IEA
            GeneID:3234 -> Biological process: GO:0006355 [regulation of transcription, DNA-dependent] evidence: NAS
            GeneID:3234 -> Biological process: GO:0008595 [anterior/posterior axis specification, embryo] evidence: NAS
            GeneID:3234 -> Biological process: GO:0048705 [skeletal system morphogenesis] evidence: IEA
            GeneID:3234 -> Cellular component: GO:0005634 [nucleus] evidence: NAS