LOCUS       NM_000523               2416 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens homeobox D13 (HOXD13), mRNA.
ACCESSION   NM_000523
VERSION     NM_000523.4
KEYWORDS    RefSeq; MANE Select.
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 2416)
  AUTHORS   Abdullah, Hussain,S., Ji,W., Khan,H., Mis,E.K., Mushtaq,R.,
            Chodhary,M., Raza,M.H., Jan,A., Ullah,I., Khokha,M.K., Lakhani,S.A.
            and Ahmad,W.
  TITLE     Sequence variants in DLX5, HOXD13 and 445 kb-microduplication
            surrounding BTRC cause split-hand/foot malformation in three
            different families
  JOURNAL   Clin Genet 105 (1), 109-111 (2024)
   PUBMED   37776184
  REMARK    GeneRIF: Sequence variants in DLX5, HOXD13 and 445
            kb-microduplication surrounding BTRC cause split-hand/foot
            malformation in three different families.
REFERENCE   2  (bases 1 to 2416)
  AUTHORS   Gottschalk,A., Sczakiel,H.L., Hulsemann,W., Schwartzmann,S.,
            Abad-Perez,A.T., Grunhagen,J., Ott,C.E., Spielmann,M., Horn,D.,
            Mundlos,S., Jamsheer,A. and Mensah,M.A.
  TITLE     HOXD13-associated synpolydactyly: Extending and validating the
            genotypic and phenotypic spectrum with 38 new and 49 published
            families
  JOURNAL   Genet Med 25 (11), 100928 (2023)
   PUBMED   37427568
  REMARK    GeneRIF: HOXD13-associated synpolydactyly: Extending and validating
            the genotypic and phenotypic spectrum with 38 new and 49 published
            families.
            Review article
REFERENCE   3  (bases 1 to 2416)
  AUTHORS   Juarez-Rendon,K.J., Castro-Garcia,M.A., Prada-Ortega,D.G.,
            Rivera,G., Ruiz-Godoy,L.M., Enriquez-Carcamo,V.I. and
            Reyes-Lopez,M.A.
  TITLE     Variants Identified in the HOXC13 and HOXD13 Genes Suggest
            Association with Cervical Cancer in a Cohort of Mexican Women
  JOURNAL   Genes (Basel) 14 (2), 358 (2023)
   PUBMED   36833285
  REMARK    GeneRIF: Variants Identified in the HOXC13 and HOXD13 Genes Suggest
            Association with Cervical Cancer in a Cohort of Mexican Women.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2416)
  AUTHORS   Apfelbaum,A.A., Wu,F., Hawkins,A.G., Magnuson,B., Jimenez,J.A.,
            Taylor,S.D., Wrenn,E.D., Waltner,O., Pfaltzgraff,E.R., Song,J.Y.,
            Hall,C., Wellik,D.M., Ljungman,M., Furlan,S.N., Ryan,R.J.H.,
            Sarthy,J.F. and Lawlor,E.R.
  TITLE     EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in Ewing Sarcoma
  JOURNAL   Clin Cancer Res 28 (20), 4466-4478 (2022)
   PUBMED   35653119
  REMARK    GeneRIF: EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in
            Ewing Sarcoma.
REFERENCE   5  (bases 1 to 2416)
  AUTHORS   Husile,H., Wu,Z., Yang,L., Cao,Y. and Wu,Q.
  TITLE     Identification of a HOXD13 variant in a Mongolian family with
            incomplete penetrance syndactyly by exon sequencing
  JOURNAL   BMC Med Genomics 15 (1), 210 (2022)
   PUBMED   36195906
  REMARK    GeneRIF: Identification of a HOXD13 variant in a Mongolian family
            with incomplete penetrance syndactyly by exon sequencing.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2416)
  AUTHORS   Goodman,F., Giovannucci-Uzielli,M.L., Hall,C., Reardon,W.,
            Winter,R. and Scambler,P.
  TITLE     Deletions in HOXD13 segregate with an identical, novel foot
            malformation in two unrelated families
  JOURNAL   Am J Hum Genet 63 (4), 992-1000 (1998)
   PUBMED   9758628
REFERENCE   7  (bases 1 to 2416)
  AUTHORS   Johnson,R.L. and Tabin,C.J.
  TITLE     Molecular models for vertebrate limb development
  JOURNAL   Cell 90 (6), 979-990 (1997)
   PUBMED   9323126
  REMARK    Review article
REFERENCE   8  (bases 1 to 2416)
  AUTHORS   Akarsu,A.N., Stoilov,I., Yilmaz,E., Sayli,B.S. and Sarfarazi,M.
  TITLE     Genomic structure of HOXD13 gene: a nine polyalanine duplication
            causes synpolydactyly in two unrelated families
  JOURNAL   Hum Mol Genet 5 (7), 945-952 (1996)
   PUBMED   8817328
  REMARK    GeneRIF: Gene Structure and Report of Nine Polyalanine Duplications
            in Families with Synpolydactyly, Type II
REFERENCE   9  (bases 1 to 2416)
  AUTHORS   D'Esposito,M., Morelli,F., Acampora,D., Migliaccio,E., Simeone,A.
            and Boncinelli,E.
  TITLE     EVX2, a human homeobox gene homologous to the even-skipped
            segmentation gene, is localized at the 5' end of HOX4 locus on
            chromosome 2
  JOURNAL   Genomics 10 (1), 43-50 (1991)
   PUBMED   1675198
REFERENCE   10 (bases 1 to 2416)
  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
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC009336.13 and BX100910.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_000523.3.
            
            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. Mutations in this particular gene cause
            synpolydactyly. [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 :: AI971733.1, AI858239.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968540, SAMEA2142348
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000392539.4/ ENSP00000376322.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-83                AC009336.13        76710-76792
            84-951              AC009336.13        76793-77660
            952-2287            AC009336.13        78469-79804
            2288-2410           BX100910.1         15-137              c
            2411-2416           AC009336.13        79928-79933
FEATURES             Location/Qualifiers
     source          1..2416
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q31.1"
     gene            1..2416
                     /gene="HOXD13"
                     /gene_synonym="BDE; BDSD; HOX4I; SPD; SPD1"
                     /note="homeobox D13"
                     /db_xref="GeneID:3239"
                     /db_xref="HGNC:HGNC:5136"
                     /db_xref="MIM:142989"
     exon            1..951
                     /gene="HOXD13"
                     /gene_synonym="BDE; BDSD; HOX4I; SPD; SPD1"
                     /inference="alignment:Splign:2.1.0"
     CDS             171..1202
                     /gene="HOXD13"
                     /gene_synonym="BDE; BDSD; HOX4I; SPD; SPD1"
                     /note="homeo box D13; homeo box 4I; homeobox protein
                     Hox-4I; synpolydactyly"
                     /codon_start=1
                     /product="homeobox protein Hox-D13"
                     /protein_id="NP_000514.2"
                     /db_xref="CCDS:CCDS2264.2"
                     /db_xref="GeneID:3239"
                     /db_xref="HGNC:HGNC:5136"
                     /db_xref="MIM:142989"
                     /translation="MSRAGSWDMDGLRADGGGAGGAPASSSSSSVAAAAASGQCRGFL
                     SAPVFAGTHSGRAAAAAAAAAAAAAAASGFAYPGTSERTGSSSSSSSSAVVAARPEAP
                     PAKECPAPTPAAAAAAPPSAPALGYGYHFGNGYYSCRMSHGVGLQQNALKSSPHASLG
                     GFPVEKYMDVSGLASSSVPANEVPARAKEVSFYQGYTSPYQHVPGYIDMVSTFGSGEP
                     RHEAYISMEGYQSWTLANGWNSQVYCTKDQPQGSHFWKSSFPGDVALNQPDMCVYRRG
                     RKKRVPYTKLQLKELENEYAINKFINKDKRRRISAATNLSERQVTIWFQNRRVKDKKI
                     VSKLKDTVS"
     exon            952..2416
                     /gene="HOXD13"
                     /gene_synonym="BDE; BDSD; HOX4I; SPD; SPD1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2388..2393
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HOXD13"
                     /gene_synonym="BDE; BDSD; HOX4I; SPD; SPD1"
                     /note="hexamer: AATAAA"
     polyA_site      2416
                     /gene="HOXD13"
                     /gene_synonym="BDE; BDSD; HOX4I; SPD; SPD1"
                     /note="major polyA site"
ORIGIN      
        1 gttggagggc aggcgggccg gaggcgggag gctcacagag ggagagaggg ctagaggaag
       61 agggcgggag cgagcgaacc agagagaaag gagaggaggg aggaggcgcg ccgcgccatg
      121 gtgtcctgcg cggggccagg gccagggccg gggccgggcc aggccgggcc atgagccgcg
      181 ccgggagctg ggacatggac gggctgcggg cagacggcgg gggcgccggt ggcgccccgg
      241 cctcttcctc ctcctcatcg gtggcggcgg cggcggcgtc aggccagtgc cgcggctttc
      301 tctccgcgcc tgtgttcgcc gggacgcatt cggggcgggc ggcggcggcg gcagcggcgg
      361 ctgcggcggc ggcggcggca gcctccggct ttgcgtaccc cgggacctct gagcgcacgg
      421 gctcttcctc gtcgtcgtcc tcttctgccg ttgtagcggc gcgcccggag gctcccccag
      481 ccaaagagtg cccagcaccc acgcctgcag cggccgctgc agcgcccccg agcgctccag
      541 cgctgggcta cggctaccac ttcggcaacg gctactacag ctgccgtatg tcgcacggcg
      601 tgggcttaca gcagaatgcg ctcaagtcat cgccgcacgc ctcgctggga ggctttcccg
      661 tggagaagta catggacgtg tcaggcctgg cgagcagcag cgtaccggcc aacgaggtgc
      721 cagcgcgagc caaggaggta tccttctacc agggctatac gagcccttac cagcacgtgc
      781 ccggctatat cgacatggtg tccactttcg gctccgggga gcctcggcac gaggcctaca
      841 tctccatgga ggggtaccag tcctggacgc tggctaacgg gtggaacagc caggtgtact
      901 gcaccaagga ccagccacag gggtcccact tttggaaatc ttcctttcca ggggatgtgg
      961 ctctaaatca gccggacatg tgcgtctacc gaagagggag gaagaagaga gtgccttaca
     1021 ccaaactgca gcttaaagaa ctggagaacg agtatgccat taacaaattc attaacaagg
     1081 acaagcggcg gcgtatctcg gctgctacga acctatctga gagacaagtg accatttggt
     1141 ttcagaaccg aagagtgaag gacaagaaaa ttgtctccaa gctcaaagat actgtctcct
     1201 gatgtggtcc aggttggcca cagacagctt agaagccatt cggttgtctc caaaaggcct
     1261 ttggaaagac ttgaatatgt atttaattcc ccccaccccc tgccaatggt ggcaaatttt
     1321 gtgaattgtt tttctctctt ccccttatct ggctctaaaa ccttctgctg cccaacctga
     1381 ctttgtagtt ctgattttta cttgtttatt attggttttg ttcttgccta gggtttttaa
     1441 aatatctgtt tttaatgttt tgtttctccc tccaggccag tataaaggga cttgaagtat
     1501 tttttaataa tccgcccccc aatgaacttc agaagtgcca ttctgattta agggtttttt
     1561 taaaaaatta ctttatttgt tcattcccag cactgattat cttcataatc cattaggaca
     1621 gaatggtttt cagtcgttca tatcctgtaa ttaggtaatt gaatcattag ctctcagcag
     1681 ttgccctgag gcaagtggaa aggcaggcag tgctctgggg tcaccgagaa agtctaaaaa
     1741 caggaggctg aaggtactgt gatggcttta aaaatggcca ccttattaaa tagggattgt
     1801 atcaatattg aaatgaagac aatctttcca actttgggtg tttcacttgc tgttttaatt
     1861 gtttgttttt aacactttgt aggtttgtgt tttcataatc tttaatttga aactcatgtg
     1921 tcctcatgga tcgtggatgc cttcatttct tgagctctca atgcagacat ttaaatggct
     1981 gcaatcagta gagtgacccg cggatggcat aaatgcacct ccttttcttg gccttggatc
     2041 tatgggtctg ggattgtggt catctcctca atcctcaaaa agaggctgaa tcaatgtggc
     2101 cgtgggtggg aacttacata cagaacccaa tgaagaactt gactgtctaa acaagggggc
     2161 ctcgcatgga gctgtaaagc atctaacaaa tatgaaaaat gtgaagttcc aaggtccaag
     2221 aagaaaaata atgatgtttc tgaaagtgat gataaataat tacttttaaa gtgctgcata
     2281 tttatacaat tgagagatta tttttgtaaa tgcaatgtct gtgagctggg atacatgggc
     2341 agtgcttcag acatttaaaa atcacttttt actcctaggg agatgccaat aaacagaact
     2401 cttttgtttc ttctga
//
