LOCUS       NM_021193               2549 bp    mRNA    linear   PRI 24-SEP-2024
DEFINITION  Homo sapiens homeobox D12 (HOXD12), mRNA.
ACCESSION   NM_021193
VERSION     NM_021193.4
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 2549)
  AUTHORS   Nuechterlein,N., Cimino,S., Shelbourn,A., Ha,V., Arora,S.,
            Rajan,S., Shapiro,L.G., Holland,E.C., Aldape,K., McGranahan,T.,
            Gilbert,M.R. and Cimino,P.J.
  TITLE     HOXD12 defines an age-related aggressive subtype of
            oligodendroglioma
  JOURNAL   Acta Neuropathol 148 (1), 41 (2024)
   PUBMED   39259414
  REMARK    GeneRIF: HOXD12 defines an age-related aggressive subtype of
            oligodendroglioma.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2549)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   3  (bases 1 to 2549)
  AUTHORS   Yin,Y., Morgunova,E., Jolma,A., Kaasinen,E., Sahu,B.,
            Khund-Sayeed,S., Das,P.K., Kivioja,T., Dave,K., Zhong,F.,
            Nitta,K.R., Taipale,M., Popov,A., Ginno,P.A., Domcke,S., Yan,J.,
            Schubeler,D., Vinson,C. and Taipale,J.
  TITLE     Impact of cytosine methylation on DNA binding specificities of
            human transcription factors
  JOURNAL   Science 356 (6337) (2017)
   PUBMED   28473536
REFERENCE   4  (bases 1 to 2549)
  AUTHORS   Woo,C.J., Kharchenko,P.V., Daheron,L., Park,P.J. and Kingston,R.E.
  TITLE     A region of the human HOXD cluster that confers polycomb-group
            responsiveness
  JOURNAL   Cell 140 (1), 99-110 (2010)
   PUBMED   20085705
  REMARK    GeneRIF: In human embryonic stem cell (hESCs)differentiation, a
            1.8kb region between HOXD11 and HOXD12 (D11.12) that is associated
            with PcG proteins was discovered, it shows alteration in nuclease
            sensitivity as hESCs differentiate.
REFERENCE   5  (bases 1 to 2549)
  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   6  (bases 1 to 2549)
  AUTHORS   Del Campo,M., Jones,M.C., Veraksa,A.N., Curry,C.J., Jones,K.L.,
            Mascarello,J.T., Ali-Kahn-Catts,Z., Drumheller,T. and McGinnis,W.
  TITLE     Monodactylous limbs and abnormal genitalia are associated with
            hemizygosity for the human 2q31 region that includes the HOXD
            cluster
  JOURNAL   Am J Hum Genet 65 (1), 104-110 (1999)
   PUBMED   10364522
REFERENCE   7  (bases 1 to 2549)
  AUTHORS   Shen,W.F., Montgomery,J.C., Rozenfeld,S., Moskow,J.J.,
            Lawrence,H.J., Buchberg,A.M. and Largman,C.
  TITLE     AbdB-like Hox proteins stabilize DNA binding by the Meis1
            homeodomain proteins
  JOURNAL   Mol Cell Biol 17 (11), 6448-6458 (1997)
   PUBMED   9343407
REFERENCE   8  (bases 1 to 2549)
  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   9  (bases 1 to 2549)
  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 2549)
  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.
            
            On Jul 17, 2019 this sequence version replaced NM_021193.3.
            
            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. The exact role of this gene has not been
            determined. [provided by RefSeq, Jul 2008].
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on 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 :: SRR14038193.2489218.1,
                                           SRR14038193.974087.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2142348, SAMEA2156266
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000406506.4/ ENSP00000385586.2
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-581               AC009336.13        83784-84364
            582-2549            AC009336.13        84511-86478
FEATURES             Location/Qualifiers
     source          1..2549
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q31.1"
     gene            1..2549
                     /gene="HOXD12"
                     /gene_synonym="HOX4H"
                     /note="homeobox D12"
                     /db_xref="GeneID:3238"
                     /db_xref="HGNC:HGNC:5135"
                     /db_xref="MIM:142988"
     exon            1..581
                     /gene="HOXD12"
                     /gene_synonym="HOX4H"
                     /inference="alignment:Splign:2.1.0"
     CDS             8..820
                     /gene="HOXD12"
                     /gene_synonym="HOX4H"
                     /note="homeo box D12; Hox-4.7, mouse, homolog of; homeobox
                     protein Hox-4H"
                     /codon_start=1
                     /product="homeobox protein Hox-D12"
                     /protein_id="NP_067016.3"
                     /db_xref="CCDS:CCDS46456.1"
                     /db_xref="GeneID:3238"
                     /db_xref="HGNC:HGNC:5135"
                     /db_xref="MIM:142988"
                     /translation="MCERSLYRAGYVGSLLNLQSPDSFYFSNLRPNGGQLAALPPISY
                     PRGALPWAATPASCAPAQPAGATAFGGFSQPYLAGSGPLGLQPPTAKDGPEEQAKFYA
                     PEAAAGPEERGRTRPSFAPESSLAPAVAALKAAKYDYAGVGRATPGSTTLLQGAPCAP
                     GFKDDTKGPLNLNMTVQAAGVASCLRPSLPDGLPWGAAPGRARKKRKPYTKQQIAELE
                     NEFLVNEFINRQKRKELSNRLNLSDQQVKIWFQNRRMKKKRVVLREQALALY"
     exon            582..2549
                     /gene="HOXD12"
                     /gene_synonym="HOX4H"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2526..2531
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HOXD12"
                     /gene_synonym="HOX4H"
                     /note="hexamer: AATAAA"
     polyA_site      2549
                     /gene="HOXD12"
                     /gene_synonym="HOX4H"
                     /note="major polyA site"
ORIGIN      
        1 gttggagatg tgtgagcgca gtctctacag agcgggctat gtgggctcgc ttctgaatct
       61 gcagtcgcca gactctttct acttctccaa cctgaggccg aatggcggcc agttggccgc
      121 gcttccccct atctcctacc cgcgcggcgc gctgccctgg gccgccacgc ccgcctcctg
      181 cgcccccgcg cagcctgcgg gcgccactgc cttcggcggc ttctcgcagc cctacctggc
      241 tggctccggg cctctcggcc tgcagccccc aacagccaaa gacggacccg aagagcaggc
      301 taagttctat gcgcccgaag cggccgctgg gccagaggag cgcggtcgta cccggccgtc
      361 cttcgccccc gagtctagcc tggctcctgc agtggctgct ctcaaagcgg ccaagtatga
      421 ctacgctggt gtgggtcgtg ccacgccggg ctccacgacc ctgctccagg gggctccctg
      481 cgcccctggc ttcaaggacg acaccaaggg cccgctcaac ttgaacatga cagtgcaggc
      541 ggcgggcgtt gcctcttgcc tgcgaccttc actgcccgac ggcctgccgt ggggggcggc
      601 cccggggagg gcccgcaaga agcggaaacc ctacacgaag cagcagattg cggagttgga
      661 gaacgaattc ctcgtcaacg aattcatcaa caggcagaaa cgcaaggaat tgtccaatag
      721 gctgaacctc agcgaccagc aagtcaaaat ctggttccag aacaggcgta tgaagaagaa
      781 gcgcgtggtg cttcgggagc aggcgctggc gctctactag ccgcgcgcgt ggccagggcc
      841 gggttggatc tgcccttttg gacagaggcc ttgtttgggg agggggatct ggggctaagg
      901 ctaaggcttt tccttcggtt ccttctctgc tggccccaga agccaccaag agatttacag
      961 accaggccag ttgggcctcc ttgctttcct cagtccctga gaagcccgtg agaaacgtgc
     1021 ggaagtacca gtgcaactct ggctggcctt aaggcttcca cgttggggga ctgaggccaa
     1081 ctctccttgc tcctggctgg ggcatttgca cccaccgctc attcttgctc cccggtacct
     1141 ggatttttct gtttccaccc aattcgttct ccctttcccc ctctctccag ccccttcagc
     1201 gtatagcagt cgcctagtta gggctcagag tggaaggcct cctgagggaa tggaaaggac
     1261 tgtgggtaca attaggtctc tgcagcagaa gccctttgtg gcaaggccag gatcttcact
     1321 ctggagaaag gaaagggcac catccaccct ccaccctcct gtctgccctg gctgatttga
     1381 gagaacaaaa gccacactag atcttcagac tttgggagga aaagggaggg aaggggaggg
     1441 gctgggtagt ggggtaaact tggagatatc tcgaaatgag aaatgcgaaa taggctggcc
     1501 tatttccagc tgggtagaat atgtggaacc ttcatttcct gagatgggat gagagagact
     1561 gggactccag acaagtgcca tctccagaca agactggcaa acattgccct actcccacct
     1621 tctcaaacat gcctaggcca ggcctatgaa ccctgtaact ggatccccag aggctagctc
     1681 tggtgaaagg agctgttggt ctgctttgaa gctctgttgc acagggagag ggaaaaatat
     1741 ccaggggagg agaagggagt gaataagagg aggaggggtg ctgcactcca actgtaaata
     1801 tggctttcca gttgaggtga gtaaaggtgt tggtgcatct ttctttcttc aattacctta
     1861 atggaacccc ataaggatag gcaaaaatcc ttctcaagag tcaaggggag gggaaggaag
     1921 tctcttagat tctctgcccc gctagctgct cttgacaaag caaagaggac cagaagttcc
     1981 tctcaccgtc tctaccatct gccaactcta ccagaggccc agctactgtg ccccttctga
     2041 ggcatgtctg gcctgtccca gtggagactt taaggccctg ggccctgcca ggcttgcctc
     2101 atggaggcag gggttcccaa atgccaggtg gagttgttct gggtgtactg gagtgtcccg
     2161 ccttaatctc agtgaaccaa gcctccccct gcgagctcat tccactatcc ctgcctcttc
     2221 tcccctctcc ttctgacatg tagcactcct ccttcgcaat tcctagcatg atgcacaaca
     2281 actcaaggat tcaggattcc ttcccaaagt ccagtgattt cttttcagtg caggacctgg
     2341 ccctaaatct ggagtgggcc cctcacagag agccctgagc cttagcccaa ctgacttcag
     2401 ttgatattta aactaatttc attttctagg ctatctaata gttatcatgc atgttttgtt
     2461 ttgattttgt caaaaacagt agcttgtata tatcagacac aatatataca aatgttttga
     2521 gtgaaaataa atatccaggt ctgagccaa
//
