LOCUS       NM_014621               1136 bp    mRNA    linear   PRI 08-JUN-2024
DEFINITION  Homo sapiens homeobox D4 (HOXD4), mRNA.
ACCESSION   NM_014621
VERSION     NM_014621.3
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 1136)
  AUTHORS   Wang,L., Wang,X., Sun,H., Wang,W. and Cao,L.
  TITLE     A pan-cancer analysis of the role of HOXD1, HOXD3, and HOXD4 and
            validation in renal cell carcinoma
  JOURNAL   Aging (Albany NY) 15 (19), 10746-10766 (2023)
   PUBMED   37827698
  REMARK    GeneRIF: A pan-cancer analysis of the role of HOXD1, HOXD3, and
            HOXD4 and validation in renal cell carcinoma.
REFERENCE   2  (bases 1 to 1136)
  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 1136)
  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 1136)
  AUTHORS   Ogura,Y., Miyake,N., Kou,I., Iida,A., Nakajima,M., Takeda,K.,
            Fujibayashi,S., Shiina,M., Okada,E., Toyama,Y., Iwanami,A.,
            Ishii,K., Ogata,K., Asahara,H., Matsumoto,N., Nakamura,M.,
            Matsumoto,M. and Ikegawa,S.
  TITLE     Identification of HOXD4 Mutations in Spinal Extradural Arachnoid
            Cyst
  JOURNAL   PLoS One 10 (11), e0142126 (2015)
   PUBMED   26545093
  REMARK    GeneRIF: identified heterozygous HOXD4 loss-of-function mutations
            in three subjects with spinal extradural arachnoid cyst (SEDAC)
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1136)
  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   6  (bases 1 to 1136)
  AUTHORS   Scott,M.P.
  TITLE     Vertebrate homeobox gene nomenclature
  JOURNAL   Cell 71 (4), 551-553 (1992)
   PUBMED   1358459
REFERENCE   7  (bases 1 to 1136)
  AUTHORS   Zappavigna,V., Renucci,A., Izpisua-Belmonte,J.C., Urier,G.,
            Peschle,C. and Duboule,D.
  TITLE     HOX4 genes encode transcription factors with potential auto- and
            cross-regulatory capacities
  JOURNAL   EMBO J 10 (13), 4177-4187 (1991)
   PUBMED   1756725
REFERENCE   8  (bases 1 to 1136)
  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   9  (bases 1 to 1136)
  AUTHORS   McAlpine,P.J. and Shows,T.B.
  TITLE     Nomenclature for human homeobox genes
  JOURNAL   Genomics 7 (3), 460 (1990)
   PUBMED   1973146
REFERENCE   10 (bases 1 to 1136)
  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
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC009336.13.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 26, 2018 this sequence version replaced NM_014621.2.
            
            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 :: SRR1163658.310802.1, X04706.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000306324.4/ ENSP00000302548.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-517               AC009336.13        135539-136055
            518-1136            AC009336.13        136597-137215
FEATURES             Location/Qualifiers
     source          1..1136
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q31.1"
     gene            1..1136
                     /gene="HOXD4"
                     /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B"
                     /note="homeobox D4"
                     /db_xref="GeneID:3233"
                     /db_xref="HGNC:HGNC:5138"
                     /db_xref="MIM:142981"
     exon            1..517
                     /gene="HOXD4"
                     /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B"
                     /inference="alignment:Splign:2.1.0"
     CDS             85..852
                     /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="CCDS:CCDS2269.1"
                     /db_xref="GeneID:3233"
                     /db_xref="HGNC:HGNC:5138"
                     /db_xref="MIM:142981"
                     /translation="MVMSSYMVNSKYVDPKFPPCEEYLQGGYLGEQGADYYGGGAQGA
                     DFQPPGLYPRPDFGEQPFGGSGPGPGSALPARGHGQEPGGPGGHYAAPGEPCPAPPAP
                     PPAPLPGARAYSQSDPKQPPSGTALKQPAVVYPWMKKVHVNSVNPNYTGGEPKRSRTA
                     YTRQQVLELEKEFHFNRYLTRRRRIEIAHTLCLSERQIKIWFQNRRMKWKKDHKLPNT
                     KGRSSSSSSSSSCSSSVAPSQHLQPMAKDHHTDLTTL"
     exon            518..1136
                     /gene="HOXD4"
                     /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1118..1123
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HOXD4"
                     /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B"
                     /note="hexamer: ATTAAA"
     polyA_site      1136
                     /gene="HOXD4"
                     /gene_synonym="HHO.C13; Hox-4.2; HOX-5.1; HOX4; HOX4B"
                     /note="major polyA site"
ORIGIN      
        1 agttgacagc aagtaggagg gccctatgga aggagaaaaa aagacaacac gagaaaaatt
       61 agtattttct accttctgaa attaatggtc atgagttcgt atatggtgaa ctccaagtat
      121 gtggacccca agttccctcc gtgcgaggag tatttgcagg gcggctacct aggcgagcag
      181 ggcgccgact actacggcgg cggcgcgcag ggcgcagact tccagccccc ggggctctac
      241 ccacggcccg acttcggtga gcagcctttc ggaggcagcg gccccgggcc tggctcggcg
      301 ctgcctgcgc ggggtcacgg acaagagcca ggcggccccg gcggtcacta cgccgctcca
      361 ggagagcctt gcccagctcc cccggcgcct ccgccggcgc ccctgcctgg cgcccgggcc
      421 tacagtcagt ccgaccccaa gcagccgccc tccgggacgg cactcaagca gccggccgtg
      481 gtctacccct ggatgaagaa ggtgcacgtg aattcggtga accccaacta caccggtggg
      541 gaacccaagc ggtcccgaac ggcctacacc cggcagcaag tcctagaact ggaaaaagaa
      601 tttcatttta acaggtatct gacaaggcgc cgtcggattg aaatcgctca caccctgtgt
      661 ctgtcggagc gccagatcaa gatctggttc cagaaccgga ggatgaagtg gaaaaaagat
      721 cataagctgc ccaacactaa aggcaggtca tcgtcctcat cttcctcctc atcttgctcc
      781 tcctcagtcg cccccagcca gcatttacag ccgatggcca aagaccacca cacggacctg
      841 acgaccttat agaagtgggg accctgggcc catctctccc tgcgcaccag gctgagccga
      901 agctgcgggg gcaggccggg cctgctgtca cctcgctggg ctctaaggta ctgtggggtg
      961 gacctgggac aagcaggccg ccctcggact aggttagcat cctgcccgag ggcagccccc
     1021 tccctagagc gggatgggga tgggaggggg ggcgggattc tctctctaag tatattatat
     1081 ggcaggagct actgagaaca taaaatcttg gcgagtcatt aaacttatga aaatca
//
