LOCUS       NM_018953               1611 bp    mRNA    linear   PRI 01-JUL-2024
DEFINITION  Homo sapiens homeobox C5 (HOXC5), transcript variant 1, mRNA.
ACCESSION   NM_018953
VERSION     NM_018953.4
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 1611)
  AUTHORS   Gao,J., Xu,Z., Song,W., Huang,J., Liu,W., He,Z. and He,L.
  TITLE     USP11 regulates proliferation and apoptosis of human spermatogonial
            stem cells via HOXC5-mediated canonical WNT/beta-catenin signaling
            pathway
  JOURNAL   Cell Mol Life Sci 81 (1), 211 (2024)
   PUBMED   38722330
  REMARK    GeneRIF: USP11 regulates proliferation and apoptosis of human
            spermatogonial stem cells via HOXC5-mediated canonical
            WNT/beta-catenin signaling pathway.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1611)
  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 1611)
  AUTHORS   Yan,T., Ooi,W.F., Qamra,A., Cheung,A., Ma,D., Sundaram,G.M., Xu,C.,
            Xing,M., Poon,L., Wang,J., Loh,Y.P., Ho,J.H.J., Ng,J.J.Q.,
            Ramlee,M.K., Aswad,L., Rozen,S.G., Ghosh,S., Bard,F.A., Sampath,P.,
            Tergaonkar,V., Davies,J.O.J., Hughes,J.R., Goh,E., Bi,X.,
            Fullwood,M.J., Tan,P. and Li,S.
  TITLE     HoxC5 and miR-615-3p target newly evolved genomic regions to
            repress hTERT and inhibit tumorigenesis
  JOURNAL   Nat Commun 9 (1), 100 (2018)
   PUBMED   29311615
  REMARK    GeneRIF: Both mir-615-3p and HOXC5 are activated upon
            differentiation, which constitute a feed-forward loop that
            coordinates transcriptional and post-transcriptional repression of
            hTERT during cellular differentiation. Deregulation of HOXC5 and
            mir-615-3p expression may contribute to the activation of hTERT in
            human cancers.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1611)
  AUTHORS   Vaquerizas,J.M., Kummerfeld,S.K., Teichmann,S.A. and Luscombe,N.M.
  TITLE     A census of human transcription factors: function, expression and
            evolution
  JOURNAL   Nat Rev Genet 10 (4), 252-263 (2009)
   PUBMED   19274049
  REMARK    Review article
REFERENCE   5  (bases 1 to 1611)
  AUTHORS   Oh,J.H., Yang,J.O., Hahn,Y., Kim,M.R., Byun,S.S., Jeon,Y.J.,
            Kim,J.M., Song,K.S., Noh,S.M., Kim,S., Yoo,H.S., Kim,Y.S. and
            Kim,N.S.
  TITLE     Transcriptome analysis of human gastric cancer
  JOURNAL   Mamm Genome 16 (12), 942-954 (2005)
   PUBMED   16341674
REFERENCE   6  (bases 1 to 1611)
  AUTHORS   Arcioni,L., Simeone,A., Guazzi,S., Zappavigna,V., Boncinelli,E. and
            Mavilio,F.
  TITLE     The upstream region of the human homeobox gene HOX3D is a target
            for regulation by retinoic acid and HOX homeoproteins
  JOURNAL   EMBO J 11 (1), 265-277 (1992)
   PUBMED   1346761
REFERENCE   7  (bases 1 to 1611)
  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
REFERENCE   8  (bases 1 to 1611)
  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   9  (bases 1 to 1611)
  AUTHORS   Simeone,A., Pannese,M., Acampora,D., D'Esposito,M. and
            Boncinelli,E.
  TITLE     At least three human homeoboxes on chromosome 12 belong to the same
            transcription unit
  JOURNAL   Nucleic Acids Res 16 (12), 5379-5390 (1988)
   PUBMED   2898768
REFERENCE   10 (bases 1 to 1611)
  AUTHORS   Rabin,M., Ferguson-Smith,A., Hart,C.P. and Ruddle,F.H.
  TITLE     Cognate homeo-box loci mapped on homologous human and mouse
            chromosomes
  JOURNAL   Proc Natl Acad Sci U S A 83 (23), 9104-9108 (1986)
   PUBMED   2878432
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC012531.11 and AC023794.37.
            
            On Jul 21, 2020 this sequence version replaced NM_018953.3.
            
            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, which are located on different
            chromosomes and consist of 9 to 11 genes arranged in tandem. This
            gene, HOXC5, is one of several homeobox HOXC genes located in a
            cluster on chromosome 12. Three genes, HOXC5, HOXC4 and HOXC6,
            share a 5' non-coding exon. Transcripts may include the shared exon
            spliced to the gene-specific exons, or they may include only the
            gene-specific exons. Two alternatively spliced variants have been
            described for HOXC5. The transcript variant which includes the
            shared exon apparently doesn't encode a protein. The protein-coding
            transcript variant contains gene-specific exons only. [provided by
            RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) represents the shorter
            transcript and is protein coding.
            
            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 :: CN309384.1, CN309383.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1968968
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000312492.3/ ENSP00000309336.2
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-527               AC012531.11        170654-171180
            528-595             AC012531.11        171882-171949
            596-1611            AC023794.37        2006-3021
FEATURES             Location/Qualifiers
     source          1..1611
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12q13.13"
     gene            1..1611
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /note="homeobox C5"
                     /db_xref="GeneID:3222"
                     /db_xref="HGNC:HGNC:5127"
                     /db_xref="MIM:142973"
     exon            1..527
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /inference="alignment:Splign:2.1.0"
     CDS             74..742
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /note="homeo box C5; homeobox protein CP11; homeobox
                     protein Hox-3D"
                     /codon_start=1
                     /product="homeobox protein Hox-C5"
                     /protein_id="NP_061826.1"
                     /db_xref="CCDS:CCDS8872.1"
                     /db_xref="GeneID:3222"
                     /db_xref="HGNC:HGNC:5127"
                     /db_xref="MIM:142973"
                     /translation="MSSYVANSFYKQSPNIPAYNMQTCGNYGSASEVQASRYCYGGLD
                     LSITFPPPAPSNSLHGVDMAANPRAHPDRPACSAAAAPGHAPGRDEAAPLNPGMYSQK
                     AARPALEERAKSSGEIKEEQAQTGQPAGLSQPPAPPQIYPWMTKLHMSHETDGKRSRT
                     SYTRYQTLELEKEFHFNRYLTRRRRIEIANNLCLNERQIKIWFQNRRMKWKKDSKMKS
                     KEAL"
     exon            528..1611
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1589..1594
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /note="hexamer: AATAAA"
     polyA_site      1611
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /note="major polyA site"
ORIGIN      
        1 ccctcaactt caaagagtca caaatcaccc ttaatcaaaa agggtgcaga aatttttttg
       61 ggccctcccc gccatgagct cctacgtagc caattcattc tataagcaga gccccaatat
      121 ccctgcctat aacatgcaaa cttgtgggaa ctatggatcg gcctcagagg tgcaggcatc
      181 caggtactgc tacggcggat tggacttaag catcactttc ccaccgcctg cgccttccaa
      241 ctctctccac ggggtagaca tggctgccaa cccccgggct caccccgacc gccccgcctg
      301 cagcgccgcg gccgctccgg gacacgctcc gggcagagac gaagcggctc ctctgaaccc
      361 cgggatgtac agtcagaagg cggctcgccc ggcgctggag gagcgagcta agagcagtgg
      421 ggagatcaaa gaggagcagg cgcagacagg gcagcccgcc ggactgagcc agccaccggc
      481 cccgccacag atttacccgt ggatgaccaa actgcacatg agccacgaga cggacggcaa
      541 gcggtcccga accagttaca cgcgctacca gactctggaa ctcgagaaag aattccactt
      601 taaccgctac ctcactcgcc gcaggcgcat agagatcgcc aacaacttgt gtctcaatga
      661 gagacagatc aagatctggt tccagaaccg caggatgaag tggaagaaag attccaaaat
      721 gaaaagcaaa gaggctcttt agaggcagcg ggggaggccc gcagagcgcg cccctagccg
      781 gttcctgtcc ctgcgccttt ccttttcgcc tttcctctct atatttcggg tcgggggcag
      841 gtgctggagc actgggctcc cgggccccac agacaaaagc gcttttcctt ggcattccgc
      901 atccctaccg acccagggtt cccgcggggc tgtcggcgct gccccatctc ccctcagctc
      961 ggctcagctc ggtacccggg gcccagggca agctccgcag gacttccccg gagggctgcg
     1021 gcgtacaggc tggcgcagaa cgaaccttgg cctgggccgt atctccggct cccagcctca
     1081 gcgcggccct cccgagttaa ggtgggcccg gcccgcgcca caggaccctc gccggaccct
     1141 ctaacctcgc cctctccttt gttcccggct ggacgggtta gacagccaaa ggctggcgag
     1201 agtctggccc tagactcggg gtgcttcctt gtagcgacta aactagattt tcacttatga
     1261 atgatttgca tatgaaagga gagcatcggc ctagggcccc cacagttgct ctatgctttc
     1321 caaaccttat ctccacaacc tcttcccccc aaaacccggg aacctcccca gcctgcgcct
     1381 gctgcatgcc ctctcaggcc ggcagcccca gcctgctagc tagctcaact agtggggttt
     1441 cctggcactg gaccccagca agtggtccta gaggcccttt gctgtcccat agtccctgcc
     1501 acgaatttct gtgccctcct gacccattgc tgttgtccaa ctatttattg actctgggtc
     1561 cttcctgaaa ctatattttg tcatatcaaa taaagagaga acaggactaa a
//
