GGRNA | NR_003084.1

LOCUS       NR_003084               1641 bp    RNA     linear   PRI 16-JUL-2013
DEFINITION  Homo sapiens homeobox C5 (HOXC5), transcript variant 2, non-coding
            RNA.
ACCESSION   NR_003084
VERSION     NR_003084.1  GI:100413100
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 1641)
  AUTHORS   Estrada,K., Styrkarsdottir,U., Evangelou,E., Hsu,Y.H., Duncan,E.L.,
            Ntzani,E.E., Oei,L., Albagha,O.M., Amin,N., Kemp,J.P., Koller,D.L.,
            Li,G., Liu,C.T., Minster,R.L., Moayyeri,A., Vandenput,L.,
            Willner,D., Xiao,S.M., Yerges-Armstrong,L.M., Zheng,H.F.,
            Alonso,N., Eriksson,J., Kammerer,C.M., Kaptoge,S.K., Leo,P.J.,
            Thorleifsson,G., Wilson,S.G., Wilson,J.F., Aalto,V., Alen,M.,
            Aragaki,A.K., Aspelund,T., Center,J.R., Dailiana,Z., Duggan,D.J.,
            Garcia,M., Garcia-Giralt,N., Giroux,S., Hallmans,G., Hocking,L.J.,
            Husted,L.B., Jameson,K.A., Khusainova,R., Kim,G.S., Kooperberg,C.,
            Koromila,T., Kruk,M., Laaksonen,M., Lacroix,A.Z., Lee,S.H.,
            Leung,P.C., Lewis,J.R., Masi,L., Mencej-Bedrac,S., Nguyen,T.V.,
            Nogues,X., Patel,M.S., Prezelj,J., Rose,L.M., Scollen,S.,
            Siggeirsdottir,K., Smith,A.V., Svensson,O., Trompet,S., Trummer,O.,
            van Schoor,N.M., Woo,J., Zhu,K., Balcells,S., Brandi,M.L.,
            Buckley,B.M., Cheng,S., Christiansen,C., Cooper,C., Dedoussis,G.,
            Ford,I., Frost,M., Goltzman,D., Gonzalez-Macias,J., Kahonen,M.,
            Karlsson,M., Khusnutdinova,E., Koh,J.M., Kollia,P., Langdahl,B.L.,
            Leslie,W.D., Lips,P., Ljunggren,O., Lorenc,R.S., Marc,J.,
            Mellstrom,D., Obermayer-Pietsch,B., Olmos,J.M.,
            Pettersson-Kymmer,U., Reid,D.M., Riancho,J.A., Ridker,P.M.,
            Rousseau,F., Slagboom,P.E., Tang,N.L., Urreizti,R., Van Hul,W.,
            Viikari,J., Zarrabeitia,M.T., Aulchenko,Y.S.,
            Castano-Betancourt,M., Grundberg,E., Herrera,L., Ingvarsson,T.,
            Johannsdottir,H., Kwan,T., Li,R., Luben,R., Medina-Gomez,C.,
            Palsson,S.T., Reppe,S., Rotter,J.I., Sigurdsson,G., van Meurs,J.B.,
            Verlaan,D., Williams,F.M., Wood,A.R., Zhou,Y., Gautvik,K.M.,
            Pastinen,T., Raychaudhuri,S., Cauley,J.A., Chasman,D.I.,
            Clark,G.R., Cummings,S.R., Danoy,P., Dennison,E.M., Eastell,R.,
            Eisman,J.A., Gudnason,V., Hofman,A., Jackson,R.D., Jones,G.,
            Jukema,J.W., Khaw,K.T., Lehtimaki,T., Liu,Y., Lorentzon,M.,
            McCloskey,E., Mitchell,B.D., Nandakumar,K., Nicholson,G.C.,
            Oostra,B.A., Peacock,M., Pols,H.A., Prince,R.L., Raitakari,O.,
            Reid,I.R., Robbins,J., Sambrook,P.N., Sham,P.C., Shuldiner,A.R.,
            Tylavsky,F.A., van Duijn,C.M., Wareham,N.J., Cupples,L.A.,
            Econs,M.J., Evans,D.M., Harris,T.B., Kung,A.W., Psaty,B.M.,
            Reeve,J., Spector,T.D., Streeten,E.A., Zillikens,M.C.,
            Thorsteinsdottir,U., Ohlsson,C., Karasik,D., Richards,J.B.,
            Brown,M.A., Stefansson,K., Uitterlinden,A.G., Ralston,S.H.,
            Ioannidis,J.P., Kiel,D.P. and Rivadeneira,F.
  TITLE     Genome-wide meta-analysis identifies 56 bone mineral density loci
            and reveals 14 loci associated with risk of fracture
  JOURNAL   Nat. Genet. 44 (5), 491-501 (2012)
   PUBMED   22504420
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1641)
  AUTHORS   Gong,L.G., Qiu,G.R., Jiang,H., Xu,X.Y., Zhu,H.Y. and Sun,K.L.
  TITLE     Analysis of single nucleotide polymorphisms and haplotypes in HOXC
            gene cluster within susceptible region 12q13 of simple congenital
            heart disease
  JOURNAL   Zhonghua Yi Xue Yi Chuan Xue Za Zhi 22 (5), 497-501 (2005)
   PUBMED   16215934
  REMARK    GeneRIF: The A17860G located in 3'flanking sequence of HOXC5 gene
            is associated with simple congenital heart disease; the haplotype
            of 3 SNPs may be linked with the susceptible gene of simple CHD.
            GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   3  (bases 1 to 1641)
  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   4  (bases 1 to 1641)
  AUTHORS   Apiou,F., Flagiello,D., Cillo,C., Malfoy,B., Poupon,M.F. and
            Dutrillaux,B.
  TITLE     Fine mapping of human HOX gene clusters
  JOURNAL   Cytogenet. Cell Genet. 73 (1-2), 114-115 (1996)
   PUBMED   8646877
REFERENCE   5  (bases 1 to 1641)
  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   6  (bases 1 to 1641)
  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 1641)
  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 1641)
  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 1641)
  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 1641)
  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 DA905719.1, BC034922.1 and
            AC023794.37.
            This sequence is a reference standard in the RefSeqGene project.
            
            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 (2) contains an alternate 5'-most
            exon, compared to variant 1. Three genes, HOXC4, HOXC5 and HOXC6,
            share this 5' non-coding exon. This variant is represented as
            non-coding due to the presence of an upstream ORF that is predicted
            to interfere with translation of the longest ORF; translation of
            the upstream ORF renders the transcript a candidate for
            nonsense-mediated mRNA decay (NMD).
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-252               DA905719.1         2-253
            253-1027            BC034922.1         1-775
            1028-1641           AC023794.37        2408-3021
FEATURES             Location/Qualifiers
     source          1..1641
                     /organism="Homo sapiens"
                     /mol_type="transcribed RNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12q13.3"
     gene            1..1641
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /note="homeobox C5"
                     /db_xref="GeneID:3222"
                     /db_xref="HGNC:5127"
                     /db_xref="MIM:142973"
     misc_RNA        1..1641
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /product="homeobox C5, transcript variant 2"
                     /db_xref="GeneID:3222"
                     /db_xref="HGNC:5127"
                     /db_xref="MIM:142973"
     exon            1..557
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    208..423
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /inference="COORDINATES: ab initio prediction:ORF Finder"
                     /note="long (>35aa) upstream ORF has strong Kozak
                     sequence; nonsense-mediated decay (NMD) candidate"
     variation       288
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:74568890"
     variation       360
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:3736210"
     variation       361
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:4133943"
     variation       376
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:4101168"
     variation       510..511
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace=""
                     /replace="ga"
                     /db_xref="dbSNP:375826581"
     exon            558..1641
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /inference="alignment:Splign:1.39.8"
     variation       561
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:145794998"
     variation       565
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:145300322"
     variation       573
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:149168463"
     variation       589
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:376228055"
     variation       617
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:376926310"
     variation       650
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:370344965"
     misc_feature    725..772
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /inference="COORDINATES:
                     alignment:Blast2seq::RefSeq|NM_018953.2"
                     /note="primary ORF"
     variation       763
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:143274247"
     variation       809
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:371365110"
     variation       860
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:113264704"
     variation       867
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:4016778"
     variation       1000
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:58994757"
     variation       1028
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:2071450"
     variation       1139
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:149895718"
     variation       1179
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:373936762"
     variation       1196
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:61921796"
     variation       1243
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:61921797"
     variation       1300
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:145357528"
     variation       1365..1367
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace=""
                     /replace="aca"
                     /db_xref="dbSNP:377514653"
     variation       1379
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:191530738"
     variation       1412
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:184371311"
     variation       1473
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:188058463"
     variation       1485
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:140104713"
     variation       1501
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:192290087"
     variation       1534
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:185833901"
     polyA_signal    1619..1624
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
     polyA_site      1641
                     /gene="HOXC5"
                     /gene_synonym="CP11; HOX3; HOX3D"
ORIGIN

ttattgtggtttgtccgttccgagcgctccgcagaacagtcctccctgtaagagcctaaccattgccagggaaacctgccctgggcgctcccttcattagcagtattttttttaaattaatctgattaataattatttttcccccatttaattttttttcctcccaggtggagttgccgaagctgggggcagctggggagggtggggatgggaggggagagacagaagttgagggcatctctctcttccttcccgaccctctggcccccaaggggcaggaggaatgcaggagcaggagttgagcttgggagctgcagatgcctccgcccctcctctctcccaggctcttcctcctgcccccttcttgcaactctccttaattttgtttggcttttggatgattataattatttttatttttgaatttatataaagtatatgtgtgtgtgtgtggagctgagacaggctcggcagcggcacagaatgagggaagacgagaaagagagtgggagagagagaggcagagagggagagagggagagtgacagcagcgctcgagacggacggcaagcggtcccgaaccagttacacgcgctaccagactctggaactcgagaaagaattccactttaaccgctacctcactcgccgcaggcgcatagagatcgccaacaacttgtgtctcaatgagagacagatcaagatctggttccagaaccgcaggatgaagtggaagaaagattccaaaatgaaaagcaaagaggctctttagaggcagcgggggaggcccgcagagcgcgcccctagccggttcctgtccctgcgcctttccttttcgcctttcctctctatatttcgggtcgggggcaggtgctggagcactgggctcccgggccccacagacaaaagcgcttttccttggcattccgcatccctaccgacccagggttcccgcggggctgtcggcgctgccccatctcccctcagctcggctcagctcggtacccggggcccagggcaagctccgcaggacttccccggagggctgcggcgtacaggctggcgcagaacgaaccttggcctgggccgtatctccggctcccagcctcagcgcggccctcccgagttaaggtgggcccggcccgcgccacaggaccctcgccggaccctctaacctcgccctctcctttgttcccggctggacgggttagacagccaaaggctggcgagagtctggccctagactcggggtgcttccttgtagcgactaaactagattttcacttatgaatgatttgcatatgaaaggagagcatcggcctagggcccccacagttgctctatgctttccaaaccttatctccacaacctcttccccccaaaacccgggaacctccccagcctgcgcctgctgcatgccctctcaggccggcagccccagcctgctagctagctcaactagtggggtttcctggcactggaccccagcaagtggtcctagaggccctttgctgtcccatagtccctgccacgaatttctgtgccctcctgacccattgctgttgtccaactatttattgactctgggtccttcctgaaactatattttgtcatatcaaataaagagagaacaggactaaa

//

Annotations: