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2024-03-29 07:53:45, GGRNA : RefSeq release 60 (20130726)

LOCUS       NR_047517               2370 bp    RNA     linear   PRI 17-JUL-2013
DEFINITION  Homo sapiens HOX transcript antisense RNA (HOTAIR), transcript
            variant 1, non-coding RNA.
ACCESSION   NR_047517
VERSION     NR_047517.1  GI:383286742
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 2370)
  AUTHORS   Kim,K., Jutooru,I., Chadalapaka,G., Johnson,G., Frank,J.,
            Burghardt,R., Kim,S. and Safe,S.
  TITLE     HOTAIR is a negative prognostic factor and exhibits pro-oncogenic
            activity in pancreatic cancer
  JOURNAL   Oncogene 32 (13), 1616-1625 (2013)
   PUBMED   22614017
  REMARK    GeneRIF: HOTAIR is a negative prognostic factor and exhibits
            pro-oncogenic activity in pancreatic cancer.
REFERENCE   2  (bases 1 to 2370)
  AUTHORS   Li,D., Feng,J., Wu,T., Wang,Y., Sun,Y., Ren,J. and Liu,M.
  TITLE     Long intergenic noncoding RNA HOTAIR is overexpressed and regulates
            PTEN methylation in laryngeal squamous cell carcinoma
  JOURNAL   Am. J. Pathol. 182 (1), 64-70 (2013)
   PUBMED   23141928
  REMARK    GeneRIF: HOTAIR is overexpressed and regulates PTEN methylation in
            laryngeal squamous cell carcinoma.
REFERENCE   3  (bases 1 to 2370)
  AUTHORS   Lu,L., Zhu,G., Zhang,C., Deng,Q., Katsaros,D., Mayne,S.T.,
            Risch,H.A., Mu,L., Canuto,E.M., Gregori,G., Benedetto,C. and Yu,H.
  TITLE     Association of large noncoding RNA HOTAIR expression and its
            downstream intergenic CpG island methylation with survival in
            breast cancer
  JOURNAL   Breast Cancer Res. Treat. 136 (3), 875-883 (2012)
   PUBMED   23124417
  REMARK    GeneRIF: intergenic DNA methylation may have important biologic
            relevance in regulating HOTAIR expression
REFERENCE   4  (bases 1 to 2370)
  AUTHORS   Pauler,F.M., Barlow,D.P. and Hudson,Q.J.
  TITLE     Mechanisms of long range silencing by imprinted macro non-coding
            RNAs
  JOURNAL   Curr. Opin. Genet. Dev. 22 (3), 283-289 (2012)
   PUBMED   22386265
  REMARK    Review article
REFERENCE   5  (bases 1 to 2370)
  AUTHORS   Niland,C.N., Merry,C.R. and Khalil,A.M.
  TITLE     Emerging Roles for Long Non-Coding RNAs in Cancer and Neurological
            Disorders
  JOURNAL   Front Genet 3, 25 (2012)
   PUBMED   22375145
REFERENCE   6  (bases 1 to 2370)
  AUTHORS   Tsai,M.C., Manor,O., Wan,Y., Mosammaparast,N., Wang,J.K., Lan,F.,
            Shi,Y., Segal,E. and Chang,H.Y.
  TITLE     Long noncoding RNA as modular scaffold of histone modification
            complexes
  JOURNAL   Science 329 (5992), 689-693 (2010)
   PUBMED   20616235
  REMARK    GeneRIF: findings show that the lincRNA HOTAIR serves as a scaffold
            for at least two distinct histone modification complexes; A 5'
            domain of HOTAIR binds polycomb repressive complex 2 (PRC2),
            whereas a 3' domain of HOTAIR binds the LSD1/CoREST/REST complex
REFERENCE   7  (bases 1 to 2370)
  AUTHORS   Gupta,R.A., Shah,N., Wang,K.C., Kim,J., Horlings,H.M., Wong,D.J.,
            Tsai,M.C., Hung,T., Argani,P., Rinn,J.L., Wang,Y., Brzoska,P.,
            Kong,B., Li,R., West,R.B., van de Vijver,M.J., Sukumar,S. and
            Chang,H.Y.
  TITLE     Long non-coding RNA HOTAIR reprograms chromatin state to promote
            cancer metastasis
  JOURNAL   Nature 464 (7291), 1071-1076 (2010)
   PUBMED   20393566
  REMARK    GeneRIF: The lincRNA termed HOTAIR is increased in expression in
            primary breast tumours and metastases, and HOTAIR expression level
            in primary tumours is a powerful predictor of eventual metastasis
            and death.
REFERENCE   8  (bases 1 to 2370)
  AUTHORS   Khalil,A.M., Guttman,M., Huarte,M., Garber,M., Raj,A., Rivea
            Morales,D., Thomas,K., Presser,A., Bernstein,B.E., van
            Oudenaarden,A., Regev,A., Lander,E.S. and Rinn,J.L.
  TITLE     Many human large intergenic noncoding RNAs associate with
            chromatin-modifying complexes and affect gene expression
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 106 (28), 11667-11672 (2009)
   PUBMED   19571010
REFERENCE   9  (bases 1 to 2370)
  AUTHORS   Rinn,J.L., Kertesz,M., Wang,J.K., Squazzo,S.L., Xu,X.,
            Brugmann,S.A., Goodnough,L.H., Helms,J.A., Farnham,P.J., Segal,E.
            and Chang,H.Y.
  TITLE     Functional demarcation of active and silent chromatin domains in
            human HOX loci by noncoding RNAs
  JOURNAL   Cell 129 (7), 1311-1323 (2007)
   PUBMED   17604720
REFERENCE   10 (bases 1 to 2370)
  AUTHORS   Woo,C.J. and Kingston,R.E.
  TITLE     HOTAIR lifts noncoding RNAs to new levels
  JOURNAL   Cell 129 (7), 1257-1259 (2007)
   PUBMED   17604716
  REMARK    Review article
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA905601.1, AC012531.11 and
            AA399272.1.
            
            Summary: This gene is located within the Homeobox C (HOXC) gene
            cluster on chromosome 12 and is co-expressed with HOXC genes. It
            represses transcription of HOXD genes on chromosome 2 in trans.
            This gene is shuttled from chromosome 12 to chromosome 2 by a
            component of Polycomb Repressive Complex 2 (PRC2). This gene
            interacts with both PRC2 and lysine specific demethylase 1 (LSD1)
            complexes through its 5' and 3' domains, respectively, and serves
            as a scaffold to assemble PRC2 and LSD1 complexes to the HOXD gene
            cluster. It couples H3K27 methylation and H3K4 demethylation for
            epigenetic silencing of HOXD genes in multiple tissues. This gene
            is highly expressed in multiple tumors. Alternatively spliced
            transcript variants have been identified. [provided by RefSeq, Feb
            2013].
            
            Transcript Variant: This variant (1) consists of six exons.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript 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 :: DA905601.1, DA906831.1 [ECO:0000332]
            RNAseq introns              :: mixed/partial sample support
                                           ERS025084, ERS025088 [ECO:0000350]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-560               DA905601.1         1-560
            561-2223            AC012531.11        100057-101719       c
            2224-2370           AA399272.1         1-147               c
FEATURES             Location/Qualifiers
     source          1..2370
                     /organism="Homo sapiens"
                     /mol_type="transcribed RNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12q13.13"
     gene            1..2370
                     /gene="HOTAIR"
                     /gene_synonym="HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072"
                     /note="HOX transcript antisense RNA"
                     /db_xref="GeneID:100124700"
                     /db_xref="HGNC:33510"
                     /db_xref="MIM:611400"
     misc_RNA        1..2370
                     /gene="HOTAIR"
                     /gene_synonym="HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072"
                     /product="HOX transcript antisense RNA, transcript variant
                     1"
                     /db_xref="GeneID:100124700"
                     /db_xref="HGNC:33510"
                     /db_xref="MIM:611400"
     exon            1..59
                     /gene="HOTAIR"
                     /gene_synonym="HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072"
                     /inference="alignment:Splign:1.39.8"
     exon            60..199
                     /gene="HOTAIR"
                     /gene_synonym="HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072"
                     /inference="alignment:Splign:1.39.8"
     exon            200..325
                     /gene="HOTAIR"
                     /gene_synonym="HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072"
                     /inference="alignment:Splign:1.39.8"
     exon            326..427
                     /gene="HOTAIR"
                     /gene_synonym="HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072"
                     /inference="alignment:Splign:1.39.8"
     exon            428..551
                     /gene="HOTAIR"
                     /gene_synonym="HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072"
                     /inference="alignment:Splign:1.39.8"
     exon            552..2368
                     /gene="HOTAIR"
                     /gene_synonym="HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072"
                     /inference="alignment:Splign:1.39.8"
     variation       965
                     /gene="HOTAIR"
                     /gene_synonym="HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:1838169"
     variation       2008
                     /gene="HOTAIR"
                     /gene_synonym="HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072"
                     /replace=""
                     /replace="c"
                     /db_xref="dbSNP:3839968"
     polyA_signal    2342..2347
                     /gene="HOTAIR"
                     /gene_synonym="HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072"
     polyA_site      2368
                     /gene="HOTAIR"
                     /gene_synonym="HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072"
ORIGIN      


ccagttctcaggcgagagccgcggctgacagggtctgggacagaaggaaagccctccagcctccaggccctgccttctgcctgcacattctgccctgatttccggaacctggaagcctaggcaggcagtggggaactctgactcgcctgtgctctggagcttgatccgaaagcttccacagtgaggactgctccgtgggggtaagagagcaccaggcactgaggcctgggagttccacagaccaacacccctgctcctggcggctcccacccgggacttagaccctcaggtccctaatatcccggaggtgctctcaatcagaaaggtcctgctccgcttcgcagtggaatggaacggatttagaagcctgcagtaggggagtggggagtggagagagggagcccagagttacagacggcggcgagaggaaggaggggcgtctttatttttttaaggccccaaagagtctgatgtttacaagaccagaaatgccacggccgcgtcctggcagagaaaaggctgaaatggaggaccggcgccttccttataagctcgttggggcctaagccagtaccgacctggtagaaaaagcaaccacgaagctagagagagagccagaggagggaagagagcgccagacgaaggtgaaagcgaaccacgcagagaaatgcaggcaagggagcaaggcggcagttcccggaacaaacgtggcagagggcaagacgggcactcacagacagaggtttatgtatttttattttttaaaatctgatttggtgttccatgaggaaaagggaaaatctagggaacgggagtacagagagaataatccgggtcctagctcgccacatgaacgcccagagaacgctggaaaaacctgagcgggtgccggggcagcacccggctcgggtcagccactgccccacaccgggcccaccaagccccgcccctcgcggccaccggggcttccttgctcttcttatcatctccatctttatgatgaggcttgttaacaagaccagagagctggccaagcacctctatctcagccgcgcccgctcagccgagcagcggtcggtggggggactgggaggcgctaattaattgattcctttggactgtaaaatatggcggcgtctacacggaacccatggactcataaacaatatatctgttgggcgtgagtgcactgtctctcaaataatttttccataggcaaatgtcagagggttctggatttttagttgctaaggaaagatccaaatgggaccaattttaggaggcccaaacagagtccgttcagtgtcagaaaatgcttccccaaaggggttgggagtgtgttttgttggaaaaaagcttgggttataggaaagcctttccctgctacttgtgtagacccagcccaatttaagaattacaaggaagcgaaggggttgtgtaggccggaagcctctctgtcccggctggatgcaggggacttgagctgctccggaatttgagaggaacatagaagcaaaggtccagcctttgcttcgtgctgattcctagacttaagattcaaaaacaaatttttaaaagtgaaaccagccctagcctttggaagctcttgaaggttcagcacccacccaggaatccacctgcctgttacacgcctctccaagacacagtggcaccgcttttctaactggcagcacagagcaactctataatatgcttatattaggtctagaagaatgcatcttgagacacatgggtaacctaattatataatgcttgttccatacaggagtgattatgcagtgggaccctgctgcaaacgggactttgcactctaaatatagaccccagcttgggacaaaagttgcagtagaaaaatagacataggagaacacttaaataagtgatgcatgtagacacagaaggggtatttaaaagacagaaataatagaagtacagaagaacagaaaaaaaatcagcagatggagattaccattcccaatgcctgaacttcctcctgctattaagattgctagagaattgtgtcttaaacagttcatgaacccagaagaatgcaatttcaatgtatttagtacacacacagtatgtatataaacacaactcacagaatatattttccatacattgggtaggtatgcactttgtgtatatataataatgtattttccatgcagttttaaaatgtagatatattaatatctggatgcattttctgtgcactggttttatatgccttatggagtatatactcacatgtagctaaatagactcaggactgcacattccttgtgtaggttgtgtgtgtgtggtggttttatgcataaataaagttttacatgtggtgaatataaa
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