LOCUS       NM_000965               3132 bp    mRNA    linear   PRI 12-OCT-2024
DEFINITION  Homo sapiens retinoic acid receptor beta (RARB), transcript variant
            1, mRNA.
ACCESSION   NM_000965 NM_015854
VERSION     NM_000965.5
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 3132)
  AUTHORS   Petty,W.J., Li,N., Biddle,A., Bounds,R., Nitkin,C., Ma,Y.,
            Dragnev,K.H., Freemantle,S.J. and Dmitrovsky,E.
  TITLE     A novel retinoic acid receptor beta isoform and retinoid resistance
            in lung carcinogenesis
  JOURNAL   J Natl Cancer Inst 97 (22), 1645-1651 (2005)
   PUBMED   16288117
  REMARK    GeneRIF: In H358 lung cancer cells transiently transfected with
            RARbeta1', RA treatment restored target gene expression compared
            with that in vector-transfected cells and suppressed cell growth
            compared with that in untreated cells.
REFERENCE   2  (bases 1 to 3132)
  AUTHORS   Peng,X., Mehta,R.G., Tonetti,D.A. and Christov,K.
  TITLE     Identification of novel RARbeta2 transcript variants with short
            5'-UTRs in normal and cancerous breast epithelial cells
  JOURNAL   Oncogene 24 (7), 1296-1301 (2005)
   PUBMED   15558014
REFERENCE   3  (bases 1 to 3132)
  AUTHORS   Peng,X., Maruo,T., Cao,Y., Punj,V., Mehta,R., Das Gupta,T.K. and
            Christov,K.
  TITLE     A novel RARbeta isoform directed by a distinct promoter P3 and
            mediated by retinoic acid in breast cancer cells
  JOURNAL   Cancer Res 64 (24), 8911-8918 (2004)
   PUBMED   15604252
REFERENCE   4  (bases 1 to 3132)
  AUTHORS   Jin,P., Fu,G.K., Wilson,A.D., Yang,J., Chien,D., Hawkins,P.R.,
            Au-Young,J. and Stuve,L.L.
  TITLE     PCR isolation and cloning of novel splice variant mRNAs from known
            drug target genes
  JOURNAL   Genomics 83 (4), 566-571 (2004)
   PUBMED   15028279
REFERENCE   5  (bases 1 to 3132)
  AUTHORS   Chen,L.I., Sommer,K.M. and Swisshelm,K.
  TITLE     Downstream codons in the retinoic acid receptor beta -2 and beta -4
            mRNAs initiate translation of a protein isoform that disrupts
            retinoid-activated transcription
  JOURNAL   J Biol Chem 277 (38), 35411-35421 (2002)
   PUBMED   12118004
  REMARK    GeneRIF: downstream codons in mRNAs initiate translation of a
            protein isoform that disrupts retinoid-activated transcription
REFERENCE   6  (bases 1 to 3132)
  AUTHORS   Sommer,K.M., Chen,L.I., Treuting,P.M., Smith,L.T. and Swisshelm,K.
  TITLE     Elevated retinoic acid receptor beta(4) protein in human breast
            tumor cells with nuclear and cytoplasmic localization
  JOURNAL   Proc Natl Acad Sci U S A 96 (15), 8651-8656 (1999)
   PUBMED   10411930
REFERENCE   7  (bases 1 to 3132)
  AUTHORS   Houle,B., Pelletier,M., Wu,J., Goodyer,C. and Bradley,W.E.
  TITLE     Fetal isoform of human retinoic acid receptor beta expressed in
            small cell lung cancer lines
  JOURNAL   Cancer Res 54 (2), 365-369 (1994)
   PUBMED   8275470
REFERENCE   8  (bases 1 to 3132)
  AUTHORS   Bardakjian,T., Weiss,A. and Schneider,A.
  TITLE     Microphthalmia/Anophthalmia/Coloboma Spectrum - RETIRED CHAPTER,
            FOR HISTORICAL REFERENCE ONLY
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301552
REFERENCE   9  (bases 1 to 3132)
  AUTHORS   Longoni,M., Pober,B.R. and High,F.A.
  TITLE     Congenital Diaphragmatic Hernia Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301533
REFERENCE   10 (bases 1 to 3132)
  AUTHORS   Nagpal,S., Zelent,A. and Chambon,P.
  TITLE     RAR-beta 4, a retinoic acid receptor isoform is generated from
            RAR-beta 2 by alternative splicing and usage of a CUG initiator
            codon
  JOURNAL   Proc Natl Acad Sci U S A 89 (7), 2718-2722 (1992)
   PUBMED   1313565
REFERENCE   11 (bases 1 to 3132)
  AUTHORS   de The,H., Marchio,A., Tiollais,P. and Dejean,A.
  TITLE     A novel steroid thyroid hormone receptor-related gene
            inappropriately expressed in human hepatocellular carcinoma
  JOURNAL   Nature 330 (6149), 667-670 (1987)
   PUBMED   2825037
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC098477.2, AC133141.2 and
            AC093416.2.
            This sequence is a reference standard in the RefSeqGene project.
            
            On May 21, 2020 this sequence version replaced NM_000965.4.
            
            Summary: This gene encodes retinoic acid receptor beta, a member of
            the thyroid-steroid hormone receptor superfamily of nuclear
            transcriptional regulators. This receptor localizes to the
            cytoplasm and to subnuclear compartments. It binds retinoic acid,
            the biologically active form of vitamin A which mediates cellular
            signalling in embryonic morphogenesis, cell growth and
            differentiation. It is thought that this protein limits growth of
            many cell types by regulating gene expression. The gene was first
            identified in a hepatocellular carcinoma where it flanks a
            hepatitis B virus integration site. Alternate promoter usage and
            differential splicing result in multiple transcript variants.
            [provided by RefSeq, Mar 2014].
            
            Transcript Variant: This variant (1), also known as beta-2, is a
            predominant transcript. This variant can initiate translation from
            an upstream AUG site and also from a downstream, in-frame AUG site
            (PMID: 12118004). The isoform (1) represented in this RefSeq is
            derived from the upstream AUG start codon.
            
            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 :: BC030234.1, SRR14038193.2999182.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000330688.9/ ENSP00000332296.4
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            regulatory uORF        :: PMID: 15558014
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-626               AC098477.2         191095-191720
            627-775             AC133141.2         29702-29850
            776-917             AC133141.2         69691-69832
            918-1078            AC093416.2         69569-69729
            1079-1255           AC093416.2         80357-80533
            1256-1460           AC093416.2         93314-93518
            1461-1619           AC093416.2         94331-94489
            1620-3132           AC093416.2         96231-97743
FEATURES             Location/Qualifiers
     source          1..3132
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3p24.2"
     gene            1..3132
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /note="retinoic acid receptor beta"
                     /db_xref="GeneID:5915"
                     /db_xref="HGNC:HGNC:9865"
                     /db_xref="MIM:180220"
     exon            1..626
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      80..94
                     /regulatory_class="uORF"
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /experiment="DESCRIPTION:regulatory uORF[PMID:15558014]"
                     /note="this uORF is predicted to encode a 4 aa peptide
                     (PMID:15558014)"
     regulatory      103..156
                     /regulatory_class="uORF"
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /experiment="DESCRIPTION:regulatory uORF[PMID:15558014]"
                     /note="this uORF is predicted to encode a 17 aa peptide
                     (PMID:15558014)"
     regulatory      267..329
                     /regulatory_class="uORF"
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /experiment="DESCRIPTION:regulatory uORF[PMID:15558014]"
                     /note="this uORF is predicted to encode a 20 aa peptide
                     (PMID:15558014)"
     regulatory      274..429
                     /regulatory_class="uORF"
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /experiment="DESCRIPTION:regulatory uORF[PMID:15558014]"
                     /note="this uORF is predicted to encode a 51 aa peptide
                     (PMID:15558014)"
     regulatory      326..385
                     /regulatory_class="uORF"
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /experiment="DESCRIPTION:regulatory uORF[PMID:15558014]"
                     /note="this uORF is predicted to encode a 19 aa peptide
                     (PMID:15558014)"
     regulatory      407..436
                     /regulatory_class="uORF"
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /experiment="DESCRIPTION:regulatory uORF[PMID:15558014]"
                     /note="this uORF is predicted to encode a 9 aa peptide
                     (PMID:15558014)"
     CDS             470..1816
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     retinoic acid receptor, beta polypeptide; hepatitis B
                     virus activated protein; HBV-activated protein;
                     RAR-epsilon; RAR-beta; nuclear receptor subfamily 1 group
                     B member 2"
                     /codon_start=1
                     /product="retinoic acid receptor beta isoform 1"
                     /protein_id="NP_000956.2"
                     /db_xref="CCDS:CCDS2642.1"
                     /db_xref="GeneID:5915"
                     /db_xref="HGNC:HGNC:9865"
                     /db_xref="MIM:180220"
                     /translation="MFDCMDVLSVSPGQILDFYTASPSSCMLQEKALKACFSGLTQTE
                     WQHRHTAQSIETQSTSSEELVPSPPSPLPPPRVYKPCFVCQDKSSGYHYGVSACEGCK
                     GFFRRSIQKNMIYTCHRDKNCVINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKKK
                     ETSKQECTESYEMTAELDDLTEKIRKAHQETFPSLCQLGKYTTNSSADHRVRLDLGLW
                     DKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDT
                     MTFSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLICGDRQD
                     LEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVITLK
                     MEIPGSMPPLIQEMLENSEGHEPLTPSSSGNTAEHSPSISPSSVENSGVSQSPLVQ"
     exon            627..775
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /inference="alignment:Splign:2.1.0"
     exon            776..917
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /inference="alignment:Splign:2.1.0"
     exon            918..1078
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /inference="alignment:Splign:2.1.0"
     exon            1079..1255
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /inference="alignment:Splign:2.1.0"
     exon            1256..1460
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /inference="alignment:Splign:2.1.0"
     exon            1461..1619
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /inference="alignment:Splign:2.1.0"
     exon            1620..3132
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3116..3121
                     /regulatory_class="polyA_signal_sequence"
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /note="hexamer: AATATA"
     polyA_site      3132
                     /gene="RARB"
                     /gene_synonym="HAP; MCOPS12; NR1B2; RARbeta; RARbeta1;
                     RRB2"
                     /note="major polyA site"
ORIGIN      
        1 gtgacagaag tagtaggaag tgagctgttc agaggcagga gggtctattc tttgccaaag
       61 gggggaccag aattccccca tgcgagctgt ttgaggactg ggatgccgag aacgcgagcg
      121 atccgagcag ggtttgtctg ggcaccgtcg gggtaggatc cggaacgcat tcggaaggct
      181 ttttgcaagc atttacttgg aaggagaact tgggatcttt ctgggaaccc cccgccccgg
      241 ctggattggc cgagcaagcc tggaaaatgg taaatgatca tttggatcaa ttacaggctt
      301 ttagctggct tgtctgtcat aattcatgat tcggggctgg gaaaaagacc aacagcctac
      361 gtgccaaaaa aggggcagag tttgatggag ttgggtggac ttttctatgc catttgcctc
      421 cacacctaga ggataagcac ttttgcagac attcagtgca agggagatca tgtttgactg
      481 tatggatgtt ctgtcagtga gtcctgggca aatcctggat ttctacactg cgagtccgtc
      541 ttcctgcatg ctccaggaga aagctctcaa agcatgcttc agtggattga cccaaaccga
      601 atggcagcat cggcacactg ctcaatcaat tgaaacacag agcaccagct ctgaggaact
      661 cgtcccaagc cccccatctc cacttcctcc ccctcgagtg tacaaaccct gcttcgtctg
      721 ccaggacaaa tcatcagggt accactatgg ggtcagcgcc tgtgagggat gtaagggctt
      781 tttccgcaga agtattcaga agaatatgat ttacacttgt caccgagata agaactgtgt
      841 tattaataaa gtcaccagga atcgatgcca atactgtcga ctccagaagt gctttgaagt
      901 gggaatgtcc aaagaatctg tcaggaatga caggaacaag aaaaagaagg agacttcgaa
      961 gcaagaatgc acagagagct atgaaatgac agctgagttg gacgatctca cagagaagat
     1021 ccgaaaagct caccaggaaa ctttcccttc actctgccag ctgggtaaat acaccacgaa
     1081 ttccagtgct gaccatcgag tccgactgga cctgggcctc tgggacaaat tcagtgaact
     1141 ggccaccaag tgcattatta agatcgtgga gtttgctaaa cgtctgcctg gtttcactgg
     1201 cttgaccatc gcagaccaaa ttaccctgct gaaggccgcc tgcctggaca tcctgattct
     1261 tagaatttgc accaggtata ccccagaaca agacaccatg actttctcag acggccttac
     1321 cctaaatcga actcagatgc acaatgctgg atttggtcct ctgactgacc ttgtgttcac
     1381 ctttgccaac cagctcctgc ctttggaaat ggatgacaca gaaacaggcc ttctcagtgc
     1441 catctgctta atctgtggag accgccagga ccttgaggaa ccgacaaaag tagataagct
     1501 acaagaacca ttgctggaag cactaaaaat ttatatcaga aaaagacgac ccagcaagcc
     1561 tcacatgttt ccaaagatct taatgaaaat cacagatctc cgtagcatca gtgctaaagg
     1621 tgcagagcgt gtaattacct tgaaaatgga aattcctgga tcaatgccac ctctcattca
     1681 agaaatgctg gagaattctg aaggacatga acccttgacc ccaagttcaa gtgggaacac
     1741 agcagagcac agtcctagca tctcacccag ctcagtggaa aacagtgggg tcagtcagtc
     1801 accactcgtg caataagaca ttttctagct acttcaaaca ttccccagta ccttcagttc
     1861 caggatttaa aatgcaagaa aaaacatttt tactgctgct tagtttttgg actgaaaaga
     1921 tattaaaact caagaaggac caagaagttt tcatatgtat caatatatat actcctcact
     1981 gtgtaactta cctagaaata caaacttttc caattttaaa aaatcagcca tttcatgcaa
     2041 ccagaaacta gttaaaagct tctattttcc tctttgaaca ctcaagattg catggcaaag
     2101 acccagtcaa aatgatttac ccctggttaa gtttctgaag actttgtaca tacagaagta
     2161 tggctctgtt ctttctatac tgtatgtttg gtgctttcct tttgtcttgc atactcaaaa
     2221 taaccatgac accaaggtta tgaaatagac tactgtacac gtctacctag gttcaaaaag
     2281 ataactgtct tgctttcatg gaatagtcaa gacatcaagg taaggaaaca ggactattga
     2341 caggactatt gtacagtatg acaagataag gctgaagata ttctacttta gttagtatgg
     2401 aagcttgtct ttgctctttc tgatgctctc aaactgcatc ttttatttca tgttgcccag
     2461 taaaagtata caaattccct gcactagcag aagagaattc tgtatcagtg taactgccag
     2521 ttcagttaat caaatgtcat ttgttcaatt gttaatgtca ctttaaatta aaagtggttt
     2581 attacttgtt taatgacata actacacagt tagttaaaaa aaattttttt acagtaatga
     2641 tagcctccaa ggcagaaaca cttttcagtg ttaagttttt gtttacttgt tcacaagcca
     2701 ttagggaaat ttcatgggat aattagcagg ctggtctacc acctggacca tgtaactcta
     2761 gtgtccttcc tgattcatgc ctgatattgg gatttttttt tccagccttc ttgatgccaa
     2821 ggggctaatt aatattaaca actcccaaag aaacaggcat agaatctgcc tcctttgacc
     2881 ttgttcaatc actatgaagc agagtgaaag ctgtggtaga gtggttaaca gatacaagtg
     2941 tcagtttctt agttctcatt taagcactag tggaattttt tttttttgat atattagcaa
     3001 gtctgtgatg tactttcact ggctctgttt gtacattgag attgtttgtt taacaatgct
     3061 ttctatgttc atatactgtt tacctttttc catggagtct cctggcaaag aataaaatat
     3121 atttatttta aa
//
