LOCUS       NM_011243               3041 bp    mRNA    linear   ROD 01-AUG-2024
DEFINITION  Mus musculus retinoic acid receptor, beta (Rarb), transcript
            variant beta2, mRNA.
ACCESSION   NM_011243 XM_127583
VERSION     NM_011243.2
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 3041)
  AUTHORS   Soussi,G., Girdziusaite,A., Jhanwar,S., Palacio,V., Notaro,M.,
            Sheth,R., Zeller,R. and Zuniga,A.
  TITLE     TBX3 is essential for establishment of the posterior boundary of
            anterior genes and upregulation of posterior genes together with
            HAND2 during the onset of limb bud development
  JOURNAL   Development 151 (11) (2024)
   PUBMED   38828908
REFERENCE   2  (bases 1 to 3041)
  AUTHORS   Queen,R., Crosier,M., Eley,L., Kerwin,J., Turner,J.E., Yu,J.,
            Alqahtani,A., Dhanaseelan,T., Overman,L., Soetjoadi,H., Baldock,R.,
            Coxhead,J., Boczonadi,V., Laude,A., Cockell,S.J., Kane,M.A.,
            Lisgo,S. and Henderson,D.J.
  TITLE     Spatial transcriptomics reveals novel genes during the remodelling
            of the embryonic human arterial valves
  JOURNAL   PLoS Genet 19 (11), e1010777 (2023)
   PUBMED   38011284
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3041)
  AUTHORS   Melis,M., Trasino,S.E., Tang,X.H., Rappa,A., Zhang,T., Qin,L. and
            Gudas,L.J.
  TITLE     Retinoic Acid Receptor beta Loss in Hepatocytes Increases Steatosis
            and Elevates the Integrated Stress Response in Alcohol-Associated
            Liver Disease
  JOURNAL   Int J Mol Sci 24 (15), 12035 (2023)
   PUBMED   37569418
  REMARK    GeneRIF: Retinoic Acid Receptor beta Loss in Hepatocytes Increases
            Steatosis and Elevates the Integrated Stress Response in
            Alcohol-Associated Liver Disease.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3041)
  AUTHORS   Reynolds,K., Zimmer,A.M. and Zimmer,A.
  TITLE     Regulation of RAR beta 2 mRNA expression: evidence for an
            inhibitory peptide encoded in the 5'-untranslated region
  JOURNAL   J Cell Biol 134 (4), 827-835 (1996)
   PUBMED   8769409
REFERENCE   5  (bases 1 to 3041)
  AUTHORS   Zimmer,A., Zimmer,A.M. and Reynolds,K.
  TITLE     Tissue specific expression of the retinoic acid receptor-beta 2:
            regulation by short open reading frames in the 5'-noncoding region
  JOURNAL   J Cell Biol 127 (4), 1111-1119 (1994)
   PUBMED   7962071
REFERENCE   6  (bases 1 to 3041)
  AUTHORS   Rochette-Egly,C., Gaub,M.P., Lutz,Y., Ali,S., Scheuer,I. and
            Chambon,P.
  TITLE     Retinoic acid receptor-beta: immunodetection and phosphorylation on
            tyrosine residues
  JOURNAL   Mol Endocrinol 6 (12), 2197-2209 (1992)
   PUBMED   1283441
REFERENCE   7  (bases 1 to 3041)
  AUTHORS   Ruberte,E., Friederich,V., Morriss-Kay,G. and Chambon,P.
  TITLE     Differential distribution patterns of CRABP I and CRABP II
            transcripts during mouse embryogenesis
  JOURNAL   Development 115 (4), 973-987 (1992)
   PUBMED   1333403
REFERENCE   8  (bases 1 to 3041)
  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   9  (bases 1 to 3041)
  AUTHORS   Morriss-Kay,G.
  TITLE     Retinoic acid receptors in normal growth and development
  JOURNAL   Cancer Surv 14, 181-193 (1992)
   PUBMED   1330302
  REMARK    Review article
REFERENCE   10 (bases 1 to 3041)
  AUTHORS   Zelent,A., Mendelsohn,C., Kastner,P., Krust,A., Garnier,J.M.,
            Ruffenach,F., Leroy,P. and Chambon,P.
  TITLE     Differentially expressed isoforms of the mouse retinoic acid
            receptor beta generated by usage of two promoters and alternative
            splicing
  JOURNAL   EMBO J 10 (1), 71-81 (1991)
   PUBMED   1846599
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            X56573.1, S56660.1 and BC076597.1.
            
            On Jan 29, 2014 this sequence version replaced NM_011243.1.
            
            Transcript Variant: This variant (beta2, also known as beta0) has
            an alternate 5' UTR and 5' coding region, compared to variant
            beta3. The resulting isoform (beta2) is shorter and has a distinct
            N-terminus, compared to isoform beta3.
            
            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 :: BC076597.1, AK078471.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849382, SAMN00849385
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            regulatory uORF        :: PMID: 7962071
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-185               X56573.1           121-305
            186-2185            S56660.1           82-2081
            2186-3041           BC076597.1         2182-3037
FEATURES             Location/Qualifiers
     source          1..3041
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="14"
                     /map="14 7.08 cM"
     gene            1..3041
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /note="retinoic acid receptor, beta"
                     /db_xref="GeneID:218772"
                     /db_xref="MGI:MGI:97857"
     exon            1..619
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      103..156
                     /regulatory_class="uORF"
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /experiment="DESCRIPTION:regulatory uORF[PMID:7962071]"
                     /note="this uORF is known as uORF1 and is predicted to
                     encode a 17 aa peptide (PMID:7962071)"
     regulatory      263..325
                     /regulatory_class="uORF"
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /experiment="DESCRIPTION:regulatory uORF[PMID:7962071]"
                     /note="this uORF is known as uORF2 and is predicted to
                     encode a 20 aa peptide (PMID:7962071)"
     regulatory      270..431
                     /regulatory_class="uORF"
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /experiment="DESCRIPTION:regulatory uORF[PMID:7962071]"
                     /note="this uORF is known as uORF3 and is predicted to
                     encode a 53 aa peptide (PMID:7962071)"
     regulatory      322..381
                     /regulatory_class="uORF"
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /experiment="DESCRIPTION:regulatory uORF[PMID:7962071]"
                     /note="this uORF is known as uORF4 and is predicted to
                     encode a 19 aa peptide (PMID:7962071)"
     regulatory      381..431
                     /regulatory_class="uORF"
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /experiment="DESCRIPTION:regulatory uORF[PMID:7962071]"
                     /note="this uORF is known as uORF5 and is predicted to
                     encode a 16 aa peptide (PMID:7962071)"
     CDS             463..1809
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /note="isoform beta2 is encoded by transcript variant
                     beta2; RAR-beta; nuclear receptor subfamily 1 group B
                     member 2"
                     /codon_start=1
                     /product="retinoic acid receptor beta isoform beta2"
                     /protein_id="NP_035373.1"
                     /db_xref="CCDS:CCDS26834.1"
                     /db_xref="GeneID:218772"
                     /db_xref="MGI:MGI:97857"
                     /translation="MFDCMDVLSVSPGQILDFYTASPSSCMLQEKALKACLSGFTQAE
                     WQHRHTAQSIETQSTSSEELVPSPPSPLPPPRVYKPCFVCQDKSSGYHYGVSACEGCK
                     GFFRRSIQKNMIYTCHRDKNCVINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKKK
                     EPSKQECTESYEMTAELDDLTEKIRKAHQETFPSLCQLGKYTTNSSADHRVRLDLGLW
                     DKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDT
                     MTFSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLICGDRQD
                     LEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVITLK
                     MEIPGSMPPLIQEMLENSEGHEPLTPSSSGNIAEHSPSVSPSSVENSGVSQSPLLQ"
     exon            620..768
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /inference="alignment:Splign:2.1.0"
     exon            769..910
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /inference="alignment:Splign:2.1.0"
     exon            911..1071
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /inference="alignment:Splign:2.1.0"
     exon            1072..1248
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /inference="alignment:Splign:2.1.0"
     exon            1249..1453
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /inference="alignment:Splign:2.1.0"
     exon            1454..1612
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /inference="alignment:Splign:2.1.0"
     exon            1613..3041
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3025..3030
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /note="hexamer: AATATA"
     polyA_site      3041
                     /gene="Rarb"
                     /gene_synonym="A830025K23; Hap; Nr1b2"
                     /note="major polyA site"
ORIGIN      
        1 gtgacagaag tggtaggaag tgagctgctc cgaggcagga gggtctattc tttgccaaag
       61 ggggggacca gagttcccgt gcgccgcggc cacaagactg ggatgcagag gacgcgagcc
      121 acccgggcag ggagcgtctg ggcaccggcg gggtaggacc cgcgcgctcc cggaggcctg
      181 cgcgggcgtc gcctggaagg gagaacttgg gatcggtgcg ggaacccccg ccctggctgg
      241 atcggccgag cgagcctgga aaatggtaaa tgatcatttg gatcaattac aggcttttag
      301 ctggcttgtc tgtcataatt catgattcgg ggctgggaaa aagaccaaca gcctacgtgc
      361 caaaaaaggg gcagagtttg atggagttcg tggacttttc tgtgcggctc gcctccacac
      421 ctagaggata agcacttttg cagagcgcgg tgcggagaga tcatgtttga ctgtatggat
      481 gttctgtcag tgagtcccgg gcagatcctg gatttctaca ccgcgagccc ttcctcctgc
      541 atgctgcagg aaaaggctct caaagcctgc ctcagtggat tcacccaggc cgaatggcag
      601 caccggcata ctgctcaatc catcgagaca cagagtacca gctctgagga gctcgtcccg
      661 agcccaccat ctccacttcc tcctcctcgg gtgtacaagc cctgcttcgt ttgccaggac
      721 aagtcatcgg gctaccacta tggcgtcagt gcctgcgagg ggtgcaaggg ctttttccgc
      781 agaagtattc agaagaacat gatctacact tgccatcgag ataagaactg cgtcattaac
      841 aaggtcacta ggaaccgatg ccagtactgc cgcctgcaga agtgctttga agtgggcatg
      901 tccaaagagt ctgttaggaa tgacaggaac aagaaaaaga aggagccttc aaagcaggaa
      961 tgcacagaga gctatgagat gacagcggag ctagacgacc tcactgagaa gatccggaaa
     1021 gcccaccagg aaacctttcc ctcactctgc cagctgggta aatacaccac gaattccagc
     1081 gctgaccacc gggtccgatt ggacttgggc ctctgggaca aattcagtga gctggccacc
     1141 aagtgcatta ttaagatcgt ggagttcgcc aagcgtctgc cgggcttcac aggtctgacc
     1201 atcgcagacc agatcaccct gctcaaagcc gcctgcttgg atatcttgat tctcagaatt
     1261 tgtaccaggt ataccccaga gcaagacacc atgactttct ctgatggcct tacactaaat
     1321 cgaactcaga tgcacaatgc tggcttcggt cctctgactg accttgtgtt cacctttgcc
     1381 aaccagctcc tgcctttgga aatggatgac acagaaacag gccttctcag tgccatctgt
     1441 ttaatctgtg gagaccgcca ggaccttgag gaaccaacaa aagtagacaa gctccaagaa
     1501 ccactgctgg aagcactaaa gatttacatt agaaaacgac gacccagcaa gcctcacatg
     1561 tttccaaaga tcttaatgaa aatcacagat ctccgcagca tcagcgcgaa aggtgccgaa
     1621 cgtgtaatta ccttgaaaat ggaaattcct ggatcaatgc cacctctcat tcaggaaatg
     1681 ctggagaatt ctgaaggaca tgaacccttg accccaagtt caagtgggaa tatagcagag
     1741 cacagtccca gcgtgtcccc cagctcagtg gagaacagtg gagtcagtca gtcaccactg
     1801 ctgcagtgag acatttccag ctgttgcaga cattccccag gaccttcagt tccagattga
     1861 aaatgcaagg aaaacatttt tactgctgct tagtttttga actgaaatat gttaaactca
     1921 aaaaggacca agaagttttc atatgtatca atatatattc cttactgtat aacttcccta
     1981 gaaatacaaa cttttcaaat tctgaaaatc agccatttca tgccaccaga atctagttta
     2041 aagcttctac tttcctctct gaatagtcaa gatgcatggc aaagacccag ttgagatgat
     2101 ttagccctgg ttaagtttct gaagactttg tacatataga agtacggctc tgttctttct
     2161 atactgtatg ttggtgcttt cttttgtctt gcatactcaa taaccaagac accgaggttg
     2221 tggagtaaac cactgtacat ccactgtacg tcctgctttc atgaataacc aggcctcacg
     2281 gtaaggaacc agggcctctg tacagtacaa gatgacacta aagacactct ggtttaagta
     2341 gtgtggaagc ttctccttgc tttttgatgc tctcaagctt cattctttcc cttatgttgc
     2401 ccagatagag tacaccactt cactgcacta gcagaattct gtatcactga aactgccagt
     2461 tcagttaatc caacatcatt gttcaattgt taatgatgtc actttaaatt aaaagtggtt
     2521 tgttccttaa tgacacaact accgaatgaa aaaaaaaatg aagcattttt acagtcatga
     2581 tagcctccaa ggcaaaaaca ctgtccagtg ttaataagtt tgtttacctg ttcacaagcc
     2641 attggagaaa tatcacagga taatcagcaa gttagtctgc cgtctggact ctagtagccc
     2701 agtgtccttg ctgactcagg cctgatcctg ggatttcccc cagtcttgat gcttgaaggt
     2761 atgggcaagt ggcctcctct ggccttgttc aatcaccatg atgcagactg acagctctgg
     2821 gagaatgagt ggttgacaga ctcaagtgtc ggcttctgag ttctcatgta agcactagtg
     2881 gaatttttgt ttgttcgttt ttgatatatt agcaaaagtc tgtgatgtac cactagctct
     2941 gtttgtacat tgagatggtt taacagtgct ttctatgttc atatactgtt tacctttttc
     3001 catggagtct cctggcaaag aataaatata tttattttaa a
//
