LOCUS       NM_001291114            2803 bp    mRNA    linear   ROD 10-FEB-2025
DEFINITION  Mus musculus RNA binding motif protein 39 (Rbm39), transcript
            variant 2, mRNA.
ACCESSION   NM_001291114 XM_006498833
VERSION     NM_001291114.1
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 2803)
  AUTHORS   Bedogni,F. and Hevner,R.F.
  TITLE     Cell-Type-Specific Gene Expression in Developing Mouse Neocortex:
            Intermediate Progenitors Implicated in Axon Development
  JOURNAL   Front Mol Neurosci 14, 686034 (2021)
   PUBMED   34321999
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2803)
  AUTHORS   Zhou,J., Wang,R., Zhang,J., Zhu,L., Liu,W., Lu,S., Chen,P., Li,H.,
            Yin,B., Yuan,J., Qiang,B., Shu,P. and Peng,X.
  TITLE     Conserved expression of ultra-conserved noncoding RNA in mammalian
            nervous system
  JOURNAL   Biochim Biophys Acta Gene Regul Mech 1860 (12), 1159-1168 (2017)
   PUBMED   29055695
REFERENCE   3  (bases 1 to 2803)
  AUTHORS   Anderson,D.M., Cannavino,J., Li,H., Anderson,K.M., Nelson,B.R.,
            McAnally,J., Bezprozvannaya,S., Liu,Y., Lin,W., Liu,N.,
            Bassel-Duby,R. and Olson,E.N.
  TITLE     Severe muscle wasting and denervation in mice lacking the
            RNA-binding protein ZFP106
  JOURNAL   Proc Natl Acad Sci U S A 113 (31), E4494-E4503 (2016)
   PUBMED   27418600
REFERENCE   4  (bases 1 to 2803)
  AUTHORS   Faherty,N., Benson,M., Sharma,E., Lee,A., Howarth,A., Lockstone,H.,
            Ebner,D. and Bhattacharya,S.
  TITLE     Negative autoregulation of BMP dependent transcription by SIN3B
            splicing reveals a role for RBM39
  JOURNAL   Sci Rep 6, 28210 (2016)
   PUBMED   27324164
  REMARK    GeneRIF: this study shows that negative autoregulation of BMP4
            dependent transcription by SIN3B splicing reveals a role for RBM39
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2803)
  AUTHORS   Kang,Y.K., Putluri,N., Maity,S., Tsimelzon,A., Ilkayeva,O., Mo,Q.,
            Lonard,D., Michailidis,G., Sreekumar,A., Newgard,C.B., Wang,M.,
            Tsai,S.Y., Tsai,M.J. and O'Malley,B.W.
  TITLE     CAPER is vital for energy and redox homeostasis by integrating
            glucose-induced mitochondrial functions via ERR-alpha-Gabpa and
            stress-induced adaptive responses via NF-kappaB-cMYC
  JOURNAL   PLoS Genet 11 (4), e1005116 (2015)
   PUBMED   25830341
  REMARK    GeneRIF: CAPER integrates mitochondrial energy metabolism by
            coactivating ERR-alpha-Gabpa and stress-induced adaptive metabolic
            responses via NF- kappaB/c-Myc.
            Erratum:[PLoS Genet. 2015 Jun 15;11(6):e1005316. doi:
            10.1371/journal.pgen.1005316.. PMID: 26075908]
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2803)
  AUTHORS   Jensen,P., Magdaleno,S., Lehman,K.M., Rice,D.S., Lavallie,E.R.,
            Collins-Racie,L., McCoy,J.M. and Curran,T.
  TITLE     A neurogenomics approach to gene expression analysis in the
            developing brain
  JOURNAL   Brain Res Mol Brain Res 132 (2), 116-127 (2004)
   PUBMED   15582152
REFERENCE   7  (bases 1 to 2803)
  AUTHORS   Blackshaw,S., Harpavat,S., Trimarchi,J., Cai,L., Huang,H.,
            Kuo,W.P., Weber,G., Lee,K., Fraioli,R.E., Cho,S.H., Yung,R.,
            Asch,E., Ohno-Machado,L., Wong,W.H. and Cepko,C.L.
  TITLE     Genomic analysis of mouse retinal development
  JOURNAL   PLoS Biol 2 (9), E247 (2004)
   PUBMED   15226823
REFERENCE   8  (bases 1 to 2803)
  AUTHORS   Shu,H., Chen,S., Bi,Q., Mumby,M. and Brekken,D.L.
  TITLE     Identification of phosphoproteins and their phosphorylation sites
            in the WEHI-231 B lymphoma cell line
  JOURNAL   Mol Cell Proteomics 3 (3), 279-286 (2004)
   PUBMED   14729942
REFERENCE   9  (bases 1 to 2803)
  AUTHORS   Stryke,D., Kawamoto,M., Huang,C.C., Johns,S.J., King,L.A.,
            Harper,C.A., Meng,E.C., Lee,R.E., Yee,A., L'Italien,L.,
            Chuang,P.T., Young,S.G., Skarnes,W.C., Babbitt,P.C. and Ferrin,T.E.
  TITLE     BayGenomics: a resource of insertional mutations in mouse embryonic
            stem cells
  JOURNAL   Nucleic Acids Res 31 (1), 278-281 (2003)
   PUBMED   12520002
REFERENCE   10 (bases 1 to 2803)
  AUTHORS   Jung,D.J., Na,S.Y., Na,D.S. and Lee,J.W.
  TITLE     Molecular cloning and characterization of CAPER, a novel
            coactivator of activating protein-1 and estrogen receptors
  JOURNAL   J Biol Chem 277 (2), 1229-1234 (2002)
   PUBMED   11704680
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL929404.19, AK147076.1, AK135289.1 and BF465342.1.
            
            On Mar 26, 2014 this sequence version replaced XM_006498833.1.
            
            Transcript Variant: This variant (2) uses an alternate in-frame
            splice site in the central coding region, compared to variant 1,
            resulting in an isoform (b) that is shorter than isoform a. Both
            variants 2 and 3 encode isoform b.
            
            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 :: AK154989.1, SRR7345562.851021.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164139, SAMN01164140
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-56                AL929404.19        21883-21938         c
            57-374              AK147076.1         2-319
            375-2089            AK135289.1         1-1715
            2090-2783           AK147076.1         2053-2746
            2784-2803           BF465342.1         1-20                c
FEATURES             Location/Qualifiers
     source          1..2803
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 77.36 cM"
     gene            1..2803
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /note="RNA binding motif protein 39"
                     /db_xref="GeneID:170791"
                     /db_xref="MGI:MGI:2157953"
     exon            1..352
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            353..416
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     CDS             366..1940
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /note="isoform b is encoded by transcript variant 2;
                     coactivator of activating protein-1 and estrogen
                     receptors; RNA-binding region (RNP1, RRM) containing 2;
                     RNA-binding protein 39; coactivator of AP-1 and ERs;
                     transcription coactivator CAPER; RNA-binding
                     region-containing protein 2; Caper alpha"
                     /codon_start=1
                     /product="RNA-binding protein 39 isoform b"
                     /protein_id="NP_001278043.1"
                     /db_xref="CCDS:CCDS71168.1"
                     /db_xref="GeneID:170791"
                     /db_xref="MGI:MGI:2157953"
                     /translation="MADDIDIEAMLEAPYKKDENKLNSANGHEERSKKRKKSKSRSRS
                     HERKRSKSKERKRSRDRERKKSKSRERKRSRSKERRRSRSRSRDRRFRGRYRSPYSGP
                     KFNSAIRGKIGLPHSIKLSRRRSRSKSPFRKDKSPVREPIDNLTPEERDARTVFCMQL
                     AARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRV
                     LGVPIIVQASQAEKNRAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRI
                     ESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTDASS
                     ASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQMSGSLAFGAVAD
                     LQTRLSQQTEASALAAAASVQPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNK
                     HGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNL
                     FPDSMTATQLLVPSRR"
     exon            417..466
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            467..661
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            662..727
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            728..781
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            782..899
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            900..1052
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            1053..1190
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            1191..1256
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            1257..1461
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            1462..1539
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            1540..1572
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            1573..1654
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            1655..1760
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            1761..1839
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     exon            1840..2792
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2072..2077
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /note="hexamer: AATAAA"
     polyA_site      2091
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /note="major polyA site"
     regulatory      2761..2766
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
                     /note="hexamer: AATAAA"
     polyA_site      2792
                     /gene="Rbm39"
                     /gene_synonym="1500012C14Rik; 2310040E03Rik;
                     B330012G18Rik; caper; Rnpc2"
ORIGIN      
        1 gcgagagccc gtgcttgcgg ctccgggaga ccccgggtgt ttgtgtgtgt gtatgtgttg
       61 gtgactgtga gtacggagga gcagcggccg ccatttcagg gagctagccg acgctgtcgc
      121 aggggtggat cctgagctgc cgaagccgct gccctgctct ccgtcgcggg ctcctttaat
      181 cccattgttt cttttagatt cgcttgggcc tagacgccct cggggcccga tattcgggtt
      241 gggcggtacc gcggcctggg cctagtggct taacagtagc gacagcagca gcggcggcgg
      301 cggcggcagc cgacttcccg tggcgagcac aggcgcgcgg aagcccgcac aggcgagtag
      361 agaaaatggc agacgatatt gatattgaag ccatgcttga ggccccttac aagaaggatg
      421 agaacaagtt gaacagtgct aacggccatg aagaacgtag caaaaagaga aaaaaaagca
      481 agagcagaag tcgtagtcat gagagaaaaa gaagcaaaag taaagaacgg aaaagaagta
      541 gagatagaga aaggaaaaag agcaaaagtc gagagcggaa acgaagtaga agcaaagaaa
      601 ggagacgaag ccgctcacgc agtcgggata gaagattccg aggccgctac agaagtccct
      661 actccggacc aaaatttaac agtgccatcc gaggaaagat tggattgcct catagcatca
      721 aattaagcag aagacgttcc cgaagcaaaa gtccatttag gaaagacaag agccctgtga
      781 gggaacctat tgataatctc actcctgagg aaagggatgc aaggactgtt ttctgcatgc
      841 aactggcagc aagaattcga ccgagagatt tggaagagtt tttctctaca gttggaaagg
      901 ttcgagatgt gagaatgatt tctgatagaa attcaagacg ttccaaagga attgcatatg
      961 tggaatttgt tgatgtcagt tcagtgcctc tagcaattgg attaactggc caacgagttt
     1021 taggagtgcc aatcatagtt caggcatcac aggcagaaaa aaacagagct gctgcaatgg
     1081 caaacaattt acaaaaggga agtgctggac ctatgaggct ctatgtaggc tcattacact
     1141 ttaacataac tgaagacatg cttcggggga tctttgaacc ttttggaagg attgaaagta
     1201 ttcagctcat gatggatagt gaaactggcc gatctaaggg atatggattt attacatttt
     1261 ctgactcaga atgtgccaaa aaggctttgg aacaactgaa tggatttgag ttagctggga
     1321 gaccaatgaa agttggtcac gttactgaac gaactgatgc ttcgagtgct agttcatttt
     1381 tggacagtga cgaactagaa aggactggaa ttgacttggg aacaactgga cgtcttcagt
     1441 taatggcaag acttgcggag ggtaccggtt tgcagattcc acctgccgca caacaagcat
     1501 tacaaatgag tggctctctg gcatttggtg ctgtggcaga tttgcaaaca cgactttccc
     1561 aacagaccga agcctcagct ttagctgcag ctgcgtctgt tcaacctctt gcaacacagt
     1621 gtttccaact ttctaacatg tttaatcctc aaacagaaga agaagttgga tgggatacag
     1681 agattaaaga tgatgtcatt gaagaatgta ataaacatgg aggagtcatt catatttatg
     1741 ttgataaaaa ttcagctcag ggcaatgtgt atgtgaagtg cccatctatt gctgcggcta
     1801 ttgctgctgt caatgcattg catggcagat ggtttgctgg taaaatgata acagcagcgt
     1861 atgtacctct tccaacttac cacaacctct ttcctgattc tatgacagca acacaactac
     1921 tggttccaag tagacgatga aggaagatac agtcccttat gtatatagct tttttttctc
     1981 ttgagaattc atcttgagtt atcttttatt tagataaaat aaagaggcaa gggtctactg
     2041 tcatttgtat acaactcctg ttaccttgaa aaataaaaat gttaacagga atgcagtgtg
     2101 ctcattatcc ctaactagca aatcctactt tatgcaaagc tgttctcttg ttctgctgtt
     2161 ttaaatgtcc atgtagaaaa tgacattaag gatctataga atagctctag gggaacaaat
     2221 gtgctttctg tataaaggca gacaggtcac gttttaatgt ttcagaaacc taacttttta
     2281 cacagcagtt acaattcaca ttcatgtatt tggctcatgg ttcagcaaag gtttccagaa
     2341 tccacattta gtgtgtgaaa agtctaagtg gctgtatggc tgcttggcat ttgatcttga
     2401 ttatttggca agaatgggat ttcaaaataa tatttctcga tggtaatttt ttcaattaat
     2461 gtctctgtaa aagtttcttt gtaaatactg tatgttttag tgtgtcttga gattccaaac
     2521 aaaatgatcc ctgcatttcc tcaaggtggc tgacgtaaca gattgagtaa gcagtcttgg
     2581 gcaagagatg ggaaatgcag aaaaaggttt tgtctggttg catataatct ttgctctttt
     2641 taagctctgt gagctctgaa atatattttt gggttacttc agtgtgtttg acaagacagc
     2701 ttgatatttc tatcaaacaa atgactttca tattgcaaca atctttgtaa gaaccactca
     2761 aataaaattc tctgaaaaag gccacaagaa aaaaaaaaaa aaa
//
