LOCUS       NM_001139513            1759 bp    mRNA    linear   ROD 21-DEC-2022
DEFINITION  Mus musculus hnRNP-associated with lethal yellow (Raly), transcript
            variant 1, mRNA.
ACCESSION   NM_001139513
VERSION     NM_001139513.1
KEYWORDS    RefSeq.
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 1759)
  AUTHORS   Pan Z, Du S, Wang K, Guo X, Mao Q, Feng X, Huang L, Wu S, Hou B,
            Chang YJ, Liu T, Chen T, Li H, Bachmann T, Bekker A, Hu H and Tao
            YX.
  TITLE     Downregulation of a Dorsal Root Ganglion-Specifically Enriched Long
            Noncoding RNA is Required for Neuropathic Pain by Negatively
            Regulating RALY-Triggered Ehmt2 Expression
  JOURNAL   Adv Sci (Weinh) 8 (13), e2004515 (2021)
   PUBMED   34383386
  REMARK    GeneRIF: Downregulation of a Dorsal Root Ganglion-Specifically
            Enriched Long Noncoding RNA is Required for Neuropathic Pain by
            Negatively Regulating RALY-Triggered Ehmt2 Expression.
REFERENCE   2  (bases 1 to 1759)
  AUTHORS   Zhang Z, Feng AC, Salisbury D, Liu X, Wu X, Kim J, Lapina I, Wang
            D, Lee B, Fraga J, Pan C, Williams KJ, Lusis AJ, Scumpia P and
            Sallam T.
  TITLE     Collaborative interactions of heterogenous ribonucleoproteins
            contribute to transcriptional regulation of sterol metabolism in
            mice
  JOURNAL   Nat Commun 11 (1), 984 (2020)
   PUBMED   32080181
  REMARK    GeneRIF: Liver-specific deletion of RALY alters hepatic lipid
            content and serum cholesterol level. RALY binds the promoter region
            of the master metabolic regulator Srebp2 and show that it directly
            interacts with coactivator Nuclear Transcription Factor Y (NFY) to
            influence cholesterogenic gene expression.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1759)
  AUTHORS   Gasperini L, Rossi A, Cornella N, Peroni D, Zuccotti P, Potrich V,
            Quattrone A and Macchi P.
  TITLE     The hnRNP RALY regulates PRMT1 expression and interacts with the
            ALS-linked protein FUS: implication for reciprocal cellular
            localization
  JOURNAL   Mol Biol Cell 29 (26), 3067-3081 (2018)
   PUBMED   30354839
REFERENCE   4  (bases 1 to 1759)
  AUTHORS   Sallam T, Jones MC, Gilliland T, Zhang L, Wu X, Eskin A, Sandhu J,
            Casero D, Vallim TQ, Hong C, Katz M, Lee R, Whitelegge J and
            Tontonoz P.
  TITLE     Feedback modulation of cholesterol metabolism by the
            lipid-responsive non-coding RNA LeXis
  JOURNAL   Nature 534 (7605), 124-128 (2016)
   PUBMED   27251289
REFERENCE   5  (bases 1 to 1759)
  AUTHORS   Pohlmeier WE, Xie F, Kurz SG, Lu N and Wood JR.
  TITLE     Progressive obesity alters the steroidogenic response to ovulatory
            stimulation and increases the abundance of mRNAs stored in the
            ovulated oocyte
  JOURNAL   Mol Reprod Dev 81 (8), 735-747 (2014)
   PUBMED   24824196
REFERENCE   6  (bases 1 to 1759)
  AUTHORS   Stryke D, Kawamoto M, Huang CC, Johns SJ, King LA, Harper CA, Meng
            EC, Lee RE, Yee A, L'Italien L, Chuang PT, Young SG, Skarnes WC,
            Babbitt PC and Ferrin TE.
  TITLE     BayGenomics: a resource of insertional mutations in mouse embryonic
            stem cells
  JOURNAL   Nucleic Acids Res 31 (1), 278-281 (2003)
   PUBMED   12520002
REFERENCE   7  (bases 1 to 1759)
  AUTHORS   Khrebtukova I, Kuklin A, Woychik RP and Michaud EJ.
  TITLE     Alternative processing of the human and mouse raly genes(1)
  JOURNAL   Biochim Biophys Acta 1447 (1), 107-112 (1999)
   PUBMED   10500250
REFERENCE   8  (bases 1 to 1759)
  AUTHORS   Duhl DM, Stevens ME, Vrieling H, Saxon PJ, Miller MW, Epstein CJ
            and Barsh GS.
  TITLE     Pleiotropic effects of the mouse lethal yellow (Ay) mutation
            explained by deletion of a maternally expressed gene and the
            simultaneous production of agouti fusion RNAs
  JOURNAL   Development 120 (6), 1695-1708 (1994)
   PUBMED   8050375
REFERENCE   9  (bases 1 to 1759)
  AUTHORS   Michaud EJ, Bultman SJ, Klebig ML, van Vugt MJ, Stubbs LJ, Russell
            LB and Woychik RP.
  TITLE     A molecular model for the genetic and phenotypic characteristics of
            the mouse lethal yellow (Ay) mutation
  JOURNAL   Proc Natl Acad Sci U S A 91 (7), 2562-2566 (1994)
   PUBMED   8146154
REFERENCE   10 (bases 1 to 1759)
  AUTHORS   Michaud EJ, Bultman SJ, Stubbs LJ and Woychik RP.
  TITLE     The embryonic lethality of homozygous lethal yellow mice (Ay/Ay) is
            associated with the disruption of a novel RNA-binding protein
  JOURNAL   Genes Dev 7 (7A), 1203-1213 (1993)
   PUBMED   8319910
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            CO812619.1, CX214615.1, L17076.1 and CF424086.1.
            
            [WARNING] On May 6, 2023 this sequence was replaced by
            NM_001139513.2.
            
            Transcript Variant: This variant (1) encodes the longer isoform.
            
            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##
            RNAseq introns :: single sample supports all introns SAMN00849374,
                              SAMN00849375 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-257               CO812619.1         14-270
            258-846             CX214615.1         1-589
            847-1744            L17076.1           612-1509
            1745-1759           CF424086.1         79-93
FEATURES             Location/Qualifiers
     source          1..1759
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 76.83 cM"
     gene            1..1759
                     /gene="Raly"
                     /gene_synonym="Merc"
                     /note="hnRNP-associated with lethal yellow"
                     /db_xref="GeneID:19383"
                     /db_xref="MGI:MGI:97850"
     exon            1..439
                     /gene="Raly"
                     /gene_synonym="Merc"
                     /inference="alignment:Splign:2.1.0"
     exon            440..704
                     /gene="Raly"
                     /gene_synonym="Merc"
                     /inference="alignment:Splign:2.1.0"
     CDS             449..1387
                     /gene="Raly"
                     /gene_synonym="Merc"
                     /note="long isoform is encoded by transcript variant 1;
                     RNA-binding protein Raly; hnRNP associated with lethal
                     yellow protein; maternally-expressed hnRNP C-related
                     protein"
                     /codon_start=1
                     /product="RNA-binding protein Raly long isoform"
                     /protein_id="NP_001132985.1"
                     /db_xref="CCDS:CCDS50767.1"
                     /db_xref="GeneID:19383"
                     /db_xref="MGI:MGI:97850"
                     /translation="MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSK
                     YGRVAGCSVHKGYAFVQYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLK
                     RAATAIYSGYSFDYDYYQDYFCARLFDYRGRLSPVPVPRAVPVKRPRVTVPLVRRVKT
                     TIPVKLFARSTAVTTGSAKIKLKSSELQTIKTELTQIKSNIDALLGRLEQIAEEQKAN
                     PDGKKKGDSSSGGGGGSSGGGGSSNVGGGSSGGSGSCSSSSRLPAPQEDTASEAGTPQ
                     GEVQTRDDGDEEGLLTHSEEELEHSQDTDAEDGALQ"
     exon            705..777
                     /gene="Raly"
                     /gene_synonym="Merc"
                     /inference="alignment:Splign:2.1.0"
     exon            778..825
                     /gene="Raly"
                     /gene_synonym="Merc"
                     /inference="alignment:Splign:2.1.0"
     exon            826..992
                     /gene="Raly"
                     /gene_synonym="Merc"
                     /inference="alignment:Splign:2.1.0"
     exon            993..1106
                     /gene="Raly"
                     /gene_synonym="Merc"
                     /inference="alignment:Splign:2.1.0"
     exon            1107..1342
                     /gene="Raly"
                     /gene_synonym="Merc"
                     /inference="alignment:Splign:2.1.0"
     exon            1343..1391
                     /gene="Raly"
                     /gene_synonym="Merc"
                     /inference="alignment:Splign:2.1.0"
     exon            1392..1759
                     /gene="Raly"
                     /gene_synonym="Merc"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gcccggcgcg aggggtgtgc agggagccca cgcgtttgga gagcccggcc cgtgcagggc
       61 ggcgctgggg actgagtgct cgggtggcag gatcctattc ggaggaccga gaggagaacc
      121 gggtaggagc cggggcggcg ggcaggccga gtgcagacgc ctgtccagca ctccccctcc
      181 ccgcgctcgc cccattggtg gcggccgagc gaaggactcg cggctgcggg gctcgcgcct
      241 ctgtcagtgc ggcggggcgc gcgagcggcg cggggtgcgg agccgaggga agccgagggg
      301 gcggaagcgg tcgcgactct cgcgcgtgtg ctcgggctcc tcacgcggcg gccagggccg
      361 cctcttccct cccgccctcc gagagcagac gcgccgtcgc ccttcggtgc cgcgcggctt
      421 cctccagacc tcggcgcggg tgaacaccat gtccttgaag attcagacca gcaatgtaac
      481 caacaagaat gaccctaagt ccatcaactc tcgggtcttc atcggaaatc taaacacagc
      541 tgtggtgaag aagtcagatg tggagaccat cttttccaag tacggccgag tggctggttg
      601 ctctgtgcac aaaggctatg cttttgtcca gtatgccaat gagcgccatg cccgggcagc
      661 tgtgctggga gagaatgggc gggtgctggc tggacagacc ctggacatca acatggctgg
      721 agagcccaag cctaatagac ccaaggggct aaagagagca gcaactgcca tctacagtgg
      781 ctacagcttt gactatgatt actaccaaga ctacttctgt gccaggctgt ttgattatcg
      841 aggccgcctt tctccagtgc ctgtgcccag ggcagttccg gtgaagcgac cccgtgttac
      901 agtccctttg gttcgccgtg tcaaaactac gatacctgtc aagctctttg cccgctccac
      961 agctgtcact actggctcag ccaaaatcaa gttaaagagc agtgagctac agaccatcaa
     1021 aacagagctg acacagatca agtccaacat cgatgccctg ttgggtcgct tggaacagat
     1081 tgctgaggaa cagaaggcca acccagatgg caagaagaag ggtgacagca gcagtggtgg
     1141 aggaggaggc agcagtggtg gaggcggcag tagcaatgtt ggtggtggca gcagcggcgg
     1201 cagcgggagc tgcagcagca gcagccggct accagcgccc caagaagaca cggcttctga
     1261 ggcaggcaca ccccaaggag aagtccaaac tcgagatgat ggtgatgagg agggactgct
     1321 aacacatagc gaggaggagc tggagcacag ccaggacaca gatgcagaag atggagcctt
     1381 gcagtaagca gcttaacagg agcattggcc accagcagaa gggcatcact gtctcaggcc
     1441 tcaagccagg cacccatctc tggatgccag tctatagcgg gtaccagagg aaagctggca
     1501 gcagtaactc tctccccatg catcctagcc agtgagtgct acatcctttg caagtggagt
     1561 tactggccta cccttacccc atgcattctt cctgtctgca ctgcctgggc caaggggcag
     1621 aaacactctg ctcttcttcc ccaggacatt cccaggcttg gggtttttct ataggtttga
     1681 aagtaaaggg gggagggtgg gaagggtggg aggaacctga caataaagag attggatcca
     1741 aatatgctct gaggtggaa
//
