LOCUS       NM_011568               1132 bp    mRNA    linear   ROD 09-FEB-2025
DEFINITION  Mus musculus Aly/REF export factor (Alyref), mRNA.
ACCESSION   NM_011568
VERSION     NM_011568.1
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 1132)
  AUTHORS   Bhattacharjee,R., Jolly,L.A., Corbett,M.A., Wee,I.C., Rao,S.R.,
            Gardner,A.E., Ritchie,T., van Hugte,E.J.H., Ciptasari,U., Piltz,S.,
            Noll,J.E., Nazri,N., van Eyk,C.L., White,M., Fornarino,D.,
            Poulton,C., Baynam,G., Collins-Praino,L.E., Snel,M.F., Nadif
            Kasri,N., Hemsley,K.M., Thomas,P.Q., Kumar,R. and Gecz,J.
  TITLE     Compromised transcription-mRNA export factor THOC2 causes R-loop
            accumulation, DNA damage and adverse neurodevelopment
  JOURNAL   Nat Commun 15 (1), 1210 (2024)
   PUBMED   38331934
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1132)
  AUTHORS   Ihashi,S., Hamanaka,M., Kaji,M., Mori,R., Nishizaki,S., Mori,M.,
            Imasato,Y., Inoue,K., Matoba,S., Ogonuki,N., Takasu,A.,
            Nakamura,M., Matsumoto,K., Anzai,M., Ogura,A., Ikawa,M. and
            Miyamoto,K.
  TITLE     Incomplete activation of Alyref and Gabpb1 leads to preimplantation
            arrest in cloned mouse embryos
  JOURNAL   Life Sci Alliance 6 (11), e202302296 (2023)
   PUBMED   37640449
  REMARK    GeneRIF: Incomplete activation of Alyref and Gabpb1 leads to
            preimplantation arrest in cloned mouse embryos.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1132)
  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   4  (bases 1 to 1132)
  AUTHORS   Yamada,R., Oguri,A., Fujiki,K., Shirahige,K., Takezoe,H.,
            Takahashi,N. and Kanai,Y.
  TITLE     Single-cell transcriptional analysis reveals developmental
            stage-dependent changes in retinal progenitors in the murine early
            optic vesicle
  JOURNAL   Biochem Biophys Res Commun 543, 80-86 (2021)
   PUBMED   33548738
REFERENCE   5  (bases 1 to 1132)
  AUTHORS   Rong,Y., Ji,S.Y., Zhu,Y.Z., Wu,Y.W., Shen,L. and Fan,H.Y.
  TITLE     ZAR1 and ZAR2 are required for oocyte meiotic maturation by
            regulating the maternal transcriptome and mRNA translational
            activation
  JOURNAL   Nucleic Acids Res 47 (21), 11387-11402 (2019)
   PUBMED   31598710
REFERENCE   6  (bases 1 to 1132)
  AUTHORS   Cheung,C.C., Martin,I.C., Zenger,K.R., Donald,J.A., Thomson,P.C.,
            Moran,C. and Buckley,M.F.
  TITLE     Quantitative trait loci for steady-state platelet count in mice
  JOURNAL   Mamm Genome 15 (10), 784-797 (2004)
   PUBMED   15520881
REFERENCE   7  (bases 1 to 1132)
  AUTHORS   Perez-Alvarado,G.C., Martinez-Yamout,M., Allen,M.M., Grosschedl,R.,
            Dyson,H.J. and Wright,P.E.
  TITLE     Structure of the nuclear factor ALY: insights into
            post-transcriptional regulatory and mRNA nuclear export processes
  JOURNAL   Biochemistry 42 (24), 7348-7357 (2003)
   PUBMED   12809490
  REMARK    GeneRIF: Structure of the nuclear factor ALY provides insights into
            post-transcriptional regulatory and mRNA nuclear export processes.
REFERENCE   8  (bases 1 to 1132)
  AUTHORS   Lejeune,F., Ishigaki,Y., Li,X. and Maquat,L.E.
  TITLE     The exon junction complex is detected on CBP80-bound but not
            eIF4E-bound mRNA in mammalian cells: dynamics of mRNP remodeling
  JOURNAL   EMBO J 21 (13), 3536-3545 (2002)
   PUBMED   12093754
REFERENCE   9  (bases 1 to 1132)
  AUTHORS   Stutz,F., Bachi,A., Doerks,T., Braun,I.C., Seraphin,B., Wilm,M.,
            Bork,P. and Izaurralde,E.
  TITLE     REF, an evolutionary conserved family of hnRNP-like proteins,
            interacts with TAP/Mex67p and participates in mRNA nuclear export
  JOURNAL   RNA 6 (4), 638-650 (2000)
   PUBMED   10786854
REFERENCE   10 (bases 1 to 1132)
  AUTHORS   Bruhn,L., Munnerlyn,A. and Grosschedl,R.
  TITLE     ALY, a context-dependent coactivator of LEF-1 and AML-1, is
            required for TCRalpha enhancer function
  JOURNAL   Genes Dev 11 (5), 640-653 (1997)
   PUBMED   9119228
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            U89876.1.
            
            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 :: U89876.1, CB201594.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164138, SAMN01164139
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
FEATURES             Location/Qualifiers
     source          1..1132
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /db_xref="taxon:10090"
                     /chromosome="11"
                     /map="11 84.31 cM"
     gene            1..1132
                     /gene="Alyref"
                     /gene_synonym="Aly; Ref1; Ref1-I; Refbp1; Tho4; Thoc4"
                     /note="Aly/REF export factor"
                     /db_xref="GeneID:21681"
                     /db_xref="MGI:MGI:1341044"
     exon            1..261
                     /gene="Alyref"
                     /gene_synonym="Aly; Ref1; Ref1-I; Refbp1; Tho4; Thoc4"
                     /inference="alignment:Splign:2.1.0"
     CDS             28..795
                     /gene="Alyref"
                     /gene_synonym="Aly; Ref1; Ref1-I; Refbp1; Tho4; Thoc4"
                     /function="transcriptional coactivator"
                     /note="Tcra enhancer-binding factor interacting protein 1;
                     RNA and export factor binding protein 1; ally of AML-1 and
                     LEF-1; transcriptional coactivator Aly/REF; THO complex 4"
                     /codon_start=1
                     /product="THO complex subunit 4"
                     /protein_id="NP_035698.1"
                     /db_xref="CCDS:CCDS25744.1"
                     /db_xref="GeneID:21681"
                     /db_xref="MGI:MGI:1341044"
                     /translation="MADKMDMSLDDIIKLNRSQRGGRGGGRGRGRAGSQGGRGGAVQA
                     AARVNRGGGPMRNRPAIARGAAGGGRNRPAPYSRPKQLPDKWQHDLFDSGFGGGAGVE
                     TGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALK
                     AMKQYNGVPLDGRPMNIQLVTSQIDTQRRPAQSINRGGMTRNRGSGGFGGGGTRRGTR
                     GGSRGRGRGTGRNSKQQLSAEELDAQLDAYNARMDTS"
     exon            262..393
                     /gene="Alyref"
                     /gene_synonym="Aly; Ref1; Ref1-I; Refbp1; Tho4; Thoc4"
                     /inference="alignment:Splign:2.1.0"
     exon            394..541
                     /gene="Alyref"
                     /gene_synonym="Aly; Ref1; Ref1-I; Refbp1; Tho4; Thoc4"
                     /inference="alignment:Splign:2.1.0"
     exon            542..605
                     /gene="Alyref"
                     /gene_synonym="Aly; Ref1; Ref1-I; Refbp1; Tho4; Thoc4"
                     /inference="alignment:Splign:2.1.0"
     exon            606..780
                     /gene="Alyref"
                     /gene_synonym="Aly; Ref1; Ref1-I; Refbp1; Tho4; Thoc4"
                     /inference="alignment:Splign:2.1.0"
     exon            781..1132
                     /gene="Alyref"
                     /gene_synonym="Aly; Ref1; Ref1-I; Refbp1; Tho4; Thoc4"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gatccgaggc ccgaatccgc gcccgccatg gccgacaaaa tggacatgtc tttggacgac
       61 atcattaagc tgaaccggag ccagcgagga ggccgcggcg ggggccgggg tcgcggcagg
      121 gccggctccc agggcggccg cggcggcgca gtgcaggccg ccgcgcgggt gaatcgaggc
      181 ggcgggccta tgaggaaccg gcccgccatc gcccgcggcg ccgcaggcgg cggcaggaac
      241 cggccggcgc cgtacagcag accgaaacaa cttcccgaca aatggcagca cgacctcttc
      301 gacagcggct tcgggggtgg agccggcgtg gagaccggcg ggaagctgct ggtgtccaac
      361 ctggacttcg gagtgtcaga tgctgatatt caggaactct ttgctgaatt tgggacattg
      421 aaaaaagctg ctgtgcacta tgatcgctct ggacgaagtt tagggacagc agatgtgcac
      481 tttgaacgga aagcagatgc cctgaaggct atgaaacagt acaatggtgt ccctttggat
      541 ggccgcccta tgaacatcca gcttgtcaca tcacagattg atacacagcg aagacctgca
      601 cagagcataa acagaggcgg catgacaaga aaccgtggct ctggaggttt tggtggtggt
      661 ggcaccagga gagggacacg tggaggcagc cggggaagag gtagaggcac cggcaggaac
      721 tcaaagcagc agctttctgc agaggagttg gacgcacagc tggatgctta caatgcaagg
      781 atggacacca gctaaacaac tgagcaaatc cacacaagta acaggaccca gaagcctcgc
      841 ctgtgatgcc tagagggagg gttggcaact gaactgtgca gacaatggtg gatttgtttt
      901 gtttcttttt atttcttttc tttttttttt tcttcctgtt ttaaaatagg atctaaaaac
      961 tcatgtaaag tttttttttt tttctttttt ggtttttgtt ttgttttttg tttttttttt
     1021 taattctgaa acagacctgt tttgtactga gttatttttg ggataaatat tactggttgc
     1081 tgttgtggag aaggtggcat tttcaccttt gccataataa aatagaaatg tg
//
