LOCUS       NM_001394394            1104 bp    mRNA    linear   ROD 03-APR-2024
DEFINITION  Rattus norvegicus Aly/REF export factor (Alyref), transcript
            variant 1, mRNA.
ACCESSION   NM_001394394 XM_006247925
VERSION     NM_001394394.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 1104)
  AUTHORS   Yang,X., Yang,Y., Sun,B.F., Chen,Y.S., Xu,J.W., Lai,W.Y., Li,A.,
            Wang,X., Bhattarai,D.P., Xiao,W., Sun,H.Y., Zhu,Q., Ma,H.L.,
            Adhikari,S., Sun,M., Hao,Y.J., Zhang,B., Huang,C.M., Huang,N.,
            Jiang,G.B., Zhao,Y.L., Wang,H.L., Sun,Y.P. and Yang,Y.G.
  TITLE     5-methylcytosine promotes mRNA export - NSUN2 as the
            methyltransferase and ALYREF as an m5C reader
  JOURNAL   Cell Res 27 (5), 606-625 (2017)
   PUBMED   28418038
REFERENCE   2  (bases 1 to 1104)
  AUTHORS   Viphakone,N., Cumberbatch,M.G., Livingstone,M.J., Heath,P.R.,
            Dickman,M.J., Catto,J.W. and Wilson,S.A.
  TITLE     Luzp4 defines a new mRNA export pathway in cancer cells
  JOURNAL   Nucleic Acids Res 43 (4), 2353-2366 (2015)
   PUBMED   25662211
REFERENCE   3  (bases 1 to 1104)
  AUTHORS   Grolimund,L., Aeby,E., Hamelin,R., Armand,F., Chiappe,D.,
            Moniatte,M. and Lingner,J.
  TITLE     A quantitative telomeric chromatin isolation protocol identifies
            different telomeric states
  JOURNAL   Nat Commun 4, 2848 (2013)
   PUBMED   24270157
REFERENCE   4  (bases 1 to 1104)
  AUTHORS   Baltz,A.G., Munschauer,M., Schwanhausser,B., Vasile,A.,
            Murakawa,Y., Schueler,M., Youngs,N., Penfold-Brown,D., Drew,K.,
            Milek,M., Wyler,E., Bonneau,R., Selbach,M., Dieterich,C. and
            Landthaler,M.
  TITLE     The mRNA-bound proteome and its global occupancy profile on
            protein-coding transcripts
  JOURNAL   Mol Cell 46 (5), 674-690 (2012)
   PUBMED   22681889
REFERENCE   5  (bases 1 to 1104)
  AUTHORS   Castello,A., Fischer,B., Eichelbaum,K., Horos,R., Beckmann,B.M.,
            Strein,C., Davey,N.E., Humphreys,D.T., Preiss,T., Steinmetz,L.M.,
            Krijgsveld,J. and Hentze,M.W.
  TITLE     Insights into RNA biology from an atlas of mammalian mRNA-binding
            proteins
  JOURNAL   Cell 149 (6), 1393-1406 (2012)
   PUBMED   22658674
REFERENCE   6  (bases 1 to 1104)
  AUTHORS   Foster,L.J., Zeemann,P.A., Li,C., Mann,M., Jensen,O.N. and
            Kassem,M.
  TITLE     Differential expression profiling of membrane proteins by
            quantitative proteomics in a human mesenchymal stem cell line
            undergoing osteoblast differentiation
  JOURNAL   Stem Cells 23 (9), 1367-1377 (2005)
   PUBMED   16210410
REFERENCE   7  (bases 1 to 1104)
  AUTHORS   Masuda,S., Das,R., Cheng,H., Hurt,E., Dorman,N. and Reed,R.
  TITLE     Recruitment of the human TREX complex to mRNA during splicing
  JOURNAL   Genes Dev 19 (13), 1512-1517 (2005)
   PUBMED   15998806
REFERENCE   8  (bases 1 to 1104)
  AUTHORS   Guo,S., Hakimi,M.A., Baillat,D., Chen,X., Farber,M.J.,
            Klein-Szanto,A.J., Cooch,N.S., Godwin,A.K. and Shiekhattar,R.
  TITLE     Linking transcriptional elongation and messenger RNA export to
            metastatic breast cancers
  JOURNAL   Cancer Res 65 (8), 3011-3016 (2005)
   PUBMED   15833825
REFERENCE   9  (bases 1 to 1104)
  AUTHORS   Jurica,M.S., Licklider,L.J., Gygi,S.R., Grigorieff,N. and
            Moore,M.J.
  TITLE     Purification and characterization of native spliceosomes suitable
            for three-dimensional structural analysis
  JOURNAL   RNA 8 (4), 426-439 (2002)
   PUBMED   11991638
REFERENCE   10 (bases 1 to 1104)
  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
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000010.1.
            
            On Apr 18, 2021 this sequence version replaced XM_006247925.4.
            
            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 :: SRR23984936.72938.1,
                                           SRR26643290.38387.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN12840111, SAMN12840115
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-264               JAXUCZ010000010.1  106373132-106373395 c
            265-396             JAXUCZ010000010.1  106372642-106372773 c
            397-544             JAXUCZ010000010.1  106371132-106371279 c
            545-608             JAXUCZ010000010.1  106370476-106370539 c
            609-783             JAXUCZ010000010.1  106370194-106370368 c
            784-1104            JAXUCZ010000010.1  106369750-106370070 c
FEATURES             Location/Qualifiers
     source          1..1104
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="10"
                     /map="10q32.3"
     gene            1..1104
                     /gene="Alyref"
                     /gene_synonym="Thoc4"
                     /note="Aly/REF export factor"
                     /db_xref="GeneID:690585"
                     /db_xref="RGD:1594679"
     exon            1..264
                     /gene="Alyref"
                     /gene_synonym="Thoc4"
                     /inference="alignment:Splign:2.1.0"
     CDS             28..798
                     /gene="Alyref"
                     /gene_synonym="Thoc4"
                     /note="THO complex 4"
                     /codon_start=1
                     /product="THO complex subunit 4"
                     /protein_id="NP_001381323.1"
                     /db_xref="GeneID:690585"
                     /db_xref="RGD:1594679"
                     /translation="MADKMDMSLDDIIKLNRSQRGGRGGGRGRGRAGSQGGRGGAVQA
                     AARVNRGGGPMRNRPAIARGAAGGGGRNRPAPYSRPKQLPDKWQHDLFDSGFGGGAGV
                     ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADAL
                     KAMKQYNGVPLDGRPMNIQLVTSQIDTQRRPAQSINRGGMTRNRGSGSFGGGGTRRGT
                     RGGSRGRGRGTGRNSKQQLSAEELDAQLDAYNARMDTS"
     exon            265..396
                     /gene="Alyref"
                     /gene_synonym="Thoc4"
                     /inference="alignment:Splign:2.1.0"
     exon            397..544
                     /gene="Alyref"
                     /gene_synonym="Thoc4"
                     /inference="alignment:Splign:2.1.0"
     exon            545..608
                     /gene="Alyref"
                     /gene_synonym="Thoc4"
                     /inference="alignment:Splign:2.1.0"
     exon            609..783
                     /gene="Alyref"
                     /gene_synonym="Thoc4"
                     /inference="alignment:Splign:2.1.0"
     exon            784..1104
                     /gene="Alyref"
                     /gene_synonym="Thoc4"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gatacgaggc 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 cggcggcagg
      241 aaccgaccgg caccatacag cagaccgaaa caacttcccg acaagtggca gcacgaccta
      301 ttcgacagcg gcttcggggg tggagccggc gtggagacgg gtgggaagct gcttgtgtca
      361 aacctggatt tcggagtgtc agacgctgat attcaggaac tgtttgccga gtttggaacg
      421 ttgaaaaaag ctgctgtgca ctatgatcgc tctggacgaa gtttagggac agcagatgta
      481 cactttgaac ggaaagcaga tgccctgaag gctatgaaac agtacaatgg tgtccctttg
      541 gatggccgcc ctatgaacat ccagcttgtc acatcacaga ttgatacaca acgaagacct
      601 gcacagagca taaacagagg tggcatgaca agaaaccgtg gttctggcag ttttggtggt
      661 ggcggcacca ggagaggcac tcgtggaggc agccggggaa gaggtagagg taccggcagg
      721 aactcaaagc agcagctttc tgcagaggag ttggacgcac agctggatgc ttacaatgca
      781 aggatggaca ccagctaaac aaccaagcaa atccgcacaa gtaacaggac ccagaagcct
      841 cgtcttgacg cctagaggga gggttggcaa ctggactgtg cagacaatgg tggatttgtt
      901 tttgtttgtt tctttttttt ttcctgtttt aaataggatc taaaaaactc atgtaaaggt
      961 ttttttttcc cccctttttt tttttttttt aattctgaaa cagacctgtt ttgtactgag
     1021 ttattttggg ataaatttta ctggttgctg ttgtggagaa ggtggcattt tcacctttgc
     1081 cataataaaa tagaaatgtg tgta
//
