LOCUS       NM_001165901            1312 bp    mRNA    linear   ROD 03-APR-2024
DEFINITION  Rattus norvegicus negative elongation factor complex member E
            (Nelfe), transcript variant 2, mRNA.
ACCESSION   NM_001165901
VERSION     NM_001165901.1
KEYWORDS    RefSeq.
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 1312)
  AUTHORS   Bastide,M.F., Bido,S., Duteil,N. and Bezard,E.
  TITLE     Striatal NELF-mediated RNA polymerase II stalling controls L-dopa
            induced dyskinesia
  JOURNAL   Neurobiol Dis 85, 93-98 (2016)
   PUBMED   26480869
  REMARK    GeneRIF: NELF-mediated RNA polymerase II stalling plays a key role
            in L-Dopa-induced dyskinesia pathophysiology
REFERENCE   2  (bases 1 to 1312)
  AUTHORS   Kwak,H. and Lis,J.T.
  TITLE     Control of transcriptional elongation
  JOURNAL   Annu Rev Genet 47, 483-508 (2013)
   PUBMED   24050178
  REMARK    Review article
REFERENCE   3  (bases 1 to 1312)
  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   4  (bases 1 to 1312)
  AUTHORS   Flynn,R.A., Almada,A.E., Zamudio,J.R. and Sharp,P.A.
  TITLE     Antisense RNA polymerase II divergent transcripts are P-TEFb
            dependent and substrates for the RNA exosome
  JOURNAL   Proc Natl Acad Sci U S A 108 (26), 10460-10465 (2011)
   PUBMED   21670248
REFERENCE   5  (bases 1 to 1312)
  AUTHORS   Saha,R.N., Wissink,E.M., Bailey,E.R., Zhao,M., Fargo,D.C.,
            Hwang,J.Y., Daigle,K.R., Fenn,J.D., Adelman,K. and Dudek,S.M.
  TITLE     Rapid activity-induced transcription of Arc and other IEGs relies
            on poised RNA polymerase II
  JOURNAL   Nat Neurosci 14 (7), 848-856 (2011)
   PUBMED   21623364
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1312)
  AUTHORS   Fujita,T., Piuz,I. and Schlegel,W.
  TITLE     Transcription elongation factors are involved in programming
            hormone production in pituitary neuroendocrine GH4C1 cells
  JOURNAL   Mol Cell Endocrinol 319 (1-2), 63-70 (2010)
   PUBMED   20097260
REFERENCE   7  (bases 1 to 1312)
  AUTHORS   Pirngruber,J., Shchebet,A., Schreiber,L., Shema,E., Minsky,N.,
            Chapman,R.D., Eick,D., Aylon,Y., Oren,M. and Johnsen,S.A.
  TITLE     CDK9 directs H2B monoubiquitination and controls
            replication-dependent histone mRNA 3'-end processing
  JOURNAL   EMBO Rep 10 (8), 894-900 (2009)
   PUBMED   19575011
REFERENCE   8  (bases 1 to 1312)
  AUTHORS   Fujita,T., Piuz,I. and Schlegel,W.
  TITLE     Negative elongation factor NELF controls transcription of immediate
            early genes in a stimulus-specific manner
  JOURNAL   Exp Cell Res 315 (2), 274-284 (2009)
   PUBMED   19014935
REFERENCE   9  (bases 1 to 1312)
  AUTHORS   Narita,T., Yamaguchi,Y., Yano,K., Sugimoto,S., Chanarat,S.,
            Wada,T., Kim,D.K., Hasegawa,J., Omori,M., Inukai,N., Endoh,M.,
            Yamada,T. and Handa,H.
  TITLE     Human transcription elongation factor NELF: identification of novel
            subunits and reconstitution of the functionally active complex
  JOURNAL   Mol Cell Biol 23 (6), 1863-1873 (2003)
   PUBMED   12612062
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            CO401737.1 and BC079427.1.
            
            Transcript Variant: This variant (2) differs in the 5' UTR compared
            to variant 1. Variants 1 and 2 encode the same protein.
            
            ##Evidence-Data-START##
            CDS exon combination :: BC079427.1 [ECO:0000331]
            RNAseq introns       :: single sample supports all introns
                                    SAMEA5760383, SAMEA5760389 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-679               CO401737.1         1-679
            680-1312            BC079427.1         712-1344
FEATURES             Location/Qualifiers
     source          1..1312
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /db_xref="taxon:10116"
                     /chromosome="20"
                     /map="20p12"
     gene            1..1312
                     /gene="Nelfe"
                     /gene_synonym="Rd; Rdbp"
                     /note="negative elongation factor complex member E"
                     /db_xref="GeneID:294258"
                     /db_xref="RGD:1303325"
     exon            1..69
                     /gene="Nelfe"
                     /gene_synonym="Rd; Rdbp"
                     /inference="alignment:Splign:2.1.0"
     exon            70..152
                     /gene="Nelfe"
                     /gene_synonym="Rd; Rdbp"
                     /inference="alignment:Splign:2.1.0"
     CDS             78..1187
                     /gene="Nelfe"
                     /gene_synonym="Rd; Rdbp"
                     /note="RD RNA-binding protein"
                     /codon_start=1
                     /product="negative elongation factor E"
                     /protein_id="NP_001159373.1"
                     /db_xref="GeneID:294258"
                     /db_xref="RGD:1303325"
                     /translation="MLVIPPGLSEEEEALQKKFNKLKKKKKALLALKKQSSSGTASQG
                     GVKRSLSEQPVVDTATATEQAKQLVKSGAISAIKAETKNSGFKRSRTLEGKLKDPEKG
                     PVPTFQPFQRSMSADEDLQEPSRRPQRKSLYESFVSSSDRLRELGQDGEEAEAPGAGE
                     GPPRGFDWSYEEHSGARSSASPPRSRSRDRSHDRSRDRDRDKERDRDRDRDRERDKDK
                     DRDRDRDRDKERDRDRDRERDREGPFRRSDSFPERRAPRKGNTLYVYGEDMTPTLLRG
                     AFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPML
                     DAATGKSVWGSLAVQNSPKGCHRDKRTQIVYSDDL"
     exon            153..222
                     /gene="Nelfe"
                     /gene_synonym="Rd; Rdbp"
                     /inference="alignment:Splign:2.1.0"
     exon            223..368
                     /gene="Nelfe"
                     /gene_synonym="Rd; Rdbp"
                     /inference="alignment:Splign:2.1.0"
     exon            369..443
                     /gene="Nelfe"
                     /gene_synonym="Rd; Rdbp"
                     /inference="alignment:Splign:2.1.0"
     exon            444..481
                     /gene="Nelfe"
                     /gene_synonym="Rd; Rdbp"
                     /inference="alignment:Splign:2.1.0"
     exon            482..813
                     /gene="Nelfe"
                     /gene_synonym="Rd; Rdbp"
                     /inference="alignment:Splign:2.1.0"
     exon            814..958
                     /gene="Nelfe"
                     /gene_synonym="Rd; Rdbp"
                     /inference="alignment:Splign:2.1.0"
     exon            959..1013
                     /gene="Nelfe"
                     /gene_synonym="Rd; Rdbp"
                     /inference="alignment:Splign:2.1.0"
     exon            1014..1116
                     /gene="Nelfe"
                     /gene_synonym="Rd; Rdbp"
                     /inference="alignment:Splign:2.1.0"
     exon            1117..1284
                     /gene="Nelfe"
                     /gene_synonym="Rd; Rdbp"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 ccgcgagccc gcgcgcagca gcccgcgcgg cggcgccgga gaccgcgggc ccgggcgccg
       61 ccccctcagg agccaacatg ttggtgatac ctccggggct gagtgaagag gaagaggcac
      121 tacagaagaa attcaacaaa ctcaagaaaa agaaaaaggc gttgctggct ctgaagaagc
      181 aaagcagcag tggtacagcg agccagggcg gtgtcaagcg ctcactgtca gagcagcctg
      241 tggtggatac tgccacagca acagaacagg ccaaacagct ggtgaagtca ggagctatca
      301 gtgccatcaa ggctgaaact aagaactcag gcttcaaacg ttctcggacc ctggaaggga
      361 agttaaagga cccagagaag gggcctgtcc ccaccttcca gccgttccag aggagcatgt
      421 ctgctgacga ggacctacag gagccatcca gacggcccca aaggaaatct ctgtatgaaa
      481 gctttgtgtc ttctagtgat cggcttcggg aactgggaca agatggagaa gaagcagagg
      541 cccctggggc tggtgaaggc ccacctcgag gttttgactg gagctatgaa gaacacagcg
      601 gtgcccgatc ctcagcctcc cctccccgaa gccgcagccg ggacagaagt catgatcgga
      661 gccgagatag ggaccgggac aaagaacgag acagagaccg ggatcgagac agagaacggg
      721 acaaagacaa agacagagac cgggaccggg acagagacaa agagcgggac agagacaggg
      781 accgggagcg agaccgagag ggccctttcc gtaggtcaga ctcattcccc gaacggaggg
      841 cccctcgaaa ggggaacact ctgtatgtgt atggagagga catgacgccc accctcctcc
      901 gaggggcctt ctctcccttt ggaaatatca tcgacctctc catggaccca cccagaaact
      961 gtgccttcgt cacctacgag aagatggagt cagcagatca ggctgttgct gagctcaatg
     1021 ggacccaggt ggaatctgtg cagctcaaag tcaacatagc ccgaaaacag cccatgctgg
     1081 acgctgctac tggcaaatct gtctggggct cccttgctgt ccagaacagc cccaagggtt
     1141 gccaccggga caagaggacc cagattgtgt acagtgacga tctataggaa accttgtgga
     1201 tggcttctag gacatgaagc tggattcctt gtgcctcata tgcccccaag ctggtctcag
     1261 taaaatcctg gggtagaagc ttttaaaaaa aaaaaaaaaa aaaaaaaaaa aa
//
