LOCUS       NM_001401979            4640 bp    mRNA    linear   ROD 30-MAR-2024
DEFINITION  Rattus norvegicus Rtf1, Paf1/RNA polymerase II complex component,
            homolog (S. cerevisiae) (Rtf1), mRNA.
ACCESSION   NM_001401979 XM_006234783
VERSION     NM_001401979.1
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 4640)
  AUTHORS   Strikoudis,A., Lazaris,C., Trimarchi,T., Galvao Neto,A.L., Yang,Y.,
            Ntziachristos,P., Rothbart,S., Buckley,S., Dolgalev,I.,
            Stadtfeld,M., Strahl,B.D., Dynlacht,B.D., Tsirigos,A. and
            Aifantis,I.
  TITLE     Regulation of transcriptional elongation in pluripotency and cell
            differentiation by the PHD-finger protein Phf5a
  JOURNAL   Nat Cell Biol 18 (11), 1127-1138 (2016)
   PUBMED   27749823
REFERENCE   2  (bases 1 to 4640)
  AUTHORS   Zhang,K., Haversat,J.M. and Mager,J.
  TITLE     CTR9/PAF1c regulates molecular lineage identity, histone H3K36
            trimethylation and genomic imprinting during preimplantation
            development
  JOURNAL   Dev Biol 383 (1), 15-27 (2013)
   PUBMED   24036311
REFERENCE   3  (bases 1 to 4640)
  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 4640)
  AUTHORS   Jaehning,J.A.
  TITLE     The Paf1 complex: platform or player in RNA polymerase II
            transcription?
  JOURNAL   Biochim Biophys Acta 1799 (5-6), 379-388 (2010)
   PUBMED   20060942
  REMARK    Review article
REFERENCE   5  (bases 1 to 4640)
  AUTHORS   Kim,J., Guermah,M. and Roeder,R.G.
  TITLE     The human PAF1 complex acts in chromatin transcription elongation
            both independently and cooperatively with SII/TFIIS
  JOURNAL   Cell 140 (4), 491-503 (2010)
   PUBMED   20178742
REFERENCE   6  (bases 1 to 4640)
  AUTHORS   Ding,L., Paszkowski-Rogacz,M., Nitzsche,A., Slabicki,M.M.,
            Heninger,A.K., de Vries,I., Kittler,R., Junqueira,M.,
            Shevchenko,A., Schulz,H., Hubner,N., Doss,M.X., Sachinidis,A.,
            Hescheler,J., Iacone,R., Anastassiadis,K., Stewart,A.F.,
            Pisabarro,M.T., Caldarelli,A., Poser,I., Theis,M. and Buchholz,F.
  TITLE     A genome-scale RNAi screen for Oct4 modulators defines a role of
            the Paf1 complex for embryonic stem cell identity
  JOURNAL   Cell Stem Cell 4 (5), 403-415 (2009)
   PUBMED   19345177
REFERENCE   7  (bases 1 to 4640)
  AUTHORS   de Jong,R.N., Truffault,V., Diercks,T., Ab,E., Daniels,M.A.,
            Kaptein,R. and Folkers,G.E.
  TITLE     Structure and DNA binding of the human Rtf1 Plus3 domain
  JOURNAL   Structure 16 (1), 149-159 (2008)
   PUBMED   18184592
REFERENCE   8  (bases 1 to 4640)
  AUTHORS   Tate,P., Lee,M., Tweedie,S., Skarnes,W.C. and Bickmore,W.A.
  TITLE     Capturing novel mouse genes encoding chromosomal and other nuclear
            proteins
  JOURNAL   J Cell Sci 111 (Pt 17), 2575-2585 (1998)
   PUBMED   9701556
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000003.1.
            
            On Mar 3, 2022 this sequence version replaced XM_006234783.2.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on transcript alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26643290.12758.1,
                                           SRR26643429.12940.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760383, SAMEA5760386
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-222               JAXUCZ010000003.1  127113171-127113392
            223-333             JAXUCZ010000003.1  127130806-127130916
            334-481             JAXUCZ010000003.1  127140538-127140685
            482-689             JAXUCZ010000003.1  127144018-127144225
            690-804             JAXUCZ010000003.1  127147981-127148095
            805-916             JAXUCZ010000003.1  127148781-127148892
            917-1052            JAXUCZ010000003.1  127157699-127157834
            1053-1230           JAXUCZ010000003.1  127158591-127158768
            1231-1313           JAXUCZ010000003.1  127162503-127162585
            1314-1401           JAXUCZ010000003.1  127164049-127164136
            1402-1509           JAXUCZ010000003.1  127164227-127164334
            1510-1587           JAXUCZ010000003.1  127164877-127164954
            1588-1709           JAXUCZ010000003.1  127165733-127165854
            1710-1767           JAXUCZ010000003.1  127166013-127166070
            1768-1845           JAXUCZ010000003.1  127167097-127167174
            1846-1941           JAXUCZ010000003.1  127167818-127167913
            1942-2053           JAXUCZ010000003.1  127169838-127169949
            2054-4640           JAXUCZ010000003.1  127170175-127172761
FEATURES             Location/Qualifiers
     source          1..4640
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="3"
                     /map="3q35"
     gene            1..4640
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /note="Rtf1, Paf1/RNA polymerase II complex component,
                     homolog (S. cerevisiae)"
                     /db_xref="GeneID:366169"
                     /db_xref="RGD:1310654"
     exon            1..222
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     CDS             13..2160
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /note="gene trap locus 7; RNA polymerase-associated
                     protein RTF1 homolog"
                     /codon_start=1
                     /product="RNA polymerase-associated protein RTF1 homolog
                     precursor"
                     /protein_id="NP_001388908.1"
                     /db_xref="GeneID:366169"
                     /db_xref="RGD:1310654"
                     /translation="MRGRLCVGRAAAVAAAVVAAVAVPLAGGQEGSPDGVRRGSRGTT
                     MVKKRKGRVVIDSDTEDSGSDENLDQELLSLAKRKRSDSEEKEPPVSQPAASSDSETS
                     DSDDEWTFGSNKNKKKGKARKVEKKGAMKKQANKAASSGSSDRDSSAESSAPEEGEVS
                     DSDSNSSSSSSDSDSSSSEDEEFHDGYGEDLMGDEEDRARLEQMTEKEREQELFNRIE
                     KREVLKRRFEIKKKLKTAKKKEKKEKKKKQEEEQEKKKLTQIQESQVTSHNKERRSKR
                     DEKLDKKSQAMEELKAEREKRKNRTAELLAKKQPLKTSEVYSDDEEEEDDDKSSEKSD
                     RSSRTSSSDEEEEKEEIPPKSQPVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFV
                     RIGIGNHNSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQ
                     EFTESEFMKWKEAMFSAGMQLPTLDEINKKEFSIKEALNYKFNDQDIEEIVKEKERFR
                     KAPPNYAMKKTQLLKEKAMAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKNISAIS
                     YINQRNREWNIVESEKALVAESHNMRNQQMDPFTRRQCKPTIVSNSRDPAVQAAILAQ
                     LNAKYGSGALPDAPKEVSKGQGKDKDLNSKSASDLSEDLFKVHDFDVKIDLQVPSSES
                     KALAITSKAPPAKDGAPRRSLNLEDYKKRRGLI"
     exon            223..333
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            334..481
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            482..689
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            690..804
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            805..916
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            917..1052
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            1053..1230
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            1231..1313
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            1314..1401
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            1402..1509
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            1510..1587
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            1588..1709
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            1710..1767
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            1768..1845
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            1846..1941
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            1942..2053
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
     exon            2054..4640
                     /gene="Rtf1"
                     /gene_synonym="Gtl7"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 agcggagcgc gcatgcgcgg tcgcctttgt gtgggtcgag cggcggcggt ggcggcggcg
       61 gtggtggcgg cagtggcggt cccactggca ggcgggcaag aggggagtcc ggacggcgtc
      121 cggcgtggga gccgggggac caccatggta aagaagcgga aaggccgtgt cgtgatcgac
      181 tcggatacgg aagacagcgg cagcgacgag aacctggatc aggagctctt gtccctggca
      241 aaacggaagc gcagtgactc tgaggagaag gagcctcctg tgagtcagcc tgcagcctcg
      301 tcagattcag agacatccga cagtgatgat gagtggacat ttgggagcaa taaaaataag
      361 aagaaaggaa aagccagaaa agtagagaag aaaggagcca tgaagaagca agccaacaaa
      421 gctgcctcct cgggcagctc agacagagac agctcagctg agagctcagc ccccgaggaa
      481 ggtgaagtgt cagactctga cagcaacagc tcctcttcca gctcagattc agactcctcg
      541 tcctcggagg atgaggagtt ccacgatggc tacggagagg accttatggg agacgaggaa
      601 gacagggccc ggctggagca gatgacggag aaggagaggg agcaggagct cttcaaccgc
      661 atagagaaga gggaggtgtt gaaaagaaga tttgaaatta agaaaaaact aaaaacagcc
      721 aaaaagaaag aaaagaaaga aaaaaagaaa aagcaggaag aagaacaaga aaagaaaaag
      781 ctgacacaga ttcaagaatc tcaggttacc tctcacaata aagaacggcg ttccaagcgc
      841 gatgagaaac tagataagaa atctcaagcc atggaggagc taaaagcaga gcgcgaaaaa
      901 cggaagaaca gaacagctga gctccttgcc aaaaaacagc cattgaaaac cagtgaggtc
      961 tactctgatg atgaggagga agaagacgat gacaagtcca gtgagaaatc agaccgctcg
     1021 tcccgaacgt catcatctga tgaagaagaa gagaaagaag aaatccctcc gaaatcacag
     1081 ccagtctcct tacccgagga actgaatcgg gttcggttat caaggcataa gctagaacgc
     1141 tggtgtcaca tgcccttctt tgctaaaact gtcacaggat gttttgtacg gattggcatt
     1201 ggaaaccata atagcaagcc agtttaccgg gtggctgaga tcacaggtgt tgtggaaact
     1261 gccaaagttt accagctggg tggtaccaga acaaacaaag ggctgcagct acggcatggc
     1321 aatgaccagc gagtgttccg tctagagttt gtgtccaacc aggaattcac tgaaagtgag
     1381 ttcatgaagt ggaaggaagc gatgttttct gctggcatgc agttgcccac actagatgaa
     1441 atcaataaaa aggaattttc tattaaggaa gccctcaatt ataaattcaa tgatcaggac
     1501 attgaggaga ttgtgaaaga gaaagaaagg tttagaaaag ctccaccaaa ctatgctatg
     1561 aagaagactc agctgctgaa ggaaaaggcc atggctgagg acctgggaga tcaggacaaa
     1621 gccaaacaaa tccaagacca gctaaatgag ctagaagagc gggcagaggc cctggaccgc
     1681 cagcggacca agaacatatc tgctatcagc tacatcaacc agcggaatcg ggagtggaac
     1741 attgtggagt ctgagaaggc tctggtggct gaaagtcaca acatgagaaa ccagcagatg
     1801 gacccgttta ccaggcgaca gtgcaaaccc accatcgtct ccaattccag ggacccagct
     1861 gttcaggctg ccattttggc ccagctaaat gcaaaatacg gttctggagc gttaccagat
     1921 gctccaaagg aagtgagcaa gggacaagga aaggataaag atttgaattc taagtcagcc
     1981 agtgacctct ccgaagactt gttcaaagtc catgactttg atgtgaagat tgacttacaa
     2041 gtcccaagct cagagtcaaa agctttggcc atcacctcca aggccccacc agccaaggat
     2101 ggagctccaa ggagatctct gaacttagaa gactataaaa aacgacgagg gcttatttga
     2161 gcacttccag cctgctgctt ccaaccctgc atgccctgtc atcgtcccgc ctttcctctt
     2221 ttcctctgat ttgccctctt tgggctggag cagcagtgga actgggaaga gactctaact
     2281 gccagtcatt gtaatataaa ccatttgctg tatagacctt ccttgtctgc accatctccc
     2341 agcaacctca ggccccgccc acggtgggtc tgggtgggtg gggcttctct tcttccaggt
     2401 ctttaggtct gcgtttgccc gccccacctg cttttggttt ttaactagca ccgtccggcc
     2461 actctgcaca ttcagtatta ccatggagct agggttcttg ctagagcccc tggtggcagg
     2521 aatggcagta ctccagtgtc ctcttcaggc tgccttgggc ccgaccatcg aacatttggc
     2581 acctaaccct gcagagagtg ggactgggcg gctgccatct tcttccctct catccttctc
     2641 ttcttcctgt gtccatggaa gagggatttt caaaccagtt tagtttccaa aaagtgtaca
     2701 tttatgggga gggagggggc ctaatttgag tgtgtgtgtg tgtgtgcgcg cgcgtgtgtg
     2761 tgtgtatgcg cgtgtgtgtg tgtatttttt atcatttttt aaaatgcagt actctttgta
     2821 ccagtctgtc atggatctag ctgtttcaga tttttttgag ctgtacttga gcatctgaaa
     2881 ctgcaagaaa gaaactgatt aaatgtgatt cttcttacta aacaggcctg actgctgtag
     2941 ctgtgtgact tccctccctg tctaccctag cactgcccta ccccacagga agctcccatc
     3001 cacccccctt gccccatagg ctgtgttctg acaggtgggc aggaaactca tggcaaggcc
     3061 caggggggca gccagagtct cgatcagtgc ccaggcacag ctgtggcttc ttgactgaac
     3121 gtagcacatc tcgtccccac ccactgttcc tctctcttcc tagtgactcc gatgtttggc
     3181 aagaataaca ctttgttctg gtttttatga aataattcaa catgaatgtg gagagcaaac
     3241 aaaaaggtgt aggttgcaaa tgttaccagc atgtgcagtg gtgcgtgtgc ccgtgtgtgt
     3301 ctgtgtgtgt gcacatatat gtggtgagca tctatatatt gtgcagtagg atgaagccag
     3361 caaagaggtg tgtatgttat gagatgtttg aaaagaaata agctgcctgc ttgataatca
     3421 ctctcaggtg taaagcgcca actgtaaata aaagtggcat ttaacaaatt taacaaattt
     3481 cttcagaaca aagtacagct gatgatatcc accaagcagt aagcgaaaga aacagctggg
     3541 agccgctgat ctccagtgct gaggactcga gctctgctct gtgcttcact gacttgtata
     3601 aggaaggggt gatgggaaat catggaatta agtagtattt aaacaaaaat ggacttacta
     3661 gctcttctga ttgaggaaag ccccggtgtt gtttcactta gtttacattt ttactttcta
     3721 aaaagcagca acggacggct ttaaagaaaa gcattgtgac gtagaatggg aaatgtggcc
     3781 tgtgcccagc ttaggtgtag ctgtggcaca gagtcgagca caggagcggt gatgggctca
     3841 ttgcaaccat acatacttga agagtccatt gaccaaagct cgctctagac ggactgtgtt
     3901 gtgtaaatgg ggaatcagcc tggggaacgc cgcctgcaca ctagcagggt cctggagctg
     3961 ccagacctct cctatcatgt cagacttgga cttttttcct tcttgtttaa aggacgtaaa
     4021 atcatagaat ccatataatc tgtggcgtca tcctgaccca catgtagatc tgtatctaat
     4081 attatttgga tttggacaag tgtcaatgac attatggctg tgtaataaaa tttttattaa
     4141 aaattccaca cactgtagcc cctttgccac tccccacctg cagctgctga gatgccaaag
     4201 caaggggcag ggagaaaagc ccaccaaaga agatggaagt tagcccagcc actgcttgcc
     4261 tgcctgctga ctgcagccac ccagcatcta cctgcggtcg gtctcagcta gtcatgggac
     4321 attggctttg tcccacccac tgggttcctg gcaggtcggt tcttctgctg gtgaatctcc
     4381 tcagtgaccc ctccatcacc ccagcttcac ttcagtgttg aagggcatag cacccaagac
     4441 tgttctaccc tctttcagtt ctgggaagta agagtcagcg tccgtatgcc tggctcattg
     4501 ctgtctgtag atctgttgtc tgtctggttt ctgacaggga cagagaacat ctgtttttgt
     4561 tatttttctg tggtttcctg atttgtcact caatttgtaa atagatttgt aaataaactc
     4621 gatgacattt taacaaggga
//
