LOCUS       NM_001100661            4234 bp    mRNA    linear   ROD 01-APR-2024
DEFINITION  Rattus norvegicus CTR9 homolog, Paf1/RNA polymerase II complex
            component (Ctr9), mRNA.
ACCESSION   NM_001100661
VERSION     NM_001100661.1
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 4234)
  AUTHORS   Cui,W., Dai,X., Marcho,C., Han,Z., Zhang,K., Tremblay,K.D. and
            Mager,J.
  TITLE     Towards Functional Annotation of the Preimplantation Transcriptome:
            An RNAi Screen in Mammalian Embryos
  JOURNAL   Sci Rep 6, 37396 (2016)
   PUBMED   27869233
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4234)
  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   3  (bases 1 to 4234)
  AUTHORS   De Gois,S., Slama,P., Pietrancosta,N., Erdozain,A.M., Louis,F.,
            Bouvrais-Veret,C., Daviet,L. and Giros,B.
  TITLE     Ctr9, a Protein in the Transcription Complex Paf1, Regulates
            Dopamine Transporter Activity at the Plasma Membrane
  JOURNAL   J Biol Chem 290 (29), 17848-17862 (2015)
   PUBMED   26048990
  REMARK    GeneRIF: Ctr9, formerly identified as a nuclei protein, interacts
            with the dopamine transporter in the cytoplasmic compartment.
REFERENCE   4  (bases 1 to 4234)
  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   5  (bases 1 to 4234)
  AUTHORS   Muntean,A.G., Tan,J., Sitwala,K., Huang,Y., Bronstein,J.,
            Connelly,J.A., Basrur,V., Elenitoba-Johnson,K.S. and Hess,J.L.
  TITLE     The PAF complex synergizes with MLL fusion proteins at HOX loci to
            promote leukemogenesis
  JOURNAL   Cancer Cell 17 (6), 609-621 (2010)
   PUBMED   20541477
REFERENCE   6  (bases 1 to 4234)
  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 4234)
  AUTHORS   Youn,M.Y., Yoo,H.S., Kim,M.J., Hwang,S.Y., Choi,Y., Desiderio,S.V.
            and Yoo,J.Y.
  TITLE     hCTR9, a component of Paf1 complex, participates in the
            transcription of interleukin 6-responsive genes through regulation
            of STAT3-DNA interactions
  JOURNAL   J Biol Chem 282 (48), 34727-34734 (2007)
   PUBMED   17911113
REFERENCE   8  (bases 1 to 4234)
  AUTHORS   Zhu,B., Zheng,Y., Pham,A.D., Mandal,S.S., Erdjument-Bromage,H.,
            Tempst,P. and Reinberg,D.
  TITLE     Monoubiquitination of human histone H2B: the factors involved and
            their roles in HOX gene regulation
  JOURNAL   Mol Cell 20 (4), 601-611 (2005)
   PUBMED   16307923
REFERENCE   9  (bases 1 to 4234)
  AUTHORS   Zhu,B., Mandal,S.S., Pham,A.D., Zheng,Y., Erdjument-Bromage,H.,
            Batra,S.K., Tempst,P. and Reinberg,D.
  TITLE     The human PAF complex coordinates transcription with events
            downstream of RNA synthesis
  JOURNAL   Genes Dev 19 (14), 1668-1673 (2005)
   PUBMED   16024656
REFERENCE   10 (bases 1 to 4234)
  AUTHORS   Malek,S.N., Yang,C.H., Earnshaw,W.C., Kozak,C.A. and Desiderio,S.
  TITLE     p150TSP, a conserved nuclear phosphoprotein that contains multiple
            tetratricopeptide repeats and binds specifically to SH2 domains
  JOURNAL   J Biol Chem 271 (12), 6952-6962 (1996)
   PUBMED   8636124
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000001.1.
            
            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 alignments.
            
            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 :: SRR26360186.1838224.1,
                                           SRR26360194.1023136.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760383, SAMEA5760386
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-168               JAXUCZ010000001.1  174571952-174572119
            169-267             JAXUCZ010000001.1  174573127-174573225
            268-507             JAXUCZ010000001.1  174577979-174578218
            508-625             JAXUCZ010000001.1  174578617-174578734
            626-715             JAXUCZ010000001.1  174580376-174580465
            716-864             JAXUCZ010000001.1  174583974-174584122
            865-972             JAXUCZ010000001.1  174586149-174586256
            973-1080            JAXUCZ010000001.1  174588291-174588398
            1081-1317           JAXUCZ010000001.1  174588501-174588737
            1318-1407           JAXUCZ010000001.1  174588910-174588999
            1408-1536           JAXUCZ010000001.1  174589105-174589233
            1537-1720           JAXUCZ010000001.1  174589321-174589504
            1721-1809           JAXUCZ010000001.1  174590814-174590902
            1810-1995           JAXUCZ010000001.1  174591521-174591706
            1996-2083           JAXUCZ010000001.1  174591783-174591870
            2084-2232           JAXUCZ010000001.1  174592027-174592175
            2233-2349           JAXUCZ010000001.1  174594206-174594322
            2350-2495           JAXUCZ010000001.1  174594494-174594639
            2496-2567           JAXUCZ010000001.1  174595418-174595489
            2568-2703           JAXUCZ010000001.1  174595921-174596056
            2704-2850           JAXUCZ010000001.1  174596195-174596341
            2851-3008           JAXUCZ010000001.1  174597396-174597553
            3009-3105           JAXUCZ010000001.1  174598418-174598514
            3106-3218           JAXUCZ010000001.1  174598778-174598890
            3219-4234           JAXUCZ010000001.1  174600959-174601974
FEATURES             Location/Qualifiers
     source          1..4234
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="1"
                     /map="1q33"
     gene            1..4234
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /note="CTR9 homolog, Paf1/RNA polymerase II complex
                     component"
                     /db_xref="GeneID:293184"
                     /db_xref="RGD:1311097"
     exon            1..168
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     CDS             124..3645
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /note="SH2 domain binding protein 1 (tetratricopeptide
                     repeat containing); Ctr9, Paf1/RNA polymerase II complex
                     component, homolog"
                     /codon_start=1
                     /product="RNA polymerase-associated protein CTR9 homolog"
                     /protein_id="NP_001094131.1"
                     /db_xref="GeneID:293184"
                     /db_xref="RGD:1311097"
                     /translation="MSRGSIEIPLRDTDEVIELDFDQLPEGDEVISILKQEHTQLHIW
                     IALALEYYKQGKTEEFVKLLEAARIDGNLDYRDHEKDQMTCLDTLAAYYVQQARKEKN
                     KDNKKDLITQATLLYTMADKIIMYDQNHLLGRACFCLLEGDKMDQADAQFHFVLNQSP
                     NNIPALLGKACISFNKKDYRGALAYYKKALRTNPGCPAEVRLGMGHCFVKLNKLEKAR
                     LAFSRALELNSKCVGALVGLAVLELNNKEADSIKNGVQLLSRAYTIDPSNPMVLNHLA
                     NHFFFKKDYSKVQHLALHAFHNTEVEAMQAESCYQLARSFHVQEDYDQAFQYYYQATQ
                     FASSSFVLPFFGLGQMYIYRGDKENASQCFEKVLKAYPNNYETMKILGSLYAASEDQE
                     KRDIAKGHLKKVTEQYPDDVEAWIELAQILEQTDIQGALSAYGTATRILQEKVQADVP
                     PEILNNVGALHFRLGNLGEAKKYFLASLDRAKAEAEHDEHYYNAISVTTSYNLARLYE
                     AMCEFHEAEKLYKNILREHPNYVDCYLRLGAMARDKGNFYEASDWFKEALQINQDHPD
                     AWSLIGNLHLAKQEWGPGQKKFERILKQPATQSDTYSMLALGNVWLQTLHQPTRDREK
                     EKRHQDRALAIYKQVLRNDAKNLYAANGIGAVLAHKGYFREARDVFAQVREATADISD
                     VWLNLAHIYVEQKQYISAVQMYENCLRKFYKHQNTEVVLYLARALFKCGKLQECKQTL
                     LKARHVAPSDTVLMFNVALVLQRLATSVLKDEKSNLKEVLNAVKELELAHRYFSYLSK
                     VGDKMRFDLALAASEARQCSDLLSQAQYHVARARKQDEEERELRAKQEQEKELLRQKL
                     LKEQEEKRLREKEEQKKLLEQRAQYVEKTKNILMFTGETEATKEKKRGGGGGRRSKKG
                     GEFDEFVNDDTDDDLPISKKKKKRKGSGSEQEGEEEEGGERKKKRRRRPPKGEEGSDD
                     DETENGPKPKKRRPPRAEKKKAPKPERLPPSMKGKIKSKAIISSSDDSSDEDKLKIAD
                     EGHPRNSNSDSDDDERPNRRASSESDSDDNQNKSGSEAGSPRRSGRQESDEDSDSDQP
                     SRKRRRSGSEQSDNESAQSGRSPSGGSENENDSRPVSPSAESDHESEQGSDNEGSGQG
                     SGNESEPEGSNNEASDRGSEHGSDDSD"
     exon            169..267
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            268..507
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            508..625
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            626..715
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            716..864
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            865..972
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            973..1080
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1081..1317
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1318..1407
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1408..1536
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1537..1720
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1721..1809
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1810..1995
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1996..2083
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            2084..2232
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            2233..2349
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            2350..2495
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            2496..2567
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            2568..2703
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            2704..2850
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            2851..3008
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            3009..3105
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            3106..3218
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
     exon            3219..4234
                     /gene="Ctr9"
                     /gene_synonym="Sh2bp1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 ggagaaggtg catctcaggc agctccgctg ggtgtgaggt gtggtaacct cttgcaagac
       61 tggaagcccg gactacgagc tccggagccg cagagtgaga agcgcctgct ttcagagctc
      121 gccatgtcgc ggggttccat cgagattccc ctccgggata ctgacgaggt cattgaactt
      181 gacttcgatc agttaccgga gggggatgaa gttatcagta ttctgaagca ggagcacaca
      241 caactgcaca tatggattgc tttggcgctg gagtactaca agcaagggaa aacagaagag
      301 tttgtgaagc tgctggaggc tgcacggata gatggcaatt tggactatcg agaccacgag
      361 aaagaccaga tgacttgctt ggatacattg gcagcctact atgtacaaca ggctcggaaa
      421 gaaaagaaca aagacaataa gaaagacctt attacgcagg caactttgtt gtatacaatg
      481 gctgataaaa ttattatgta tgatcagaac catttgttgg gaagagcctg cttctgcctg
      541 ctcgagggtg acaaaatgga ccaagctgac gcacagtttc attttgtact taaccagtct
      601 ccaaacaata ttccagccct tcttgggaaa gcttgtatct cattcaacaa gaaggactac
      661 agaggagccc ttgcttacta taaaaaagca ttgcgcacta acccaggatg tccagctgaa
      721 gttcgtctag gaatgggcca ttgctttgtc aaactgaaca aactggaaaa agcccgacta
      781 gcattcagca gagccctgga actcaactct aagtgtgtgg gagcactggt cggactggct
      841 gttctagaac tcaacaataa agaggctgat tccatcaaaa atggtgtgca gcttctttcc
      901 agagcctaca ctattgatcc tagcaaccct atggtactga accatttggc aaaccacttt
      961 ttcttcaaga aggattatag taaagtgcag cacctggctc tccacgcgtt ccacaacaca
     1021 gaggtggagg ccatgcaagc agagagctgt taccagctgg ctcggtcctt ccatgttcag
     1081 gaagattatg accaggcctt tcagtactac tatcaagcca cacagtttgc ttcatcttct
     1141 tttgtcctac cattttttgg tttgggacaa atgtatattt atcgaggtga caaagaaaat
     1201 gcatctcagt gtttcgagaa agttttgaaa gcttatccga acaattatga aactatgaaa
     1261 attcttggct ctctctatgc tgcttcagaa gatcaggaga aaagagacat agccaagggc
     1321 catttgaaga aggttacaga acagtatcct gatgacgtgg aagcttggat tgagttggcc
     1381 cagatcttag aacagactga catacagggt gccctttcag cctatggaac ggcaacacga
     1441 atcctgcagg agaaggtgca ggccgatgtc ccgcctgaga ttttgaataa tgttggggcc
     1501 ctccatttta gacttggaaa cctaggcgaa gcaaagaagt acttcctggc ctcactggac
     1561 cgagcaaagg cagaggcgga gcatgatgaa cactattaca atgccatctc tgtcaccaca
     1621 tcctacaatt tagccaggct ctacgaggcc atgtgtgaat ttcatgaagc agagaaactg
     1681 tacaaaaaca ttttacgaga gcatcctaac tatgttgatt gctatctgcg cctaggagcc
     1741 atggccagag ataaaggaaa cttctatgaa gcttcagatt ggtttaagga agcccttcag
     1801 atcaatcagg accatcccga tgcctggtct ttgattggta acctccatct ggcaaaacaa
     1861 gagtggggcc caggtcagaa gaagtttgag aggatcttaa aacagccagc cacacagagt
     1921 gacacctact ctatgctggc ccttggcaat gtgtggctcc agactttgca tcagccaacc
     1981 cgagaccgag aaaaggaaaa gcgccatcaa gaccgtgcgc tggccatcta caaacaagtc
     2041 ctgagaaatg atgccaagaa cctgtatgct gccaatggca taggagctgt cttggcccac
     2101 aaaggatatt tccgtgaagc tcgtgatgtg ttcgcccaag tgagagaagc aacagcagat
     2161 atcagtgacg tgtggctgaa cttagcacac atctacgtcg agcagaagca gtatatcagc
     2221 gccgttcaga tgtatgagaa ctgcctccga aagttctata agcaccaaaa cactgaagtt
     2281 gtgctctacc tggcccgtgc cctcttcaag tgtggcaagt tgcaggagtg caagcagact
     2341 ctgctgaagg cccgacacgt ggcacccagc gacacagttc tgatgtttaa tgtggccttg
     2401 gtcttgcaaa gattagctac ctctgtcctg aaagatgaaa aaagtaattt gaaggaagtc
     2461 cttaatgctg tgaaagagct ggagcttgca cacagatact tcagttactt gagtaaagtt
     2521 ggagataaga tgagatttga tttggccctt gctgcctctg aagccaggca gtgctctgac
     2581 ttactgagcc aggcccaata ccatgtggct cgggcacgca agcaggatga ggaggaacgg
     2641 gagctgcggg ccaagcagga gcaggagaag gagctcctaa gacagaagct tctcaaagag
     2701 caggaagaaa aacgtctcag agaaaaggaa gagcaaaaga aacttttgga acagcgggcc
     2761 cagtatgtgg agaagaccaa aaatatcctc atgttcactg gcgagactga agcaacaaaa
     2821 gagaagaaaa gaggtggagg tggagggcgg cgttccaaga aaggaggcga gtttgatgag
     2881 tttgtcaacg atgacactga tgacgacctc cctatatcca agaagaagaa gaaaaggaag
     2941 ggcagtggca gtgaacagga aggcgaagag gaggaaggtg gagagaggaa gaagaagagg
     3001 aggagaagac ctccaaaggg agaagaagga tctgatgatg atgaaacaga aaatggcccc
     3061 aaaccaaaga agcgccgtcc accgagagca gagaaaaaga aggctcccaa gccagaacgc
     3121 ctgcctcctt caatgaaagg aaaaataaaa tccaaagcca ttatatcatc aagcgatgat
     3181 tcttcagatg aggataaact gaaaattgct gatgaaggac atcccaggaa cagcaacagc
     3241 gactctgatg atgacgagag gcccaacaga cgcgcctcat cggagagcga ctcagatgac
     3301 aaccagaaca agtctggcag cgaggcgggt agcccccgga ggtctggtag gcaggagtcc
     3361 gatgaggatt ccgacagtga ccagccgtcc agaaagagaa ggcgctccgg ctctgagcag
     3421 tcggacaatg agtctgcgca gtccgggagg agcccctccg gaggctcaga gaatgagaac
     3481 gattctcgcc cggtttctcc aagtgcagag tcggaccacg aatcagagca gggctctgac
     3541 aacgaaggtt ctggccaagg ctctggaaat gaatcggaac cagagggctc aaacaatgag
     3601 gcctcagacc gaggctcaga acatggatca gatgatagcg actaggttca tttcatcaaa
     3661 gactccatag ggtgggggga gctttatata tataaaagct gtgataaaaa acatttcaga
     3721 tagtcgtttg tgaaattttc ttaaggcaat tttttttttc tacttgtata tttactaact
     3781 tccaagagac atttcctgtg ctggagagtc cagtgtctga ccctggagca atgagactcc
     3841 tgcgttgtgg tgcagcccca cctgccatat gtgaaaactg cagtgataac agatgctaaa
     3901 gcattcctgc aaggcttgcc caggctagcc ccatctcctc tccggttagc agcatgctgc
     3961 tatgtacggt tttgttgcaa acttgtacca aatgttgcag aagccgagat atatgccttt
     4021 gttccctttt gagttgagac tgaaagtttt atttccagag gaagacatgt ccctgtactg
     4081 aactctgaaa ggcaggtgtt tacagtgtga ggctccacca tgagtcggag tggccaacac
     4141 tggggagggt gaggggtgga gagtgttttt ctgttgttag agtgggaaga gcttcccagc
     4201 cgcttaataa actctttacc aactgtgctg ggta
//
