LOCUS       NM_001399391            1879 bp    mRNA    linear   ROD 27-MAR-2024
DEFINITION  Rattus norvegicus poly-U binding splicing factor 60 (Puf60),
            transcript variant 1, mRNA.
ACCESSION   NM_001399391 XM_006241894
VERSION     NM_001399391.1
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 1879)
  AUTHORS   Guo,Z., Neilson,L.J., Zhong,H., Murray,P.S., Zanivan,S. and
            Zaidel-Bar,R.
  TITLE     E-cadherin interactome complexity and robustness resolved by
            quantitative proteomics
  JOURNAL   Sci Signal 7 (354), rs7 (2014)
   PUBMED   25468996
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1879)
  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   3  (bases 1 to 1879)
  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 1879)
  AUTHORS   Hegele,A., Kamburov,A., Grossmann,A., Sourlis,C., Wowro,S.,
            Weimann,M., Will,C.L., Pena,V., Luhrmann,R. and Stelzl,U.
  TITLE     Dynamic protein-protein interaction wiring of the human spliceosome
  JOURNAL   Mol Cell 45 (4), 567-580 (2012)
   PUBMED   22365833
REFERENCE   5  (bases 1 to 1879)
  AUTHORS   Yu,H., Tardivo,L., Tam,S., Weiner,E., Gebreab,F., Fan,C.,
            Svrzikapa,N., Hirozane-Kishikawa,T., Rietman,E., Yang,X.,
            Sahalie,J., Salehi-Ashtiani,K., Hao,T., Cusick,M.E., Hill,D.E.,
            Roth,F.P., Braun,P. and Vidal,M.
  TITLE     Next-generation sequencing to generate interactome datasets
  JOURNAL   Nat Methods 8 (6), 478-480 (2011)
   PUBMED   21516116
REFERENCE   6  (bases 1 to 1879)
  AUTHORS   Sandrock,B. and Egly,J.M.
  TITLE     A yeast four-hybrid system identifies Cdk-activating kinase as a
            regulator of the XPD helicase, a subunit of transcription factor
            IIH
  JOURNAL   J Biol Chem 276 (38), 35328-35333 (2001)
   PUBMED   11445587
REFERENCE   7  (bases 1 to 1879)
  AUTHORS   Liu,J., Akoulitchev,S., Weber,A., Ge,H., Chuikov,S., Libutti,D.,
            Wang,X.W., Conaway,J.W., Harris,C.C., Conaway,R.C., Reinberg,D. and
            Levens,D.
  TITLE     Defective interplay of activators and repressors with TFIH in
            xeroderma pigmentosum
  JOURNAL   Cell 104 (3), 353-363 (2001)
   PUBMED   11239393
REFERENCE   8  (bases 1 to 1879)
  AUTHORS   Bouffard,P., Barbar,E., Briere,F. and Boire,G.
  TITLE     Interaction cloning and characterization of RoBPI, a novel protein
            binding to human Ro ribonucleoproteins
  JOURNAL   RNA 6 (1), 66-78 (2000)
   PUBMED   10668799
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000007.1.
            
            On Jan 7, 2022 this sequence version replaced XM_006241894.4.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26360172.287597.1,
                                           SRR26360194.1351870.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA5760389,
                                           SAMEA5760475 [ECO:0006172]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-63                JAXUCZ010000007.1  109674352-109674414 c
            64-165              JAXUCZ010000007.1  109670971-109671072 c
            166-261             JAXUCZ010000007.1  109668849-109668944 c
            262-351             JAXUCZ010000007.1  109668653-109668742 c
            352-402             JAXUCZ010000007.1  109667718-109667768 c
            403-564             JAXUCZ010000007.1  109665525-109665686 c
            565-657             JAXUCZ010000007.1  109665350-109665442 c
            658-871             JAXUCZ010000007.1  109665025-109665238 c
            872-1062            JAXUCZ010000007.1  109664751-109664941 c
            1063-1198           JAXUCZ010000007.1  109664481-109664616 c
            1199-1434           JAXUCZ010000007.1  109664052-109664287 c
            1435-1879           JAXUCZ010000007.1  109663490-109663934 c
FEATURES             Location/Qualifiers
     source          1..1879
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="7"
                     /map="7q34"
     gene            1..1879
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /note="poly-U binding splicing factor 60"
                     /db_xref="GeneID:84401"
                     /db_xref="RGD:621674"
     exon            1..63
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /inference="alignment:Splign:2.1.0"
     CDS             40..1734
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     poly(U)-binding-splicing factor PUF60; siah-binding
                     protein 1; RNA-binding protein Siah-BP; 60 kDa
                     poly(U)-binding-splicing factor; FBP interacting
                     repressor; pyrimidine tract binding splicing factor; Ro
                     ribonucleoprotein-binding protein 1; siah binding protein
                     1; FBP interacting repressor; pyrimidine tract binding
                     splicing factor; Ro ribonucleoprotein-binding protein 1;
                     poly-U binding splicing factor 60K"
                     /codon_start=1
                     /product="poly(U)-binding-splicing factor PUF60 isoform 1"
                     /protein_id="NP_001386320.1"
                     /db_xref="GeneID:84401"
                     /db_xref="RGD:621674"
                     /translation="MATATIALQVNGQQGGGSEPAAAAAAAAAAVVAAGDKWKPPQGT
                     ESIKMENGQSTGTKLGLPPLTPEQQEALQKAKKYAMEQSIKSVLVKQTIAHQQQQLTN
                     LQMAAVTMGFGDPLSPLQSMAAQRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPI
                     KSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQP
                     IIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGF
                     IEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATPGGLPPAAAVAAAAA
                     TAKITAQEAVAGAAVLGTLATPGLVSPALTLAQPLGALPQAVMAAQAPGVITGVTPAR
                     PPIPVTIPSVGVVNPILASPPTLGLLEPKKEKEEEELFPESERPEMLSEQEHMSISGS
                     SARHMVMQKLLRKQESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQ
                     GEEEDAEIIVKIFVEFSMASETHKAIQALNGRWFGGRKVVAEVYDQERFDNSDLSA"
     exon            64..165
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /inference="alignment:Splign:2.1.0"
     exon            166..261
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /inference="alignment:Splign:2.1.0"
     exon            262..351
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /inference="alignment:Splign:2.1.0"
     exon            352..402
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /inference="alignment:Splign:2.1.0"
     exon            403..564
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /inference="alignment:Splign:2.1.0"
     exon            565..657
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /inference="alignment:Splign:2.1.0"
     exon            658..871
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /inference="alignment:Splign:2.1.0"
     exon            872..1062
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1063..1198
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1199..1434
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1435..1879
                     /gene="Puf60"
                     /gene_synonym="Siahbp1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gatgcttgtg gcgcgcgcgg cggccgcgac ggacgcaaga tggcgacggc aactatagct
       61 ctccaggtca atggccaaca aggagggggg tcggagccag cagcagcggc tgcagcggcg
      121 gcggcggcag tggtggcagc aggagacaaa tggaaacctc cacagggcac agaatccatc
      181 aagatggaaa atgggcaaag cacaggcacc aagctggggc tgcctcccct gacgcccgag
      241 cagcaggagg ccctccagaa ggccaagaaa tatgcaatgg agcagagcat caagagtgtg
      301 ctggtgaagc agaccatcgc ccaccagcag cagcagctca ccaacctgca gatggcagca
      361 gtgacaatgg gctttggaga tcctctctca cctttgcaat cgatggcagc tcagcggcag
      421 cgggcactgg ctatcatgtg ccgggtgtat gtgggttcca tctactatga gctgggagaa
      481 gacactattc gccaggcctt tgctcccttt ggccccatca agagcattga tatgtcctgg
      541 gactccgtta ccatgaagca taagggcttt gccttcgtgg agtatgaggt cccagaagct
      601 gcacagctgg ctttggagca gatgaactct gtgatgcttg ggggcaggaa catcaaggtg
      661 ggaagaccta gcaacatcgg acaagcccaa cccatcatag accagctggc tgaggaggct
      721 agggctttca accgaatata cgtggcctcc gtacatcagg acctgtctga tgatgatatc
      781 aagagtgtgt ttgaagcctt cggcaagatc aagtcttgta cgctggcccg ggaccccaca
      841 actggcaagc acaagggcta tggttttatc gaatatgaga aggcccagtc gtcccaggat
      901 gctgtgtcct ccatgaacct ctttgatctg ggtggccagt acttgagggt gggcaaggcc
      961 gtcacacccc caatgcccct gctaacacct gccacgcctg gaggtctccc gcctgctgct
     1021 gctgtggccg cagctgcagc cacagccaag attacagctc aggaagcagt ggctggagct
     1081 gcagtgctgg gtactttagc cacaccagga ctagtgtccc cagcactgac actggcccag
     1141 cccttagggg ccctacccca ggctgtcatg gctgcccaag cccctggagt catcacaggt
     1201 gtgacaccag cccgccctcc tattccggtc accatcccct ctgtgggagt ggtgaacccc
     1261 atcctagcca gcccgccaac gctgggtctg ttggaaccca agaaggagaa ggaagaggag
     1321 gagctgtttc cagagtcaga gcggccagag atgttgagtg agcaggagca catgagcatc
     1381 tctggcagca gtgctcgaca catggtcatg caaaagctac tcagaaaaca ggagtctaca
     1441 gtgatggttc tccgaaacat ggtggatccc aaggacattg atgatgacct ggagggagag
     1501 gtgacagagg aatgtggcaa atttggtgct gtgaaccggg tcattatcta ccaagaaaaa
     1561 cagggcgagg aggaagatgc agaaatcatc gtcaagattt ttgtggaatt ttccatggct
     1621 tcagagactc acaaggccat ccaggccctc aatgggcgct ggtttggtgg tcgcaaggtg
     1681 gtggctgaag tgtatgacca ggagcgtttt gataacagcg acctctctgc gtgactttgg
     1741 cctcatttcc tggacttgca cttgcccctt ccttcctttg ggttttgtaa agtgttaaaa
     1801 gtggtgtgtc cctgggacca ggcactctgc ccagcccacc ctgtagtgta cataaagatg
     1861 cagatactgc tggccctga
//
