LOCUS       NM_029078               5804 bp    mRNA    linear   ROD 03-JUN-2024
DEFINITION  Mus musculus PCF11 cleavage and polyadenylation factor subunit
            (Pcf11), mRNA.
ACCESSION   NM_029078 XM_485961
VERSION     NM_029078.3
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 5804)
  AUTHORS   Wang,R., Zheng,D., Wei,L., Ding,Q. and Tian,B.
  TITLE     Regulation of Intronic Polyadenylation by PCF11 Impacts mRNA
            Expression of Long Genes
  JOURNAL   Cell Rep 26 (10), 2766-2778 (2019)
   PUBMED   30840896
  REMARK    GeneRIF: PCF11 is autoregulated through a conserved IPA site, the
            removal of which leads to global activation of PASs close to gene
            promotors. Therefore, PCF11 uses distinct mechanisms to regulate
            genes of different sizes, and its autoregulation maintains
            homeostasis of PAS usage in the cell.
REFERENCE   2  (bases 1 to 5804)
  AUTHORS   Okazaki,N., F-Kikuno,R., Ohara,R., Inamoto,S., Koseki,H.,
            Hiraoka,S., Saga,Y., Seino,S., Nishimura,M., Kaisho,T., Hoshino,K.,
            Kitamura,H., Nagase,T., Ohara,O. and Koga,H.
  TITLE     Prediction of the coding sequences of mouse homologues of KIAA
            gene: IV. The complete nucleotide sequences of 500 mouse
            KIAA-homologous cDNAs identified by screening of terminal sequences
            of cDNA clones randomly sampled from size-fractionated libraries
  JOURNAL   DNA Res 11 (3), 205-218 (2004)
   PUBMED   15368895
REFERENCE   3  (bases 1 to 5804)
  AUTHORS   Stryke,D., Kawamoto,M., Huang,C.C., Johns,S.J., King,L.A.,
            Harper,C.A., Meng,E.C., Lee,R.E., Yee,A., L'Italien,L.,
            Chuang,P.T., Young,S.G., Skarnes,W.C., Babbitt,P.C. and Ferrin,T.E.
  TITLE     BayGenomics: a resource of insertional mutations in mouse embryonic
            stem cells
  JOURNAL   Nucleic Acids Res 31 (1), 278-281 (2003)
   PUBMED   12520002
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            CJ046746.1, AK173035.1 and BC030492.1.
            
            On Nov 17, 2009 this sequence version replaced NM_029078.2.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660813.25945.1,
                                           SRR1660819.10193.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164138, SAMN01164139
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-314               CJ046746.1         25-338
            315-5261            AK173035.1         287-5233
            5262-5804           BC030492.1         1212-1754
FEATURES             Location/Qualifiers
     source          1..5804
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="7"
                     /map="7 51.56 cM"
     gene            1..5804
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /note="PCF11 cleavage and polyadenylation factor subunit"
                     /db_xref="GeneID:74737"
                     /db_xref="MGI:MGI:1919579"
     exon            1..484
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     CDS             293..4954
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /note="cleavage and polyadenylation factor subunit
                     homolog; pre-mRNA cleavage complex II protein Pcf11"
                     /codon_start=1
                     /product="pre-mRNA cleavage complex 2 protein Pcf11"
                     /protein_id="NP_083354.3"
                     /db_xref="CCDS:CCDS52311.1"
                     /db_xref="GeneID:74737"
                     /db_xref="MGI:MGI:1919579"
                     /translation="MSEQTPAEAGAAGAREDACRDYQSSLEDLTFNSKPHINMLTILA
                     EENLPFAKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNVGREYLTAFTKNLVATFIC
                     VFEKVDENTRKSLFKLRSTWDEIFPLKKLYALDVRVNSLDPAWPIKPLPPNVNTSSIH
                     VNPKFLNKSPDEPSTPGTVVSSPSISTPPIVPDIQKNLTQEQLIRQQLLAKQKQLLEL
                     QQKKLELELEQAKAQLAVSLSVQQETANLGPGSVPSKLHVPQIPTMAVKTPHQVPVQP
                     DKSRAGPSLQMQDLKGTNRDPRLNRMSQHSSHGKEQSHRKEFVMNTINQSDIKTSKNV
                     PSEKLNSSKQEKSKSGERITKKELDQLDSKSKSKSKSPSPLKNKLSHTKDLKNQDSES
                     MRLSDMSKRDPRLKKHLQDKAEGKDEDVKEKRKTAEKKEKDEHMKSSEHRVIGSRSKI
                     INGIVQKQDMVTEELEKQGTKPGRSSTRKRSRSRSPKSRSPIIHSPKRRDRRSPKRRQ
                     RSMSPNLAPKAGKMRQSGLKQSHMEEFPPPSREERNIKRSAKQDVRDPRRLKKMDEDR
                     PQETAGQHSMKSGGDPKENIENWQSSKSAKRWKSGWEENKSLQQGDEHSKPPHLRHRE
                     SWSSTKGILSPRAPKQQHRLSVDANLQIPKELTLASKRELLQKTSERLASGEITQDEF
                     LVVVHQIRQLFQYQEGVREEQRSPFNDRFPLKRPRYEDSDKPFVDGPASRFAGLDTNQ
                     RLTALAEDRPLFDGPGRPSVTRDGPAKMIFEGPNKLSPRIDGPPTPGSLRFDGSPGQM
                     GGGGPMRFEGPQGQLGGGCPLRFEGPPGPVGTPLRFEGPIGQGGGGGFRFEGSPSLRF
                     EGSTGGLRFEGPGGQPVGGLRFEGHRGQPVGGLRFEGPHGQPVGSLRFDNPRGQPVGG
                     LRFEGGHGPSGAAIRFDGPHGQPGGGGGIRFEGPLLQQGVGMRFEGPHGQSVAGLRFE
                     GHNQLGGNLRFEGPHGQPGVGIRFEGPIVQQGGGMRFEGPVPGGGLRIEGPLGQGGPR
                     FEGCHSLRFDGQPGQPSLLPRFDGLHGQPGPRFERTGQPGPQRFDGPPGQQVQPRFDG
                     VPQRFDGPQHQQASRFDIPLGLQGTRFDNHPSQRIESFNHSGPYNDPPGNTFNVPSQG
                     LQFQRHEQIFDTPQGPNFNGPHGPGNQNFPNPINRASGHYFDEKNLQSSQFGNFGNLP
                     TPISVGNIQASQQVLTGVAQPVAFGQGQQFLPVHPQNPGAFIQNPSGGLPKAYPDNHL
                     SQVDVNELFSKLLKTGILKLSQPDSATAQVTEAVAQPPPEEDEDQNEDQDVPDLTNFT
                     IEELKQRYDSVINRLYTGIQCYSCGMRFTTSQTDVYADHLDWHYRQNRTEKDVSRKVT
                     HRRWYYSLTDWIEFEEIADLEERAKSQFFEKVHEEVVLKTQEAAKEKEFQSVPAGPAG
                     AVESCEICQEQFEQYWDEEEEEWHLKNAIRVDGKIYHPSCYEDYQNTSSFDCTPSPSK
                     TPVENPLNIMLNIVKNELQEPCESPKVKEEQIDAPPACSEESVATPTEIKTESDTVES
                     V"
     exon            485..610
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            611..799
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            800..994
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            995..2112
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            2113..2293
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            2294..2384
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            2385..3943
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            3944..4043
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            4044..4163
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            4164..4269
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            4270..4453
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            4454..4609
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            4610..4702
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            4703..4738
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     exon            4739..5804
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /inference="alignment:Splign:2.1.0"
     regulatory      5784..5789
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /note="hexamer: AATAAA"
     polyA_site      5804
                     /gene="Pcf11"
                     /gene_synonym="2500001H09Rik; 5730417B17Rik"
                     /note="major polyA site"
ORIGIN      
        1 ggaacacaga cattttcgga gctggagccg ccactgccgc cgccattttg tgtctgtgga
       61 gaaagaagcc ccggcggcgg ctggaagcgg acggagattc cccgtgaggc tgcggcgttt
      121 cttccccgag gttccccctg ggtcgtcccc catcccccct ccgtggtcag catgtggtga
      181 agccgcagcc gccggagacc cggggagcga ggccgaggcg tcggaaggga ggcggggtgt
      241 cgagcggctt cagcttcggc ggcggcggac ctcggagggg ggccgcggcg caatgtcaga
      301 gcagacgccg gcggaggccg gggctgcggg ggcccgggag gacgcctgtc gggattatca
      361 gtcgtcgctg gaagacctga ccttcaatag caaaccgcac atcaatatgc tgaccattct
      421 agccgaggag aacctgccct tcgccaagga gatcgtctct ctcatcgagg cccaaaccgc
      481 caaggctcct tcctcagaga agcttccagt tatgtacctt atggattcta tcgtgaaaaa
      541 tgttggaaga gaatatctca ctgcctttac taaaaatcta gttgcaacat ttatttgtgt
      601 gtttgaaaag gtggatgaaa atactagaaa aagtttattt aaattacgtt ccacatggga
      661 tgaaatattc cctttgaaga aactttatgc cttggatgtc agagtcaatt cattagatcc
      721 tgcttggcct attaaacctc tgcctcctaa tgtgaataca tctagcatcc atgtgaatcc
      781 caaattttta aataaatcgc ctgatgagcc ttcaacacct ggcacagtgg tcagttcccc
      841 cagtatctcc actcctccca ttgtacctga tatacaaaag aatcttaccc aagaacaact
      901 aataaggcaa cagttactgg caaaacaaaa acagttgtta gaacttcagc agaaaaagct
      961 ggagcttgag ttagaacaag ctaaggcaca gctggcagta tctctgagtg ttcagcagga
     1021 aacagccaac ttgggtcctg gatcagtgcc gtctaaatta catgttccac aaattcccac
     1081 aatggctgtt aaaactcccc atcaggtccc tgtacaacct gacaaaagcc gagcaggtcc
     1141 atccttacaa atgcaagact tgaaaggaac taaccgggat ccccgtctta acaggatgag
     1201 ccaacattct tcccatggca aagagcagag tcataggaaa gaatttgtaa tgaacacaat
     1261 aaaccagtct gatattaaaa caagtaagaa tgtaccctct gaaaagctaa attcatccaa
     1321 acaagaaaaa agtaaatcag gtgaaagaat aaccaagaaa gaacttgacc agttagattc
     1381 taaatccaaa tctaagtcta aatcaccatc acctttgaaa aacaaattat cccacacaaa
     1441 agacttgaaa aatcaagact ctgaaagtat gaggttgtct gatatgagta agagagatcc
     1501 acgattaaag aagcatcttc aggataaagc tgagggcaaa gatgaagatg taaaagaaaa
     1561 gagaaaaact gcagaaaaga aggagaaaga tgagcacatg aaatcatctg aacacagggt
     1621 gattggaagt agaagtaaaa tcataaatgg cattgtccaa aaacaagaca tggttacaga
     1681 ggagttggaa aaacagggga caaaaccagg gagatcgagt actagaaaga gatcaagatc
     1741 aaggtcacct aagtctcggt caccaattat acattcccca aagagaagag atagacggtc
     1801 acccaaacga aggcaaagaa gtatgtctcc caatttggca cccaaagctg gaaagatgcg
     1861 tcagtcggga ctaaaacagt cacatatgga agaattccca ccaccttcca gggaagaaag
     1921 aaatattaag agaagtgcta agcaggatgt tagagatccc agacgactga aaaagatgga
     1981 tgaggaccgg cctcaagaaa ctgcaggtca acattctatg aagtcaggtg gtgacccaaa
     2041 ggagaatata gagaattggc aaagctctaa gtctgccaaa agatggaaat ctggctggga
     2101 agaaaataaa agcttgcagc agggtgatga acatagtaaa cctcctcatc taaggcatag
     2161 ggagagctgg tcaagcacta aagggatctt gtcacctcga gcccccaagc agcagcaccg
     2221 actaagtgta gatgccaatc ttcaaattcc taaagagtta actcttgcaa gcaaaagaga
     2281 attgcttcaa aagacgagcg aacgtttagc atctggtgaa attacacagg atgagttcct
     2341 tgttgttgtg catcaaattc gacagctatt tcagtatcaa gaaggtgtac gagaggagca
     2401 gagatcacca ttcaatgatc gttttccact taagcgacct agatatgaag attcagataa
     2461 accatttgta gatggcccag catcaagatt tgctggcctt gatacaaatc agcgacttac
     2521 agctctagct gaagaccgac cattatttga tggacctggt aggccatctg tgacgagaga
     2581 tggcccagcc aagatgattt ttgaaggacc taataaatta agccctagaa ttgatggacc
     2641 tcctacacca ggttctcttc ggtttgatgg gtcaccagga caaatggggg gaggaggccc
     2701 tatgagattt gaaggaccac aaggtcagtt aggaggtggg tgtcctttga gatttgaagg
     2761 tcctccagga ccagtaggaa cacctctgcg gtttgaaggg ccaattggtc aaggaggagg
     2821 aggtggtttt cgatttgaag gttcacctag tttgaggttt gagggatcta caggtggttt
     2881 acgatttgaa ggaccagggg gtcagcccgt gggtggtctc aggtttgaag gacatcgtgg
     2941 tcaacctgtg ggtggtctca ggtttgaagg acctcatgga cagcctgtgg gcagtcttag
     3001 atttgataat cctcgaggtc agcctgtagg aggacttaga tttgaagggg gtcatggtcc
     3061 atcaggggct gcaattaggt ttgatgggcc tcatggtcag ccaggtggtg gtggtggtat
     3121 cagatttgag ggccctttgc tacagcaagg agttggaatg aggtttgagg gtccccatgg
     3181 tcagtctgta gctggtctga gatttgaagg acataatcaa ctaggtggga accttaggtt
     3241 tgagggacca catggtcaac caggggttgg gatcaggttt gaaggaccta tagttcaaca
     3301 aggaggtgga atgaggtttg aaggtcctgt accaggaggt ggcctgagaa ttgaagggcc
     3361 tctgggtcaa ggtggtccta gatttgaagg ttgtcactct ttaaggtttg atggacagcc
     3421 aggtcaacca tcacttttgc caagatttga tggattacat ggccagccag gtcctagatt
     3481 tgaaagaact ggtcagccag gtccacagag gtttgatgga ccacctggac agcaggttca
     3541 accaagattt gatggtgtac ctcaaagatt tgatgggcca caacaccagc aagcatcaag
     3601 atttgatatt cctcttggtc tacaaggaac tcgatttgac aatcatcctt cacaaaggat
     3661 tgaatctttc aatcattctg gcccatataa tgatccacct ggcaatactt ttaatgttcc
     3721 atctcaagga ttacagttcc aaagacacga acaaatattt gatacacctc aaggaccaaa
     3781 ttttaatgga ccacatggcc ctggaaatca gaatttccca aatcccatta acagagcttc
     3841 tggacactat tttgatgaaa agaatcttca gagttctcag tttggaaact ttggcaattt
     3901 gcctacacca atatcagtag gaaatattca ggcatctcaa caggttctta ctggtgttgc
     3961 tcagccagta gcgtttggcc aaggacaaca gttcttacca gttcatccac agaatcctgg
     4021 agcttttatt caaaatcctt caggcggtct tcccaaggca tatcctgata atcatctcag
     4081 tcaggtggat gtaaacgaat tgttttcaaa actgctaaaa acaggaattc tcaaattgtc
     4141 acagcctgat tcagctacag cacaggtaac cgaggctgtt gctcagcctc cccctgagga
     4201 ggacgaggat cagaatgaag atcaggatgt tccagatctt accaatttca ccattgaaga
     4261 attgaagcaa cgttatgaca gtgttataaa ccggctgtac actgggattc aatgttactc
     4321 gtgtggaatg aggttcacga catcccagac agatgtttat gcagatcact tggattggca
     4381 ttatcggcaa aacagaaccg agaaagatgt tagcagaaaa gtcactcata gacgttggta
     4441 ctacagtcta acagattgga tagaatttga agaaatagct gatctggaag aacgtgcaaa
     4501 aagccagttt tttgaaaagg ttcatgaaga ggttgtcctt aaaactcagg aggctgctaa
     4561 agaaaaggag ttccaaagtg tacctgctgg accagctgga gcagttgaga gttgtgaaat
     4621 ctgtcaagaa caatttgaac agtactggga tgaagaggag gaagaatggc acttaaaaaa
     4681 tgctattaga gtagacggaa agatttacca tccatcatgt tatgaagatt atcaaaatac
     4741 atcttcattt gattgcacac catctcccag caagacacca gttgaaaacc ctttgaacat
     4801 tatgttgaac attgtcaaaa acgaattgca agaaccctgt gaaagtccca aagttaagga
     4861 agaacaaatt gatgccccac cagcttgttc agaagaaagt gtagcaacac ccactgaaat
     4921 taaaacagaa agtgatacag ttgagtcagt ttaaataaaa tgagaaaagt atgcttttct
     4981 ttttaaacaa aagctgctgt tggatctagg tgaagaattt ttttatgtat atatagaaat
     5041 atctatatta attgtctagc tgtggcaggg ccttcagcta tcatttggtt aataaataca
     5101 ttttagtatt tgcatttcct actgcctgca cagtttcagg tgcttgttgt gtgaaagttc
     5161 tgtagatgag tgcaaatgta acaaaatgaa attgtatgtg tacaaatgta caattttcac
     5221 ttgtgaactg taaattataa ataaaaaata tttttgctat ccatggagtg taatatttat
     5281 gcacaccatc aaataaagac agtgtttcta tacttttatt gggcaagaat ggaactgaac
     5341 agcaatctta acatgatggt tttttttcta gtagcttcct gggacttaat gcagcaaagt
     5401 ttcaaactta gtttttctca aatagaaaag caagattaaa aaaacaaaaa ggacatatgt
     5461 gcttacatat agatatgtat ctccagctag agtcatccac aatgtccact tttggaaagt
     5521 atgtaatgaa acagtaatgc ttatttaaac ttggacactg atgccatcaa gcaactaaca
     5581 aatatattta agtactaaaa gtgattttac tttttagaaa atatttttaa aattgtcaat
     5641 ttaatgcaga tgaacacatt tctattttaa gttacaggga ttctgtataa gaatgttcat
     5701 atgaaaaaca tggttaactt tttttctttg ttggttttga ttgaattaga tgggtaacat
     5761 gagatgttaa tattcataca tgtaataaac tgaatgatga acaa
//
