LOCUS       NM_133840               1849 bp    mRNA    linear   ROD 05-JUN-2024
DEFINITION  Mus musculus CLP1, cleavage and polyadenylation factor I subunit
            (Clp1), transcript variant 1, mRNA.
ACCESSION   NM_133840
VERSION     NM_133840.3
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 1849)
  AUTHORS   LaForce,G.R., Farr,J.S., Liu,J., Akesson,C., Gumus,E., Pinkard,O.,
            Miranda,H.C., Johnson,K., Sweet,T.J., Ji,P., Lin,A., Coller,J.,
            Philippidou,P., Wagner,E.J. and Schaffer,A.E.
  TITLE     Suppression of premature transcription termination leads to reduced
            mRNA isoform diversity and neurodegeneration
  JOURNAL   Neuron 110 (8), 1340-1357 (2022)
   PUBMED   35139363
REFERENCE   2  (bases 1 to 1849)
  AUTHORS   Monaghan,C.E., Adamson,S.I., Kapur,M., Chuang,J.H. and
            Ackerman,S.L.
  TITLE     The Clp1 R140H mutation alters tRNA metabolism and mRNA 3'
            processing in mouse models of pontocerebellar hypoplasia
  JOURNAL   Proc Natl Acad Sci U S A 118 (39) (2021)
   PUBMED   34548404
  REMARK    GeneRIF: The Clp1 R140H mutation alters tRNA metabolism and mRNA 3'
            processing in mouse models of pontocerebellar hypoplasia.
REFERENCE   3  (bases 1 to 1849)
  AUTHORS   Morisaki,I., Shiraishi,H., Fujinami,H., Shimizu,N., Hikida,T.,
            Arai,Y., Kobayashi,T., Hanada,R., Penninger,J.M., Fujiki,M. and
            Hanada,T.
  TITLE     Modeling a human CLP1 mutation in mouse identifies an accumulation
            of tyrosine pre-tRNA fragments causing pontocerebellar hypoplasia
            type 10
  JOURNAL   Biochem Biophys Res Commun 570, 60-66 (2021)
   PUBMED   34273619
REFERENCE   4  (bases 1 to 1849)
  AUTHORS   Fujinami,H., Shiraishi,H., Hada,K., Inoue,M., Morisaki,I., Higa,R.,
            Shin,T., Kobayashi,T., Hanada,R., Penninger,J.M., Mimata,H. and
            Hanada,T.
  TITLE     CLP1 acts as the main RNA kinase in mice
  JOURNAL   Biochem Biophys Res Commun (2020) In press
   PUBMED   32081435
  REMARK    Publication Status: Available-Online prior to print
REFERENCE   5  (bases 1 to 1849)
  AUTHORS   Karaca,E., Weitzer,S., Pehlivan,D., Shiraishi,H., Gogakos,T.,
            Hanada,T., Jhangiani,S.N., Wiszniewski,W., Withers,M.,
            Campbell,I.M., Erdin,S., Isikay,S., Franco,L.M.,
            Gonzaga-Jauregui,C., Gambin,T., Gelowani,V., Hunter,J.V., Yesil,G.,
            Koparir,E., Yilmaz,S., Brown,M., Briskin,D., Hafner,M., Morozov,P.,
            Farazi,T.A., Bernreuther,C., Glatzel,M., Trattnig,S., Friske,J.,
            Kronnerwetter,C., Bainbridge,M.N., Gezdirici,A., Seven,M.,
            Muzny,D.M., Boerwinkle,E., Ozen,M., Clausen,T., Tuschl,T.,
            Yuksel,A., Hess,A., Gibbs,R.A., Martinez,J., Penninger,J.M. and
            Lupski,J.R.
  CONSRTM   Baylor Hopkins Center for Mendelian Genomics
  TITLE     Human CLP1 mutations alter tRNA biogenesis, affecting both
            peripheral and central nervous system function
  JOURNAL   Cell 157 (3), 636-650 (2014)
   PUBMED   24766809
REFERENCE   6  (bases 1 to 1849)
  AUTHORS   Hanada,T., Weitzer,S., Mair,B., Bernreuther,C., Wainger,B.J.,
            Ichida,J., Hanada,R., Orthofer,M., Cronin,S.J., Komnenovic,V.,
            Minis,A., Sato,F., Mimata,H., Yoshimura,A., Tamir,I., Rainer,J.,
            Kofler,R., Yaron,A., Eggan,K.C., Woolf,C.J., Glatzel,M., Herbst,R.,
            Martinez,J. and Penninger,J.M.
  TITLE     CLP1 links tRNA metabolism to progressive motor-neuron loss
  JOURNAL   Nature 495 (7442), 474-480 (2013)
   PUBMED   23474986
  REMARK    GeneRIF: loss of CLP1 activity results in accumulation of a novel
            set of small RNA fragments derived from aberrant processing of
            tyrosine pre-transfer RNA; these tRNA fragments sensitize cells to
            oxidative-stress-induced p53 activation and p53-dependent cell
            death
REFERENCE   7  (bases 1 to 1849)
  AUTHORS   Nishimura,M., Yokoi,N., Miki,T., Horikawa,Y., Yoshioka,H.,
            Takeda,J., Ohara,O. and Seino,S.
  TITLE     Construction of a multi-functional cDNA library specific for mouse
            pancreatic islets and its application to microarray
  JOURNAL   DNA Res 11 (5), 315-323 (2004)
   PUBMED   15747579
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL928914.15.
            
            On Apr 26, 2018 this sequence version replaced NM_133840.2.
            
            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 alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC003237.1, AK169709.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849386, SAMN01164134
                                           [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
            1-125               AL928914.15        9516-9640           c
            126-753             AL928914.15        7882-8509           c
            754-1849            AL928914.15        5475-6570           c
FEATURES             Location/Qualifiers
     source          1..1849
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 49.45 cM"
     gene            1..1849
                     /gene="Clp1"
                     /gene_synonym="Heab"
                     /note="CLP1, cleavage and polyadenylation factor I
                     subunit"
                     /db_xref="GeneID:98985"
                     /db_xref="MGI:MGI:2138968"
     exon            1..125
                     /gene="Clp1"
                     /gene_synonym="Heab"
                     /inference="alignment:Splign:2.1.0"
     exon            126..753
                     /gene="Clp1"
                     /gene_synonym="Heab"
                     /inference="alignment:Splign:2.1.0"
     CDS             148..1425
                     /gene="Clp1"
                     /gene_synonym="Heab"
                     /EC_number="2.7.1.78"
                     /note="ATP/GTP-binding protein; polynucleotide kinase
                     Clp1; pre-mRNA cleavage complex II protein Clp1"
                     /codon_start=1
                     /product="polyribonucleotide 5'-hydroxyl-kinase Clp1"
                     /protein_id="NP_598601.1"
                     /db_xref="CCDS:CCDS16191.1"
                     /db_xref="GeneID:98985"
                     /db_xref="MGI:MGI:2138968"
                     /translation="MSEESNDDKKPTTKFELERETELRFEVEASQSVQLELLAGMAEI
                     FGTELTRNKKFTFDAGAKVAVFTWHGCSLQLSGRTEVAYVSKDTPMLLYLNTHTALEQ
                     MRRQAEKEEERGPRVMVVGPTDVGKSTVCRLLLNYAVRLGRRPTYVELDVGQGSVSIP
                     GTMGALYIERPADVEEGFSIQAPLVYHFGSTTPGTNIKLYNKITSRLADVFNQRCEVN
                     RRASVSGCVINTCGWVKGYGYQALVHAASAFEVDVVVVLDQERLYNELKRDLPHFVRT
                     VLLPKSGGVVERSKDFRRECRDERIREYFYGFRGCFYPHAFNVKFSDVKIYKVGAPTI
                     PDSCLPLGMSQEDNQLKLVPVTPGRDMVHHLLSVSTAEGTEENLSETSVAGFIVVTSV
                     DVEHQVFTVLSPAPRPLPKNFLLIMDIRFMDLK"
     exon            754..1849
                     /gene="Clp1"
                     /gene_synonym="Heab"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1828..1833
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Clp1"
                     /gene_synonym="Heab"
                     /note="hexamer: AATAAA"
     polyA_site      1849
                     /gene="Clp1"
                     /gene_synonym="Heab"
                     /note="major polyA site"
ORIGIN      
        1 gctttccggc tagtatttag gtgaacgtta ttcgtggttt gctgaggtcc gaggtttgct
       61 gaggtcggag gtttccagag gtcccaggtt tctgtgaagc tggttttgag tccgtgcccg
      121 tataggcacg tcagctttac tggaaagatg agcgaggaat ccaatgatga caagaagcca
      181 acgactaagt ttgaactaga gcgagaaaca gagcttcgat ttgaggtgga ggcctctcaa
      241 tcggttcagt tggagttgtt ggctggcatg gcggagatct ttggcacaga gctgaccaga
      301 aacaagaaat tcacttttga tgctggtgcc aaggtggctg ttttcacttg gcatggctgt
      361 tctctgcagt tgagtggccg gactgaggtg gcttatgtct ctaaggacac ccctatgttg
      421 ctttacctca acactcatac agccttggag cagatgcgga ggcaggcaga aaaggaagaa
      481 gagagaggtc cccgagtgat ggtagtaggt cctactgatg tgggcaagtc cactgtgtgt
      541 cgactgctac tcaactacgc agtgcgtttg ggccgccgtc ctacttacgt ggagttagat
      601 gtaggccagg gctctgtgtc catccctggt accatggggg ccctgtacat tgagcgtcca
      661 gcagatgtgg aagaaggttt ctccatccag gcccctcttg tgtatcattt tggctccacc
      721 acgcctggca ccaacatcaa gctttacaat aagattacat ctcgcttagc agatgtgttc
      781 aaccaaaggt gtgaagtgaa cagaagggct tctgtgagtg gctgtgtcat caacacctgt
      841 ggctgggtca agggctatgg ttaccaagcc ctggtgcacg cagcgtcggc ctttgaggtg
      901 gatgtggttg tggttctgga tcaagagcga ctgtacaacg aattgaaaag ggacctgcct
      961 cattttgttc gaactgtgtt gcttccaaaa tcagggggtg tggtagaacg ttccaaggac
     1021 ttccggcggg aatgtagaga tgaacgtatc cgtgagtatt tctatggatt tcgaggctgt
     1081 ttctatcccc atgccttcaa cgtcaaattt tctgatgtga aaatctacaa agttggagca
     1141 cccaccattc cagattcctg tttacctctg ggtatgtctc aggaagacaa ccagctcaag
     1201 ttagtgcctg tcacccctgg tagagatatg gtgcaccatc tcctgagtgt gagcactgct
     1261 gagggcacag aagagaacct ttctgagacc agtgtggctg gattcattgt tgtgaccagt
     1321 gtggatgtgg aacaccaagt gtttactgtc ctgtctccag ccccccgccc attgcctaag
     1381 aactttcttc tcatcatgga tatccggttc atggatctca agtagtaatt gcaagaagcc
     1441 tcactttctg ggccatagag ttctggtcat caccaaaggc agatggaatg gactatagca
     1501 atcttattaa ggcagctgac aaggcccaac tagcagaaag cacatttgct acctcttgaa
     1561 actggtagta gccagactcc tggctattat ttggttcatt tactctgaac caaaaggaga
     1621 cagctcaaaa agaaaatctg aatatttttt taagatcacc taaggtacca ttttaaagat
     1681 tccaagaccc tagaaaattc cacgtcttcc acatgtgctt ccatgtgggt tttcttgtta
     1741 ccactttctt gtatctctgt atagtatttg ctatatcatt taaccaggat gaaagtgaga
     1801 gagttcaaac ttgaaaacaa ttattttaat aaatatgatt gtgatagaa
//
