LOCUS       NM_006831               1828 bp    mRNA    linear   PRI 20-SEP-2024
DEFINITION  Homo sapiens cleavage factor polyribonucleotide kinase subunit 1
            (CLP1), transcript variant 1, mRNA.
ACCESSION   NM_006831
VERSION     NM_006831.3
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1828)
  AUTHORS   Boreikaite,V., Elliott,T.S., Chin,J.W. and Passmore,L.A.
  TITLE     RBBP6 activates the pre-mRNA 3' end processing machinery in humans
  JOURNAL   Genes Dev 36 (3-4), 210-224 (2022)
   PUBMED   35177536
REFERENCE   2  (bases 1 to 1828)
  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
  REMARK    GeneRIF: Modeling a human CLP1 mutation in mouse identifies an
            accumulation of tyrosine pre-tRNA fragments causing pontocerebellar
            hypoplasia type 10.
REFERENCE   3  (bases 1 to 1828)
  AUTHORS   Wu,J., Li,X., Gao,Z., Pang,L., Liu,X., Huang,X., Wang,Y. and
            Wang,Z.
  TITLE     RNA kinase CLP1/Cbc regulates meiosis initiation in spermatogenesis
  JOURNAL   Hum Mol Genet 30 (17), 1569-1578 (2021)
   PUBMED   33864361
  REMARK    GeneRIF: RNA kinase CLP1/Cbc regulates meiosis initiation in
            spermatogenesis.
REFERENCE   4  (bases 1 to 1828)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   5  (bases 1 to 1828)
  AUTHORS   Ramirez,A., Shuman,S. and Schwer,B.
  TITLE     Human RNA 5'-kinase (hClp1) can function as a tRNA splicing enzyme
            in vivo
  JOURNAL   RNA 14 (9), 1737-1745 (2008)
   PUBMED   18648070
  REMARK    GeneRIF: Expression of hClp1 in budding yeast can complement
            conditional and lethal mutations in the essential 5'-OH RNA kinase
            module of yeast or plant tRNA ligases.
REFERENCE   6  (bases 1 to 1828)
  AUTHORS   Weitzer,S. and Martinez,J.
  TITLE     The human RNA kinase hClp1 is active on 3' transfer RNA exons and
            short interfering RNAs
  JOURNAL   Nature 447 (7141), 222-226 (2007)
   PUBMED   17495927
  REMARK    GeneRIF: the kinase hClp1 phosphorylates and licenses synthetic
            siRNAs to become assembled into RISC for subsequent target RNA
            cleavage
REFERENCE   7  (bases 1 to 1828)
  AUTHORS   Paushkin,S.V., Patel,M., Furia,B.S., Peltz,S.W. and Trotta,C.R.
  TITLE     Identification of a human endonuclease complex reveals a link
            between tRNA splicing and pre-mRNA 3' end formation
  JOURNAL   Cell 117 (3), 311-321 (2004)
   PUBMED   15109492
REFERENCE   8  (bases 1 to 1828)
  AUTHORS   Zhou,Z., Licklider,L.J., Gygi,S.P. and Reed,R.
  TITLE     Comprehensive proteomic analysis of the human spliceosome
  JOURNAL   Nature 419 (6903), 182-185 (2002)
   PUBMED   12226669
REFERENCE   9  (bases 1 to 1828)
  AUTHORS   de Vries,H., Ruegsegger,U., Hubner,W., Friedlein,A., Langen,H. and
            Keller,W.
  TITLE     Human pre-mRNA cleavage factor II(m) contains homologs of yeast
            proteins and bridges two other cleavage factors
  JOURNAL   EMBO J 19 (21), 5895-5904 (2000)
   PUBMED   11060040
  REMARK    GeneRIF: HEAB is a pre-mRNA 3'-end processing factor, which bridges
            two other pre-mRNA processing factors (CF Im and CPSF) and is
            involved in cleavage of the pre-mRNA. It can be UV-crosslinked to
            GTP.
REFERENCE   10 (bases 1 to 1828)
  AUTHORS   Tanabe,S., Bohlander,S.K., Vignon,C.V., Espinosa,R. 3rd, Zhao,N.,
            Strissel,P.L., Zeleznik-Le,N.J. and Rowley,J.D.
  TITLE     AF10 is split by MLL and HEAB, a human homolog to a putative
            Caenorhabditis elegans ATP/GTP-binding protein in an
            invins(10;11)(p12;q23q12)
  JOURNAL   Blood 88 (9), 3535-3545 (1996)
   PUBMED   8896421
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA922553.1 and BC000446.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_006831.2.
            
            Summary: This gene encodes a member of the Clp1 family. The encoded
            protein is a multifunctional kinase which is a component of the
            tRNA splicing endonuclease complex and a component of the pre-mRNA
            cleavage complex II. This protein is implicated in tRNA, mRNA, and
            siRNA maturation. Mutations in this gene are associated with
            pontocerebellar hypoplasia type 10 (PCH10). Alternatively splice
            transcript variants encoding different isoforms have been found for
            this gene. [provided by RefSeq, Sep 2014].
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes a longer protein (isoform 1).
            
            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 :: U73524.1, SRR1803612.125930.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000533682.2/ ENSP00000434995.1
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-4                 DA922553.1         19-22
            5-1828              BC000446.1         11-1834
FEATURES             Location/Qualifiers
     source          1..1828
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11q12.1"
     gene            1..1828
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /note="cleavage factor polyribonucleotide kinase subunit
                     1"
                     /db_xref="GeneID:10978"
                     /db_xref="HGNC:HGNC:16999"
                     /db_xref="MIM:608757"
     exon            1..99
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /inference="alignment:Splign:2.1.0"
     exon            100..727
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /inference="alignment:Splign:2.1.0"
     CDS             122..1399
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /EC_number="2.7.1.78"
                     /note="isoform 1 is encoded by transcript variant 1;
                     homolog of yeast CFIA subunit Clp1p; ATP/GTP-binding
                     protein; polyribonucleotide 5'-hydroxyl-kinase Clp1;
                     polynucleotide kinase Clp1; pre-mRNA cleavage complex II
                     protein Clp1; polyadenylation factor Clp1; cleavage and
                     polyadenylation factor I subunit 1"
                     /codon_start=1
                     /product="polyribonucleotide 5'-hydroxyl-kinase Clp1
                     isoform 1"
                     /protein_id="NP_006822.1"
                     /db_xref="CCDS:CCDS7964.1"
                     /db_xref="GeneID:10978"
                     /db_xref="HGNC:HGNC:16999"
                     /db_xref="MIM:608757"
                     /translation="MGEEANDDKKPTTKFELERETELRFEVEASQSVQLELLTGMAEI
                     FGTELTRNKKFTFDAGAKVAVFTWHGCSVQLSGRTEVAYVSKDTPMLLYLNTHTALEQ
                     MRRQAEKEEERGPRVMVVGPTDVGKSTVCRLLLNYAVRLGRRPTYVELDVGQGSVSIP
                     GTMGALYIERPADVEEGFSIQAPLVYHFGSTTPGTNIKLYNKITSRLADVFNQRCEVN
                     RRASVSGCVINTCGWVKGSGYQALVHAASAFEVDVVVVLDQERLYNELKRDLPHFVRT
                     VLLPKSGGVVERSKDFRRECRDERIREYFYGFRGCFYPHAFNVKFSDVKIYKVGAPTI
                     PDSCLPLGMSQEDNQLKLVPVTPGRDMVHHLLSVSTAEGTEENLSETSVAGFIVVTSV
                     DLEHQVFTVLSPAPRPLPKNFLLIMDIRFMDLK"
     exon            728..1828
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /inference="alignment:Splign:2.1.0"
     polyA_site      1582
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /note="major polyA site"
     regulatory      1805..1810
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /note="hexamer: AATAAA"
     polyA_site      1828
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /note="major polyA site"
ORIGIN      
        1 gtttccggcg tgggtccggg caagaaccgc ttgtagtttg gtttaaattc tgcacgggag
       61 gaccttctga gtttacctgt tgggctcctg gctgcgcagg cacagcagct acacagaaga
      121 gatgggagaa gaggctaatg atgacaagaa gccaaccact aaatttgaac tagagcgaga
      181 aacagaactt cgctttgagg tggaggcatc tcagtcagtt cagttggagt tgttgactgg
      241 catggcagag atctttggca cagagctgac ccgaaacaag aaattcacct ttgatgctgg
      301 tgccaaggtg gctgttttca cttggcatgg ctgttctgtg caactgagcg gccgcactga
      361 ggtggcttat gtctccaagg acactcctat gttgctttac ctcaacactc acacagcctt
      421 ggaacagatg cggaggcaag cggaaaagga agaagagcga ggtccccgag tgatggtagt
      481 gggccccact gatgtgggca agtctacagt gtgtcgcctt ctgctcaact acgcagtgcg
      541 tttgggccgc cgtcccactt atgtggagct ggatgtgggc cagggttctg tgtccatccc
      601 tggtaccatg ggggccctct acatcgagcg gcctgcagat gtcgaagagg gtttctctat
      661 ccaggcccct ctggtgtatc attttggttc caccactcct ggcactaaca tcaagcttta
      721 taataagatt acatctcgtt tagcagatgt gttcaaccaa aggtgtgagg tgaaccgaag
      781 ggcatctgtg agtggctgtg tcattaacac ctgtggctgg gtcaagggct ctggttacca
      841 ggctctggtg catgcagcct cagcttttga ggtggatgtc gttgttgttc tggatcaaga
      901 acgactgtac aatgaactga aacgggacct cccccacttt gtacgcactg tgctgctccc
      961 taaatctggg ggtgtggtgg agcgctccaa ggacttccgg cgggaatgta gggatgagcg
     1021 tatccgtgag tatttttatg gattccgagg ctgtttctat ccccatgcct tcaatgtcaa
     1081 attttcagat gtgaaaatct acaaagttgg ggcacccacc atcccagact cctgtttacc
     1141 tttgggcatg tctcaagagg ataatcagct caagctagta cctgtcactc ctgggcgaga
     1201 tatggtgcac cacctactga gtgttagcac tgccgagggt acagaggaga acctgtccga
     1261 gacaagtgta gctggcttca ttgtggtgac cagtgtggac ctggagcatc aggtgtttac
     1321 tgttctgtct ccagcccctc gcccactgcc taagaacttc cttctcatca tggatatccg
     1381 gttcatggat ctgaagtaga gatcagcagg aagccttgct gcctgggaca tagagatcat
     1441 ctggccaccc ctagaggcag atgggctgag ataaaagact gttggggcca cctgaccagt
     1501 aaactgtgga ctagtagaaa gttcatattc tacctctaaa aacaggtagt ggtaacctga
     1561 ctcttctaat cttgaaccaa aaggaaaacc atgagactgt aattggtttc ttagaccacc
     1621 taagatgcca ctttgaattc tctaagaccc tggagaattg catttctttc actgtgctac
     1681 tatgtggttt ttaaaaaatc aatgctttat attccatatg tggttcttac ccatttatct
     1741 aggatgaaag tgtgaattag agggactcct tccaataaag ttcaaactta aaaaaaatca
     1801 ttttaataaa tatttttgcc atatcata
//
