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2024-03-29 06:27:09, GGRNA : RefSeq release 60 (20130726)

LOCUS       NM_006831               1864 bp    mRNA    linear   PRI 17-APR-2013
DEFINITION  Homo sapiens cleavage and polyadenylation factor I subunit 1
            (CLP1), transcript variant 1, mRNA.
ACCESSION   NM_006831
VERSION     NM_006831.2  GI:217272857
KEYWORDS    RefSeq.
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 1864)
  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   2  (bases 1 to 1864)
  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   3  (bases 1 to 1864)
  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   4  (bases 1 to 1864)
  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   5  (bases 1 to 1864)
  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   6  (bases 1 to 1864)
  AUTHORS   Tanabe,S., Bohlander,S.K., Vignon,C.V., Espinosa,R. III, 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     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DA922553.1 and BC000446.1.
            On Dec 11, 2008 this sequence version replaced gi:5803028.
            
            Transcript Variant: This variant (1) uses an alternate splice donor
            site and encodes a longer protein (isoform 1).
            
            ##Evidence-Data-START##
            Transcript exon combination :: U73524.1, BG339978.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           ERS025081, ERS025083 [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-22                DA922553.1         1-22
            23-1864             BC000446.1         11-1852
FEATURES             Location/Qualifiers
     source          1..1864
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11q12"
     gene            1..1864
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /note="cleavage and polyadenylation factor I subunit 1"
                     /db_xref="GeneID:10978"
                     /db_xref="HGNC:16999"
                     /db_xref="HPRD:16382"
                     /db_xref="MIM:608757"
     exon            1..117
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /inference="alignment:Splign:1.39.8"
     variation       13
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:117284601"
     variation       31
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:185853414"
     variation       40
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:373729660"
     variation       73
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:376913568"
     misc_feature    86..88
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /note="upstream in-frame stop codon"
     exon            118..745
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /inference="alignment:Splign:1.39.8"
     variation       132
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:374267974"
     CDS             140..1417
                     /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; CLP1, cleavage and polyadenylation factor I
                     subunit, homolog; polyadenylation factor Clp1"
                     /codon_start=1
                     /product="polyribonucleotide 5'-hydroxyl-kinase Clp1
                     isoform 1"
                     /protein_id="NP_006822.1"
                     /db_xref="GI:5803029"
                     /db_xref="CCDS:CCDS7964.1"
                     /db_xref="GeneID:10978"
                     /db_xref="HGNC:16999"
                     /db_xref="HPRD:16382"
                     /db_xref="MIM:608757"
                     /translation="
MGEEANDDKKPTTKFELERETELRFEVEASQSVQLELLTGMAEIFGTELTRNKKFTFDAGAKVAVFTWHGCSVQLSGRTEVAYVSKDTPMLLYLNTHTALEQMRRQAEKEEERGPRVMVVGPTDVGKSTVCRLLLNYAVRLGRRPTYVELDVGQGSVSIPGTMGALYIERPADVEEGFSIQAPLVYHFGSTTPGTNIKLYNKITSRLADVFNQRCEVNRRASVSGCVINTCGWVKGSGYQALVHAASAFEVDVVVVLDQERLYNELKRDLPHFVRTVLLPKSGGVVERSKDFRRECRDERIREYFYGFRGCFYPHAFNVKFSDVKIYKVGAPTIPDSCLPLGMSQEDNQLKLVPVTPGRDMVHHLLSVSTAEGTEENLSETSVAGFIVVTSVDLEHQVFTVLSPAPRPLPKNFLLIMDIRFMDLK
"
     misc_feature    224..1408
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /note="Predicted GTPase subunit of the pre-mRNA cleavage
                     complex [Translation, ribosomal structure and biogenesis];
                     Region: CLP1; COG5623"
                     /db_xref="CDD:35182"
     misc_feature    482..829
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /note="Molybdopterin guanine dinucleotide synthesis
                     protein B; Region: MobB; pfam03205"
                     /db_xref="CDD:190563"
     misc_feature    833..1408
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /note="Pre-mRNA cleavage complex II protein Clp1; Region:
                     Clp1; pfam06807"
                     /db_xref="CDD:191613"
     variation       171
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:141320814"
     variation       172
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:150722524"
     variation       187
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:139128549"
     variation       226
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:57281140"
     variation       241
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:143977407"
     variation       242
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:368377553"
     variation       265
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:113685226"
     variation       316
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:202017683"
     variation       317
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:200305079"
     variation       354
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:371072021"
     variation       371
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:374658636"
     variation       396
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:368779092"
     variation       423
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:200951285"
     variation       432
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:139859258"
     variation       454
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:371746577"
     variation       460
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:184720631"
     variation       490
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:373867004"
     variation       550
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:376558702"
     variation       551
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:368119334"
     variation       553
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:372083969"
     variation       568
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:150037684"
     variation       583
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:142356287"
     variation       625
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:149223879"
     variation       662
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:145927880"
     variation       672
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:34572579"
     variation       691
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:142476927"
     exon            746..1846
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /inference="alignment:Splign:1.39.8"
     variation       783
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:370085533"
     variation       789
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:147951568"
     variation       795
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:372647012"
     variation       806
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:375721461"
     variation       819
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:78489374"
     variation       874
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:141596718"
     variation       937
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:17152015"
     variation       940
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:138402857"
     variation       946
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:140965892"
     variation       950
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:200588495"
     variation       971
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:200917931"
     variation       1029
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:1804745"
     variation       1037
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:150146614"
     variation       1087
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:145579673"
     variation       1090
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:111754731"
     variation       1206
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:377065634"
     variation       1214
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:371222945"
     variation       1252
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:146281104"
     variation       1272
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:375674736"
     variation       1280
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:148451233"
     variation       1295
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:371843068"
     variation       1324
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:200297908"
     variation       1339
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:367955593"
     variation       1384
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:113696908"
     STS             1419..1651
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /standard_name="RH70702"
                     /db_xref="UniSTS:45493"
     variation       1439
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:372139047"
     STS             1448..1684
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /standard_name="RH80129"
                     /db_xref="UniSTS:88220"
     variation       1570
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:184089253"
     variation       1738
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:142223022"
     variation       1820
                     /gene="CLP1"
                     /gene_synonym="hClp1; HEAB"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:113003927"
ORIGIN      
aagtgcggaactgcgtttgtttccggcgtgggtccgggcaagaaccgcttgtagtttggtttaaattctgcacgggaggaccttctgagtttacctgttgggctcctggctgcgcaggcacagcagctacacagaagagatgggagaagaggctaatgatgacaagaagccaaccactaaatttgaactagagcgagaaacagaacttcgctttgaggtggaggcatctcagtcagttcagttggagttgttgactggcatggcagagatctttggcacagagctgacccgaaacaagaaattcacctttgatgctggtgccaaggtggctgttttcacttggcatggctgttctgtgcaactgagcggccgcactgaggtggcttatgtctccaaggacactcctatgttgctttacctcaacactcacacagccttggaacagatgcggaggcaagcggaaaaggaagaagagcgaggtccccgagtgatggtagtgggccccactgatgtgggcaagtctacagtgtgtcgccttctgctcaactacgcagtgcgtttgggccgccgtcccacttatgtggagctggatgtgggccagggttctgtgtccatccctggtaccatgggggccctctacatcgagcggcctgcagatgtcgaagagggtttctctatccaggcccctctggtgtatcattttggttccaccactcctggcactaacatcaagctttataataagattacatctcgtttagcagatgtgttcaaccaaaggtgtgaggtgaaccgaagggcatctgtgagtggctgtgtcattaacacctgtggctgggtcaagggctctggttaccaggctctggtgcatgcagcctcagcttttgaggtggatgtcgttgttgttctggatcaagaacgactgtacaatgaactgaaacgggacctcccccactttgtacgcactgtgctgctccctaaatctgggggtgtggtggagcgctccaaggacttccggcgggaatgtagggatgagcgtatccgtgagtatttttatggattccgaggctgtttctatccccatgccttcaatgtcaaattttcagatgtgaaaatctacaaagttggggcacccaccatcccagactcctgtttacctttgggcatgtctcaagaggataatcagctcaagctagtacctgtcactcctgggcgagatatggtgcaccacctactgagtgttagcactgccgagggtacagaggagaacctgtccgagacaagtgtagctggcttcattgtggtgaccagtgtggacctggagcatcaggtgtttactgttctgtctccagcccctcgcccactgcctaagaacttccttctcatcatggatatccggttcatggatctgaagtagagatcagcaggaagccttgctgcctgggacatagagatcatctggccacccctagaggcagatgggctgagataaaagactgttggggccacctgaccagtaaactgtggactagtagaaagttcatattctacctctaaaaacaggtagtggtaacctgactcttctaatcttgaaccaaaaggaaaaccatgagactgtaattggtttcttagaccacctaagatgccactttgaattctctaagaccctggagaattgcatttctttcactgtgctactatgtggtttttaaaaaatcaatgctttatattccatatgtggttcttacccatttatctaggatgaaagtgtgaattagagggactccttccaataaagttcaaacttaaaaaaaatcattttaataaatatttttgccatatcataaaaaaaaaaaaaaaaaaa
//

Annotations:

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:10978 -> Molecular function: GO:0005524 [ATP binding] evidence: TAS
            GeneID:10978 -> Molecular function: GO:0046404 [ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity] evidence: IEA
            GeneID:10978 -> Molecular function: GO:0051733 [polydeoxyribonucleotide kinase activity] evidence: IDA
            GeneID:10978 -> Molecular function: GO:0051736 [ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity] evidence: IDA
            GeneID:10978 -> Biological process: GO:0000398 [mRNA splicing, via spliceosome] evidence: TAS
            GeneID:10978 -> Biological process: GO:0006366 [transcription from RNA polymerase II promoter] evidence: TAS
            GeneID:10978 -> Biological process: GO:0006369 [termination of RNA polymerase II transcription] evidence: TAS
            GeneID:10978 -> Biological process: GO:0006388 [tRNA splicing, via endonucleolytic cleavage and ligation] evidence: IDA
            GeneID:10978 -> Biological process: GO:0008380 [RNA splicing] evidence: TAS
            GeneID:10978 -> Biological process: GO:0010467 [gene expression] evidence: TAS
            GeneID:10978 -> Biological process: GO:0030423 [targeting of mRNA for destruction involved in RNA interference] evidence: IMP
            GeneID:10978 -> Biological process: GO:0031124 [mRNA 3'-end processing] evidence: TAS
            GeneID:10978 -> Biological process: GO:0035087 [siRNA loading onto RISC involved in RNA interference] evidence: IDA
            GeneID:10978 -> Cellular component: GO:0000214 [tRNA-intron endonuclease complex] evidence: IDA
            GeneID:10978 -> Cellular component: GO:0005654 [nucleoplasm] evidence: TAS
ANNOTATIONS from NCBI Entrez Gene (20130726):
            NP_006822 -> EC 2.7.1.78

by @meso_cacase at DBCLS
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