2024-03-29 21:27:18, GGRNA : RefSeq release 60 (20130726)
LOCUS NM_001142597 1672 bp mRNA linear PRI 17-APR-2013 DEFINITION Homo sapiens cleavage and polyadenylation factor I subunit 1 (CLP1), transcript variant 2, mRNA. ACCESSION NM_001142597 VERSION NM_001142597.1 GI:217272858 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 1672) 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 1672) 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 1672) 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 1672) 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 1672) 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 1672) 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, AK300232.1 and BC000446.1. Transcript Variant: This variant (2) uses an alternate splice donor site and encodes a shorter protein (isoform 2) compared to transcript variant 1. ##Evidence-Data-START## Transcript exon combination :: AK300232.1, BG338247.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support ERS025081, ERS025082 [ECO:0000350] ##Evidence-Data-END## PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-19 DA922553.1 1-19 20-1289 AK300232.1 3-1272 1290-1672 BC000446.1 1470-1852 FEATURES Location/Qualifiers source 1..1672 /organism="Homo sapiens" /mol_type="mRNA" /db_xref="taxon:9606" /chromosome="11" /map="11q12" gene 1..1672 /gene="CLP1" /gene_synonym="hClp1; HEAB" /note="cleavage and polyadenylation factor I subunit 1" /db_xref="GeneID:10978" /db_xref="HGNC:16999" /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..553 /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..1225 /gene="CLP1" /gene_synonym="hClp1; HEAB" /EC_number="2.7.1.78" /note="isoform 2 is encoded by transcript variant 2; 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 2" /protein_id="NP_001136069.1" /db_xref="GI:217272859" /db_xref="CCDS:CCDS44600.1" /db_xref="GeneID:10978" /db_xref="HGNC:16999" /db_xref="MIM:608757" /translation="
MGEEANDDKKPTTKFELERETELRFEVEASQSVQLELLTGMAEIFGTELTRNKKFTFDAGAKVAVFTWHGCSVQLSGRTEVAYVSKDTPMLLYLNTHTALEQMRRQAEKEEERGPRVMVVGPTDVGKSTVCRLLLNYAITSRLADVFNQRCEVNRRASVSGCVINTCGWVKGSGYQALVHAASAFEVDVVVVLDQERLYNELKRDLPHFVRTVLLPKSGGVVERSKDFRRECRDERIREYFYGFRGCFYPHAFNVKFSDVKIYKVGAPTIPDSCLPLGMSQEDNQLKLVPVTPGRDMVHHLLSVSTAEGTEENLSETSVAGFIVVTSVDLEHQVFTVLSPAPRPLPKNFLLIMDIRFMDLK
" misc_feature 482..>553 /gene="CLP1" /gene_synonym="hClp1; HEAB" /note="P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099" /db_xref="CDD:214148" misc_feature 641..1216 /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" exon 554..1654 /gene="CLP1" /gene_synonym="hClp1; HEAB" /inference="alignment:Splign:1.39.8" variation 591 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="a" /replace="g" /db_xref="dbSNP:370085533" variation 597 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:147951568" variation 603 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="a" /replace="g" /db_xref="dbSNP:372647012" variation 614 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="a" /replace="g" /db_xref="dbSNP:375721461" variation 627 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="g" /replace="t" /db_xref="dbSNP:78489374" variation 682 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="a" /replace="g" /db_xref="dbSNP:141596718" variation 745 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="a" /replace="g" /db_xref="dbSNP:17152015" variation 748 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="a" /replace="g" /db_xref="dbSNP:138402857" variation 754 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:140965892" variation 758 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:200588495" variation 779 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:200917931" variation 837 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="g" /replace="t" /db_xref="dbSNP:1804745" variation 845 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:150146614" variation 895 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:145579673" variation 898 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:111754731" variation 1014 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:377065634" variation 1022 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:371222945" variation 1060 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:146281104" variation 1080 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:375674736" variation 1088 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="a" /replace="g" /db_xref="dbSNP:148451233" variation 1103 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:371843068" variation 1132 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="a" /replace="g" /db_xref="dbSNP:200297908" variation 1147 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:367955593" variation 1192 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:113696908" STS 1227..1459 /gene="CLP1" /gene_synonym="hClp1; HEAB" /standard_name="RH70702" /db_xref="UniSTS:45493" variation 1247 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="a" /replace="g" /db_xref="dbSNP:372139047" STS 1256..1492 /gene="CLP1" /gene_synonym="hClp1; HEAB" /standard_name="RH80129" /db_xref="UniSTS:88220" variation 1378 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="a" /replace="g" /db_xref="dbSNP:184089253" variation 1546 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="a" /replace="g" /db_xref="dbSNP:142223022" variation 1628 /gene="CLP1" /gene_synonym="hClp1; HEAB" /replace="c" /replace="t" /db_xref="dbSNP:113003927" ORIGIN
aagtgcggaactgcgtttgtttccggcgtgggtccgggcaagaaccgcttgtagtttggtttaaattctgcacgggaggaccttctgagtttacctgttgggctcctggctgcgcaggcacagcagctacacagaagagatgggagaagaggctaatgatgacaagaagccaaccactaaatttgaactagagcgagaaacagaacttcgctttgaggtggaggcatctcagtcagttcagttggagttgttgactggcatggcagagatctttggcacagagctgacccgaaacaagaaattcacctttgatgctggtgccaaggtggctgttttcacttggcatggctgttctgtgcaactgagcggccgcactgaggtggcttatgtctccaaggacactcctatgttgctttacctcaacactcacacagccttggaacagatgcggaggcaagcggaaaaggaagaagagcgaggtccccgagtgatggtagtgggccccactgatgtgggcaagtctacagtgtgtcgccttctgctcaactacgcaattacatctcgtttagcagatgtgttcaaccaaaggtgtgaggtgaaccgaagggcatctgtgagtggctgtgtcattaacacctgtggctgggtcaagggctctggttaccaggctctggtgcatgcagcctcagcttttgaggtggatgtcgttgttgttctggatcaagaacgactgtacaatgaactgaaacgggacctcccccactttgtacgcactgtgctgctccctaaatctgggggtgtggtggagcgctccaaggacttccggcgggaatgtagggatgagcgtatccgtgagtatttttatggattccgaggctgtttctatccccatgccttcaatgtcaaattttcagatgtgaaaatctacaaagttggggcacccaccatcccagactcctgtttacctttgggcatgtctcaagaggataatcagctcaagctagtacctgtcactcctgggcgagatatggtgcaccacctactgagtgttagcactgccgagggtacagaggagaacctgtccgagacaagtgtagctggcttcattgtggtgaccagtgtggacctggagcatcaggtgtttactgttctgtctccagcccctcgcccactgcctaagaacttccttctcatcatggatatccggttcatggatctgaagtagagatcagcaggaagccttgctgcctgggacatagagatcatctggccacccctagaggcagatgggctgagataaaagactgttggggccacctgaccagtaaactgtggactagtagaaagttcatattctacctctaaaaacaggtagtggtaacctgactcttctaatcttgaaccaaaaggaaaaccatgagactgtaattggtttcttagaccacctaagatgccactttgaattctctaagaccctggagaattgcatttctttcactgtgctactatgtggtttttaaaaaatcaatgctttatattccatatgtggttcttacccatttatctaggatgaaagtgtgaattagagggactccttccaataaagttcaaacttaaaaaaaatcattttaataaatatttttgccatatcataaaaaaaaaaaaaaaaaaa
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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_001136069 -> EC 2.7.1.78
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