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CLP1 cleavage factor polyribonucleotide kinase subunit 1 [ Homo sapiens (human) ]

Gene ID: 10978, updated on 5-Apr-2020

Summary

Official Symbol
CLP1provided by HGNC
Official Full Name
cleavage factor polyribonucleotide kinase subunit 1provided by HGNC
Primary source
HGNC:HGNC:16999
See related
Ensembl:ENSG00000172409 MIM:608757
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HEAB; hClp1
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]
Expression
Ubiquitous expression in bone marrow (RPKM 9.5), appendix (RPKM 6.4) and 25 other tissues See more
Orthologs

Genomic context

See CLP1 in Genome Data Viewer
Location:
11q12.1
Exon count:
3
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (57657744..57661865)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (57425216..57429337)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene microRNA 130a Neighboring gene yippee like 4 Neighboring gene zinc finger DHHC-type palmitoyltransferase 5 Neighboring gene mediator complex subunit 19

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Pontocerebellar hypoplasia, type 10
MedGen: C4014347 OMIM: 615803 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
RNA processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cerebellar cortex development IMP
Inferred from Mutant Phenotype
more info
PubMed 
mRNA 3'-end processing TAS
Traceable Author Statement
more info
PubMed 
mRNA polyadenylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
phosphorylation IEA
Inferred from Electronic Annotation
more info
 
siRNA loading onto RISC involved in RNA interference IDA
Inferred from Direct Assay
more info
PubMed 
tRNA splicing, via endonucleolytic cleavage and ligation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
tRNA splicing, via endonucleolytic cleavage and ligation IDA
Inferred from Direct Assay
more info
PubMed 
tRNA splicing, via endonucleolytic cleavage and ligation IMP
Inferred from Mutant Phenotype
more info
PubMed 
tRNA splicing, via endonucleolytic cleavage and ligation TAS
Traceable Author Statement
more info
 
targeting of mRNA for destruction involved in RNA interference IMP
Inferred from Mutant Phenotype
more info
PubMed 
termination of RNA polymerase II transcription TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
mRNA cleavage factor complex IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
tRNA-intron endonuclease complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
polyribonucleotide 5'-hydroxyl-kinase Clp1
Names
ATP/GTP-binding protein
cleavage and polyadenylation factor I subunit 1
homolog of yeast CFIA subunit Clp1p
polyadenylation factor Clp1
polynucleotide kinase Clp1
pre-mRNA cleavage complex II protein Clp1
NP_001136069.1
NP_006822.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_034248.1 RefSeqGene

    Range
    5019..9122
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001142597.1NP_001136069.1  polyribonucleotide 5'-hydroxyl-kinase Clp1 isoform 2

    See identical proteins and their annotated locations for NP_001136069.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice donor site and encodes a shorter protein (isoform 2) compared to transcript variant 1.
    Source sequence(s)
    AK300232, BC000446, DA922553
    Consensus CDS
    CCDS44600.1
    UniProtKB/Swiss-Prot
    Q92989
    Related
    ENSP00000304704.4, ENST00000302731.4
    Conserved Domains (1) summary
    cl25635
    Location:14359
    CLP1_N; N-terminal beta-sandwich domain of polyadenylation factor
  2. NM_006831.3NP_006822.1  polyribonucleotide 5'-hydroxyl-kinase Clp1 isoform 1

    See identical proteins and their annotated locations for NP_006822.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes a longer protein (isoform 1).
    Source sequence(s)
    BC000446, DA922553
    Consensus CDS
    CCDS7964.1
    UniProtKB/Swiss-Prot
    Q92989
    Related
    ENSP00000434995.1, ENST00000533682.2
    Conserved Domains (2) summary
    COG5623
    Location:14423
    CLP1; Predicted GTPase subunit of the pre-mRNA cleavage complex [Translation, ribosomal structure and biogenesis]
    pfam16575
    Location:121306
    CLP1_P; mRNA cleavage and polyadenylation factor CLP1 P-loop

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    57657744..57661865
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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