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CLP1 cleavage and polyadenylation factor I subunit 1 [ Homo sapiens (human) ]

Gene ID: 10978, updated on 13-Jan-2019

Summary

Official Symbol
CLP1provided by HGNC
Official Full Name
cleavage and polyadenylation factor I 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 current GRCh38.p12 (GCF_000001405.38) 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 containing 5 Neighboring gene TMX2-CTNND1 readthrough (NMD candidate) Neighboring gene mediator complex subunit 19 Neighboring gene thioredoxin related transmembrane protein 2

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 FunctionsWhat'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 BioSystems

  • Cleavage of Growing Transcript in the Termination Region, organism-specific biosystem (from REACTOME)
    Cleavage of Growing Transcript in the Termination Region, organism-specific biosystemThis section includes the cleavage of both polyadenylated and non-polyadenylated transcripts. In the former case polyadenylation has to precede transcript cleavage, while in the latter case there is ...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Processing of Capped Intronless Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intronless Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Processing of Intronless Pre-mRNAs, organism-specific biosystem (from REACTOME)
    Processing of Intronless Pre-mRNAs, organism-specific biosystemThe 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3' processing consists of two steps: The mRNA is first cleaved ...
  • RNA Polymerase II Transcription, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription, organism-specific biosystem
    RNA Polymerase II Transcription
  • RNA Polymerase II Transcription Termination, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription Termination, organism-specific biosystemThe detailed annotation of this section will be completed in the next release.
  • mRNA 3'-end processing, organism-specific biosystem (from REACTOME)
    mRNA 3'-end processing, organism-specific biosystemThe 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3'-end processing consists of two steps: (i) the mRNA is first ...
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA surveillance pathway, organism-specific biosystem (from KEGG)
    mRNA surveillance pathway, organism-specific biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
  • mRNA surveillance pathway, conserved biosystem (from KEGG)
    mRNA surveillance pathway, conserved biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
  • tRNA processing, organism-specific biosystem (from REACTOME)
    tRNA processing, organism-specific biosystemGenes encoding transfer RNAs (tRNAs) are transcribed by RNA polymerase III in the nucleus and by mitochondrial RNA polymerase in the mitochondrion.In the nucleus transcription reactions produce precu...
  • tRNA processing in the nucleus, organism-specific biosystem (from REACTOME)
    tRNA processing in the nucleus, organism-specific biosystemGenes encoding transfer RNAs are transcribed in the nucleus by RNA polymerase III. (Distinct processes of transcription and processing also occur in mitochondria.) The initial transcripts, pre-tRNAs,...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
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 
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
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
    5001..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, ENST00000533682.1
    Conserved Domains (2) summary
    pfam16575
    Location:121306
    CLP1_P; mRNA cleavage and polyadenylation factor CLP1 P-loop
    cl25635
    Location:14423
    CLP1_N; N-terminal beta-sandwich domain of polyadenylation factor

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

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