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

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; AllianceGenome:HGNC:16999
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: mouse all
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Genomic context

Location:: 11q12.1

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (57657762..57661865)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (57607935..57612038)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (57425234..57429337)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RNA kinase CLP1/Cbc regulates meiosis initiation in spermatogenesis.
Title: RNA kinase CLP1/Cbc regulates meiosis initiation in spermatogenesis.
Modeling a human CLP1 mutation in mouse identifies an accumulation of tyrosine pre-tRNA fragments causing pontocerebellar hypoplasia type 10.
Title: Modeling a human CLP1 mutation in mouse identifies an accumulation of tyrosine pre-tRNA fragments causing pontocerebellar hypoplasia type 10.
We have reconstituted CF II as a heterodimer of hPcf11 and hClp1. The heterodimer is active in partially reconstituted cleavage reactions, whereas hClp1 by itself is not. Pcf11 moderately stimulates the RNA 5' kinase activity of hClp1; the kinase activity is dispensable for RNA cleavage
Title: Reconstitution of mammalian cleavage factor II involved in 3' processing of mRNA precursors.
Data link tRNA maturation to neuronal development and neurodegeneration through defective CLP1 function in humans.
Title: CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration.
Study reports the identification of a human CLP1 mutation that impairs tRNA splicing in vitro and causes a neurological syndrome involving both the central nervous system (CNS) and peripheral nervous system (PNS).
Title: Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function.
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.
Title: Human RNA 5'-kinase (hClp1) can function as a tRNA splicing enzyme in vivo.
the kinase hClp1 phosphorylates and licenses synthetic siRNAs to become assembled into RISC for subsequent target RNA cleavage
Title: The human RNA kinase hClp1 is active on 3' transfer RNA exons and short interfering RNAs.
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.
Title: Human pre-mRNA cleavage factor II(m) contains homologs of yeast proteins and bridges two other cleavage factors.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Pontocerebellar hypoplasia type 10 MedGen: C5190575 OMIM: 615803 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH80129 (e-PCR)
- UniSTS:88220

RH70702 (e-PCR)
- UniSTS:45493

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	TAS Traceable Author Statement more info	PubMed
enables ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables polynucleotide 5'-hydroxyl-kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RISC complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in cerebellar cortex development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in global gene silencing by mRNA cleavage	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA 3'-end processing	TAS Traceable Author Statement more info	PubMed
involved_in tRNA splicing, via endonucleolytic cleavage and ligation	IBA Inferred from Biological aspect of Ancestor more info
involved_in tRNA splicing, via endonucleolytic cleavage and ligation	IDA Inferred from Direct Assay more info	PubMed
involved_in tRNA splicing, via endonucleolytic cleavage and ligation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info
part_of mRNA cleavage factor complex	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of tRNA-intron endonuclease complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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

EC 2.7.1.78

NP_006822.1

EC 2.7.1.78

NCBI Reference Sequences (RefSeq)

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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

NG_034248.1 RefSeqGene

Range

5019..9122

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001142597.2 → NP_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/TrEMBL

E9PL17

Related

ENSP00000304704.4, ENST00000302731.4

Conserved Domains (1) summary

cl25635
Location:14 → 359

CLP1_N; N-terminal beta-sandwich domain of polyadenylation factor
NM_006831.3 → NP_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

B2R7J6, B4DTI8, Q92989

UniProtKB/TrEMBL

E9PL17

Related

ENSP00000434995.1, ENST00000533682.2

Conserved Domains (2) summary

COG5623
Location:14 → 423

CLP1; Predicted GTPase subunit of the pre-mRNA cleavage complex [Translation, ribosomal structure and biogenesis]

pfam16575
Location:121 → 306

CLP1_P; mRNA cleavage and polyadenylation factor CLP1 P-loop