Clp1 CLP1, cleavage and polyadenylation factor I subunit [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Clp1provided by MGI
Official Full Name: CLP1, cleavage and polyadenylation factor I subunitprovided by MGI
Primary source: MGI:MGI:2138968
See related: Ensembl:ENSMUSG00000027079 AllianceGenome:MGI:2138968
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Heab
Summary: Predicted to enable polydeoxyribonucleotide kinase activity and polyribonucleotide 5'-hydroxyl-kinase activity. Involved in cerebellar cortex development. Predicted to be located in cytosol and nucleoplasm. Predicted to be part of tRNA-intron endonuclease complex. Predicted to be active in nucleus. Is expressed in genitourinary system; liver lobe; and thymus primordium. Used to study pontocerebellar hypoplasia type 10. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 10. Orthologous to human CLP1 (cleavage factor polyribonucleotide kinase subunit 1). [provided by Alliance of Genome Resources, Apr 2022]
Annotation information: Note: Hexim1 (Gene ID: 192231) and Clp1 (Gene ID: 98985) loci share the Clp1 symbol/alias in common. [08 Feb 2019]
Expression: Ubiquitous expression in liver E14 (RPKM 18.5), liver E14.5 (RPKM 16.5) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 D; 2 49.45 cM

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (84553466..84557631, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (84723122..84727287, complement)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Clp1 R140H mutation alters tRNA metabolism and mRNA 3' processing in mouse models of pontocerebellar hypoplasia.
Title: The Clp1 R140H mutation alters tRNA metabolism and mRNA 3' processing in mouse models of pontocerebellar hypoplasia.
loss of CLP1 activity results in accumulation of a novel set of small RNA fragments derived from aberrant processing of tyrosine pre-transfer RNA; these tRNA fragments sensitize cells to oxidative-stress-induced p53 activation and p53-dependent cell death
Title: CLP1 links tRNA metabolism to progressive motor-neuron loss.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (7) 1 citation
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI462438 (e-PCR)
- UniSTS:158977

RH139104 (e-PCR)
- UniSTS:221190

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	ISO Inferred from Sequence Orthology more info
enables ATP-dependent polynucleotide 5'-hydroxyl-kinase activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity	ISO Inferred from Sequence Orthology more info
enables kinase activity	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables polynucleotide 5'-hydroxyl-kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in RISC complex assembly	ISO Inferred from Sequence Orthology more info
involved_in RNA processing	IEA Inferred from Electronic Annotation more info
involved_in cerebellar cortex development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cerebellar cortex development	ISO Inferred from Sequence Orthology more info
involved_in global gene silencing by mRNA cleavage	ISO Inferred from Sequence Orthology more info
involved_in mRNA 3'-end processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within phosphorylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within tRNA processing	IEA Inferred from Electronic Annotation more info
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	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytosol	ISO Inferred from Sequence Orthology more info
part_of mRNA cleavage factor complex	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of tRNA-intron endonuclease complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: polyribonucleotide 5'-hydroxyl-kinase Clp1

Names: ATP/GTP-binding protein; polynucleotide kinase Clp1; pre-mRNA cleavage complex II protein Clp1

NP_598601.1

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.

mRNA and Protein(s)

NM_133840.3 → NP_598601.1 polyribonucleotide 5'-hydroxyl-kinase Clp1

See identical proteins and their annotated locations for NP_598601.1

Status: VALIDATED

Source sequence(s)

AL928914

Consensus CDS

CCDS16191.1

UniProtKB/Swiss-Prot

Q3TEC7, Q3ULZ9, Q99LI9

Related

ENSMUSP00000028475.9, ENSMUST00000028475.9

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