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

    Gene ID: 10978, updated on 2-May-2024

    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
    NEW
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    Try the new Transcript table

    Genomic context

    See CLP1 in Genome Data Viewer
    Location:
    11q12.1
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (57657762..57661865)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (57607935..57612038)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (57425234..57429337)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene MIR130A host gene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:57410743-57411242 Neighboring gene microRNA 130a Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4725 Neighboring gene yippee like 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4727 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:57435387-57436026 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:57436027-57436664 Neighboring gene zinc finger DHHC-type palmitoyltransferase 5 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:57471607-57472806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3357 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: C5190575 OMIM: 615803 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    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

    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)

    NEW Try the new Transcript table

    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_001142597.2NP_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: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
      B2R7J6, B4DTI8, Q92989
      UniProtKB/TrEMBL
      E9PL17
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      57657762..57661865
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      57607935..57612038
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)