Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CLP1 Gene

Aliases for CLP1 Gene

  • Cleavage And Polyadenylation Factor I Subunit 1 2 3
  • Pre-MRNA Cleavage Complex II Protein Clp1 3 4
  • Polyadenylation Factor Clp1 3 4
  • Polynucleotide Kinase Clp1 3 4
  • EC 2.7.1.78 4 63
  • HEAB 3 4
  • CLP1, Cleavage And Polyadenylation Factor I Subunit, Homolog (S. Cerevisiae) 2
  • Polyribonucleotide 5-Hydroxyl-Kinase Clp1 3
  • Polyribonucleotide 5-Hydroxyl-Kinase 2
  • Homolog Of Yeast CFIA Subunit Clp1p 3
  • ATP/GTP-Binding Protein 3
  • ATP/GTPbinding Protein 2
  • HCLP1 3

External Ids for CLP1 Gene

Previous GeneCards Identifiers for CLP1 Gene

  • GC11P057182
  • GC11P057425
  • GC11P053774

Summaries for CLP1 Gene

Entrez Gene Summary for CLP1 Gene

  • 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]

GeneCards Summary for CLP1 Gene

CLP1 (Cleavage And Polyadenylation Factor I Subunit 1) is a Protein Coding gene. Diseases associated with CLP1 include pontocerebellar hypoplasia, type 10. Among its related pathways are Gene Expression and mRNA Splicing - Major Pathway. GO annotations related to this gene include ATP-dependent polydeoxyribonucleotide 5-hydroxyl-kinase activity and ATP-dependent polyribonucleotide 5-hydroxyl-kinase activity.

UniProtKB/Swiss-Prot for CLP1 Gene

  • Polynucleotide kinase that can phosphorylate the 5-hydroxyl groups of double-stranded RNA (dsRNA), single-stranded RNA (ssRNA), double-stranded DNA (dsDNA) and double-stranded DNA:RNA hybrids. dsRNA is phosphorylated more efficiently than dsDNA, and the RNA component of a DNA:RNA hybrid is phosphorylated more efficiently than the DNA component. Plays a key role in both tRNA splicing and mRNA 3-end formation. Component of the tRNA splicing endonuclease complex: phosphorylates the 5-terminus of the tRNA 3-exon during tRNA splicing; this phosphorylation event is a prerequisite for the subsequent ligation of the two exon halves and the production of a mature tRNA (PubMed:24766809, PubMed:24766810). Its role in tRNA splicing and maturation is required for cerebellar development (PubMed:24766809, PubMed:24766810). Component of the pre-mRNA cleavage complex II (CF-II), which seems to be required for mRNA 3-end formation. Also phosphorylates the 5-terminus of exogenously introduced short interfering RNAs (siRNAs), which is a necessary prerequisite for their incorporation into the RNA-induced silencing complex (RISC). However, endogenous siRNAs and microRNAs (miRNAs) that are produced by the cleavage of dsRNA precursors by DICER1 already contain a 5-phosphate group, so this protein may be dispensible for normal RNA-mediated gene silencing.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLP1 Gene

Genomics for CLP1 Gene

Regulatory Elements for CLP1 Gene

Genomic Location for CLP1 Gene

Start:
57,648,992 bp from pter
End:
57,661,868 bp from pter
Size:
12,877 bases
Orientation:
Plus strand

Genomic View for CLP1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLP1 Gene

Proteins for CLP1 Gene

  • Protein details for CLP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92989-CLP1_HUMAN
    Recommended name:
    Polyribonucleotide 5-hydroxyl-kinase Clp1
    Protein Accession:
    Q92989
    Secondary Accessions:
    • B2R7J6
    • B4DTI8

    Protein attributes for CLP1 Gene

    Size:
    425 amino acids
    Molecular mass:
    47646 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
    Quaternary structure:
    • Component of the tRNA splicing endonuclease complex, composed of CLP1, TSEN2, TSEN15, TSEN34 and TSEN54 (PubMed:24766809). Component of pre-mRNA cleavage complex II (CF-II). Also associates with numerous components of the pre-mRNA cleavage complex I (CF-I/CFIm), including NUDT21, CPSF2, CPSF3, CPSF6 and CPSF7. Interacts with CSTF2 and SYMPK.

    Alternative splice isoforms for CLP1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLP1 Gene

Proteomics data for CLP1 Gene at MOPED

Post-translational modifications for CLP1 Gene

  • Ubiquitination at Lys127
  • Modification sites at PhosphoSitePlus

Other Protein References for CLP1 Gene

Domains for CLP1 Gene

Suggested Antigen Peptide Sequences for CLP1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q92989

UniProtKB/Swiss-Prot:

CLP1_HUMAN :
  • Q92989
Family:
  • Belongs to the Clp1 family. Clp1 subfamily.
genes like me logo Genes that share domains with CLP1: view

No data available for Gene Families for CLP1 Gene

Function for CLP1 Gene

Molecular function for CLP1 Gene

UniProtKB/Swiss-Prot CatalyticActivity: ATP + 5-dephospho-DNA = ADP + 5-phospho-DNA.
UniProtKB/Swiss-Prot CatalyticActivity: ATP + 5-dephospho-RNA = ADP + 5-phospho-RNA.
UniProtKB/Swiss-Prot Function: Polynucleotide kinase that can phosphorylate the 5-hydroxyl groups of double-stranded RNA (dsRNA), single-stranded RNA (ssRNA), double-stranded DNA (dsDNA) and double-stranded DNA:RNA hybrids. dsRNA is phosphorylated more efficiently than dsDNA, and the RNA component of a DNA:RNA hybrid is phosphorylated more efficiently than the DNA component. Plays a key role in both tRNA splicing and mRNA 3-end formation. Component of the tRNA splicing endonuclease complex: phosphorylates the 5-terminus of the tRNA 3-exon during tRNA splicing; this phosphorylation event is a prerequisite for the subsequent ligation of the two exon halves and the production of a mature tRNA (PubMed:24766809, PubMed:24766810). Its role in tRNA splicing and maturation is required for cerebellar development (PubMed:24766809, PubMed:24766810). Component of the pre-mRNA cleavage complex II (CF-II), which seems to be required for mRNA 3-end formation. Also phosphorylates the 5-terminus of exogenously introduced short interfering RNAs (siRNAs), which is a necessary prerequisite for their incorporation into the RNA-induced silencing complex (RISC). However, endogenous siRNAs and microRNAs (miRNAs) that are produced by the cleavage of dsRNA precursors by DICER1 already contain a 5-phosphate group, so this protein may be dispensible for normal RNA-mediated gene silencing.

Enzyme Numbers (IUBMB) for CLP1 Gene

Gene Ontology (GO) - Molecular Function for CLP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005524 ATP binding TAS 8896421
GO:0046404 ATP-dependent polydeoxyribonucleotide 5-hydroxyl-kinase activity IEA --
GO:0051733 polydeoxyribonucleotide kinase activity IDA 17495927
GO:0051736 ATP-dependent polyribonucleotide 5-hydroxyl-kinase activity IMP 24766809
genes like me logo Genes that share ontologies with CLP1: view
genes like me logo Genes that share phenotypes with CLP1: view

Animal Model Products

CRISPR Products

miRNA for CLP1 Gene

miRTarBase miRNAs that target CLP1

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for CLP1 Gene

Localization for CLP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLP1 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CLP1 Gene COMPARTMENTS Subcellular localization image for CLP1 gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1
mitochondrion 1
peroxisome 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for CLP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000214 tRNA-intron endonuclease complex IDA 17495927
GO:0005634 nucleus IDA 24766810
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IDA --
GO:0005849 mRNA cleavage factor complex IEA --
genes like me logo Genes that share ontologies with CLP1: view

Pathways for CLP1 Gene

genes like me logo Genes that share pathways with CLP1: view

Gene Ontology (GO) - Biological Process for CLP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006366 transcription from RNA polymerase II promoter TAS --
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006378 mRNA polyadenylation IBA --
GO:0006379 mRNA cleavage IBA --
genes like me logo Genes that share ontologies with CLP1: view

Transcripts for CLP1 Gene

Unigene Clusters for CLP1 Gene

Cleavage and polyadenylation factor I subunit 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLP1

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLP1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c · 2d ^ 3a · 3b
SP1:
SP2: - -
SP3: -

Relevant External Links for CLP1 Gene

GeneLoc Exon Structure for
CLP1
ECgene alternative splicing isoforms for
CLP1

Expression for CLP1 Gene

mRNA expression in normal human tissues for CLP1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for CLP1 Gene

SOURCE GeneReport for Unigene cluster for CLP1 Gene Hs.523687

genes like me logo Genes that share expressions with CLP1: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for CLP1 Gene

Orthologs for CLP1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CLP1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia CLP1 35
  • 89.49 (n)
  • 99.53 (a)
CLP1 36
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CLP1 35
  • 93.73 (n)
  • 99.53 (a)
CLP1 36
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Clp1 35
  • 90.04 (n)
  • 98.59 (a)
Clp1 16
Clp1 36
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 97 (a)
OneToMany
-- 36
  • 97 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Clp1 35
  • 90.67 (n)
  • 98.59 (a)
chicken
(Gallus gallus)
Aves CLP1 35
  • 79.69 (n)
  • 93.18 (a)
CLP1 36
  • 93 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLP1 36
  • 94 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clp1 35
  • 68.92 (n)
  • 79.04 (a)
zebrafish
(Danio rerio)
Actinopterygii CR855307.1 36
  • 76 (a)
OneToOne
LOC565621 35
  • 71.03 (n)
  • 81.11 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta CLP1_ANOGA 35
  • 59.55 (n)
  • 59.95 (a)
fruit fly
(Drosophila melanogaster)
Insecta cbc 35
  • 58.76 (n)
  • 56.97 (a)
cbc 36
  • 56 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea clpf-1 35
  • 51.34 (n)
  • 48.9 (a)
clpf-1 36
  • 47 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CLP1 36
  • 24 (a)
OneToOne
CLP1 38
thale cress
(Arabidopsis thaliana)
eudicotyledons CLPS3 35
  • 48.77 (n)
  • 42.89 (a)
rice
(Oryza sativa)
Liliopsida Os02g0217500 35
  • 48.36 (n)
  • 39.81 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.15542 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 63 (a)
OneToOne
Species with no ortholog for CLP1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CLP1 Gene

ENSEMBL:
Gene Tree for CLP1 (if available)
TreeFam:
Gene Tree for CLP1 (if available)

Paralogs for CLP1 Gene

No data available for Paralogs for CLP1 Gene

Variants for CLP1 Gene

Sequence variations from dbSNP and Humsavar for CLP1 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs525645 -- 57,659,239(-) GGGCA(C/T)GGTGG intron-variant
rs526747 -- 57,659,393(+) cCCAT(G/T)GGATG intron-variant
rs681764 -- 57,660,722(-) CAGAC(A/C)AACCC intron-variant
rs1613592 -- 57,656,528(+) tatct(G/T)agtct upstream-variant-2KB
rs1647401 -- 57,658,031(+) GTTTC(C/T)TTGCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLP1 Gene

Variant ID Type Subtype PubMed ID
nsv832163 CNV Gain 17160897
nsv832164 CNV Loss 17160897
nsv508633 CNV Loss 20534489

Relevant External Links for CLP1 Gene

HapMap Linkage Disequilibrium report
CLP1
Human Gene Mutation Database (HGMD)
CLP1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLP1 Gene

Disorders for CLP1 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (1) Diseases for CLP1 Gene including...

Search for CLP1 Gene in MalaCards »

UniProtKB/Swiss-Prot

CLP1_HUMAN
  • Pontocerebellar hypoplasia 10 (PCH10) [MIM:615803]: A form of pontocerebellar hypoplasia, a disorder characterized by structural defects of the pons and cerebellum, evident upon brain imaging. PCH10 features include cortical dysgenesis marked by a simplified gyral pattern, cortical atrophy, mild or focal cerebellar vermian volume loss, delayed myelination, progressive microcephaly, global growth and developmental delays, severe intellectual disabilities, and seizures refractory to treatment. {ECO:0000269 PubMed:24766809, ECO:0000269 PubMed:24766810}. Note=The disease is caused by mutations affecting the gene represented in this entry. Neurodegeneration is due to defects in tRNA splicing (PubMed:24766809, PubMed:24766810). {ECO:0000269 PubMed:24766809, ECO:0000269 PubMed:24766810}.
genes like me logo Genes that share disorders with CLP1: view

Publications for CLP1 Gene

  1. The human RNA kinase hClp1 is active on 3' transfer RNA exons and short interfering RNAs. (PMID: 17495927) Weitzer S. … Martinez J. (Nature 2007) 3 4 23
  2. Human RNA 5'-kinase (hClp1) can function as a tRNA splicing enzyme in vivo. (PMID: 18648070) Ramirez A. … Schwer B. (RNA 2008) 3 4 23
  3. AF10 is split by MLL and HEAB, a human homolog to a putative Caenorhabditis elegans ATP/GTP-binding protein in an invins(10;11)(p12;q23q12). (PMID: 8896421) Tanabe S. … Rowley J.D. (Blood 1996) 2 3 4
  4. Human pre-mRNA cleavage factor II(m) contains homologs of yeast proteins and bridges two other cleavage factors. (PMID: 11060040) de Vries H. … Keller W. (EMBO J. 2000) 2 3 4
  5. Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function. (PMID: 24766809) Karaca E. … Lupski J.R. (Cell 2014) 3 4

Products for CLP1 Gene

Sources for CLP1 Gene

Back to Top

Content