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CLK3 CDC like kinase 3 [ Homo sapiens (human) ]

Gene ID: 1198, updated on 9-Feb-2020

Summary

Official Symbol
CLK3provided by HGNC
Official Full Name
CDC like kinase 3provided by HGNC
Primary source
HGNC:HGNC:2071
See related
Ensembl:ENSG00000179335 MIM:602990
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
PHCLK3; PHCLK3/152
Summary
This gene encodes a protein belonging to the serine/threonine type protein kinase family. This protein is a nuclear dual-specificity kinase that regulates the intranuclear distribution of the serine/arginine-rich (SR) family of splicing factors. Two transcript variants encoding different isoforms have been found for this gene. Related pseudogenes are located on chromosomes 1 and 9. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 16.0), testis (RPKM 5.8) and 25 other tissues See more
Orthologs

Genomic context

See CLK3 in Genome Data Viewer
Location:
15q24.1
Exon count:
14
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (74608372..74630201)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (74898327..74922542)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene AT-rich interaction domain 3B Neighboring gene VISTA enhancer hs1510 Neighboring gene Sharpr-MPRA regulatory region 315 Neighboring gene uncharacterized LOC102723750 Neighboring gene enhancer of mRNA decapping 3 Neighboring gene CYP1A1 5' regulatory region Neighboring gene cytochrome P450 family 1 subfamily A member 1

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

Phenotypes

NHGRI GWAS Catalog

Description
Genome wide association study identified SNP on 15q24 associated with bladder cancer risk in Japanese population.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ22858

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
RNA binding HDA PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein serine/threonine kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
protein serine/threonine/tyrosine kinase activity IEA
Inferred from Electronic Annotation
more info
 
protein tyrosine kinase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
peptidyl-tyrosine phosphorylation IEA
Inferred from Electronic Annotation
more info
 
protein autophosphorylation IEA
Inferred from Electronic Annotation
more info
 
protein phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of RNA splicing IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
acrosomal vesicle IEA
Inferred from Electronic Annotation
more info
 
intermediate filament cytoskeleton IDA
Inferred from Direct Assay
more info
 
membrane HDA PubMed 
nuclear speck IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
dual specificity protein kinase CLK3
NP_001123500.1
NP_003983.2

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.

mRNA and Protein(s)

  1. NM_001130028.1NP_001123500.1  dual specificity protein kinase CLK3 isoform a

    See identical proteins and their annotated locations for NP_001123500.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AK091692, BC002555, BQ183959
    Consensus CDS
    CCDS45304.1
    UniProtKB/Swiss-Prot
    P49761
    UniProtKB/TrEMBL
    B3KRI8
    Related
    ENSP00000378505.3, ENST00000395066.7
    Conserved Domains (3) summary
    smart00220
    Location:304620
    S_TKc; Serine/Threonine protein kinases, catalytic domain
    cd14214
    Location:290620
    PKc_CLK3; Catalytic domain of the Dual-specificity protein kinase, CDC-like kinase 3
    pfam15730
    Location:60136
    DUF4680; Domain of unknown function (DUF4680)
  2. NM_003992.4NP_003983.2  dual specificity protein kinase CLK3 isoform b

    See identical proteins and their annotated locations for NP_003983.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (b) has a shorter and distinct N-terminus compared to isoform a.
    Source sequence(s)
    BC002555, BQ183959, L29217
    Consensus CDS
    CCDS10265.1
    UniProtKB/Swiss-Prot
    P49761
    Related
    ENSP00000344112.4, ENST00000345005.8
    Conserved Domains (1) summary
    cd14214
    Location:142472
    PKc_CLK3; Catalytic domain of the Dual-specificity protein kinase, CDC-like kinase 3

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    74608372..74630201
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001292.1: Suppressed sequence

    Description
    NM_001292.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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