Human Gene CLK4 (ENST00000316308.9_7) from GENCODE V47lift37
  Description: CDC like kinase 4 (from RefSeq NM_020666.3)
Gencode Transcript: ENST00000316308.9_7
Gencode Gene: ENSG00000113240.14_11
Transcript (Including UTRs)
   Position: hg19 chr5:178,029,665-178,054,051 Size: 24,387 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr5:178,030,618-178,050,417 Size: 19,800 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:178,029,665-178,054,051)mRNA (may differ from genome)Protein (481 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CLK4_HUMAN
DESCRIPTION: RecName: Full=Dual specificity protein kinase CLK4; EC=2.7.12.1; AltName: Full=CDC-like kinase 4;
FUNCTION: Dual specificity kinase acting on both serine/threonine and tyrosine-containing substrates. Phosphorylates serine- and arginine-rich (SR) proteins of the spliceosomal complex and may be a constituent of a network of regulatory mechanisms that enable SR proteins to control RNA splicing. Phosphorylates SRSF1 and SRSF3. Required for the regulation of alternative splicing of MAPT/TAU. Regulates the alternative splicing of tissue factor (F3) pre-mRNA in endothelial cells.
CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.
ENZYME REGULATION: TG003 inhibits its kinase activity and affects the regulation of alternative splicing mediated by phosphorylation of SR proteins (By similarity).
SUBUNIT: Interacts with UBL5.
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Expressed in liver, kidney, heart, muscle, brain and endothelial cells.
PTM: Autophosphorylates on all three types of residues.
SIMILARITY: Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. Lammer subfamily.
SIMILARITY: Contains 1 protein kinase domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 74.60 RPKM in Brain - Cerebellum
Total median expression: 579.68 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -39.20105-0.373 Picture PostScript Text
3' UTR -197.60953-0.207 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011009 - Kinase-like_dom
IPR000719 - Prot_kinase_cat_dom
IPR017441 - Protein_kinase_ATP_BS
IPR002290 - Ser/Thr_dual-sp_kinase_dom
IPR008271 - Ser/Thr_kinase_AS

Pfam Domains:
PF00069 - Protein kinase domain
PF07714 - Protein tyrosine and serine/threonine kinase

SCOP Domains:
56112 - Protein kinase-like (PK-like)

ModBase Predicted Comparative 3D Structure on Q9HAZ1
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004712 protein serine/threonine/tyrosine kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity

Biological Process:
GO:0006468 protein phosphorylation
GO:0016310 phosphorylation
GO:0018108 peptidyl-tyrosine phosphorylation
GO:0043484 regulation of RNA splicing
GO:0046777 protein autophosphorylation

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC151233 - Homo sapiens cDNA clone IMAGE:8860324.
AK311485 - Homo sapiens cDNA, FLJ18527.
BX647323 - Homo sapiens mRNA; cDNA DKFZp779C0615 (from clone DKFZp779C0615).
AF294429 - Homo sapiens protein serine threonine kinase Clk4 mRNA, complete cds.
CR749504 - Homo sapiens mRNA; cDNA DKFZp686A20267 (from clone DKFZp686A20267).
BC063116 - Homo sapiens CDC-like kinase 4, mRNA (cDNA clone IMAGE:30324121), partial cds.
BC136261 - Homo sapiens CDC-like kinase 4, mRNA (cDNA clone MGC:167871 IMAGE:9020248), complete cds.
BC143547 - Homo sapiens CDC-like kinase 4, mRNA (cDNA clone MGC:177075 IMAGE:9052058), complete cds.
BC046211 - Homo sapiens CDC-like kinase 4, mRNA (cDNA clone IMAGE:6189079), partial cds.
BC015942 - Homo sapiens CDC-like kinase 4, mRNA (cDNA clone IMAGE:3908500).
BC143538 - Homo sapiens cDNA clone IMAGE:9052049, with apparent retained intron.
AK304614 - Homo sapiens cDNA FLJ53767 complete cds, highly similar to Dual specificity protein kinase CLK4 (EC 2.7.12.1).
BC034633 - Homo sapiens CDC-like kinase 4, mRNA (cDNA clone IMAGE:4831263), complete cds.
AK294921 - Homo sapiens cDNA FLJ51841 complete cds, highly similar to Dual specificity protein kinase CLK4 (EC 2.7.12.1).
AK310427 - Homo sapiens cDNA, FLJ17469.
AK308674 - Homo sapiens cDNA, FLJ98715.
AK308879 - Homo sapiens cDNA, FLJ98920.
AK308578 - Homo sapiens cDNA, FLJ98619.
AK309215 - Homo sapiens cDNA, FLJ99256.
BC065732 - Homo sapiens CDC-like kinase 4, mRNA (cDNA clone IMAGE:30318368), complete cds.
KJ902949 - Synthetic construct Homo sapiens clone ccsbBroadEn_12343 CLK4 gene, encodes complete protein.
LF325678 - JP 2014500723-A/133181: Polycomb-Associated Non-Coding RNAs.
MA561255 - JP 2018138019-A/133181: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: CLK4_HUMAN, ENST00000316308.1, ENST00000316308.2, ENST00000316308.3, ENST00000316308.4, ENST00000316308.5, ENST00000316308.6, ENST00000316308.7, ENST00000316308.8, NM_020666, Q9HAZ1, uc317pzi.1, uc317pzi.2
UCSC ID: ENST00000316308.9_7
RefSeq Accession: NM_020666.3
Protein: Q9HAZ1 (aka CLK4_HUMAN)

-  Gene Model Information
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.