Human Gene CLK1 (uc002uwe.2) Description and Page Index
  Description: Homo sapiens CDC-like kinase 1 (CLK1), transcript variant 1, mRNA.
RefSeq Summary (NM_004071): This gene encodes a member of the CDC2-like (or LAMMER) family of dual specificity protein kinases. In the nucleus, the encoded protein phosphorylates serine/arginine-rich proteins involved in pre-mRNA processing, releasing them into the nucleoplasm. The choice of splice sites during pre-mRNA processing may be regulated by the concentration of transacting factors, including serine/arginine rich proteins. Therefore, the encoded protein may play an indirect role in governing splice site selection. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009].
Transcript (Including UTRs)
   Position: hg19 chr2:201,717,732-201,729,467 Size: 11,736 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr2:201,718,029-201,726,585 Size: 8,557 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:201,717,732-201,729,467)mRNA (may differ from genome)Protein (484 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: CLK1_HUMAN
DESCRIPTION: RecName: Full=Dual specificity protein kinase CLK1; EC=2.7.12.1; AltName: Full=CDC-like kinase 1;
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, SRSF3 and PTPN1. Regulates the alternative splicing of tissue factor (F3) pre-mRNA in endothelial cells and adenovirus E1A pre-mRNA.
CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.
ENZYME REGULATION: Regulates splicing of its own pre-mRNA according to its kinase activity; increased expression of the catalytically active form influences splicing to generate the catalytically inactive splicing variant lacking the kinase domain. Leucettine L41 inhibits its kinase activity and affects the regulation of alternative splicing mediated by phosphorylation of SR proteins (By similarity).
SUBUNIT: Interacts with PPIG and UBL5.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Endothelial cells.
PTM: Autophosphorylates on all three types of residues (By similarity).
SIMILARITY: Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. Lammer subfamily.
SIMILARITY: Contains 1 protein kinase domain.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D000082 Acetaminophen
  • D016604 Aflatoxin B1
  • D004997 Ethinyl Estradiol
  • D013749 Tetrachlorodibenzodioxin
  • C517041 (4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)
  • D015084 2,4-Dichlorophenoxyacetic Acid
  • C012796 2-butenal
  • C472791 3-(4'-hydroxy-3'-adamantylbiphenyl-4-yl)acrylic acid
  • D000111 Acetylcysteine
  • D017638 Asbestos, Crocidolite
          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: 113.84 RPKM in Nerve - Tibial
Total median expression: 3218.96 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 -67.10181-0.371 Picture PostScript Text
3' UTR -56.89297-0.192 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 kinase

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

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1Z57
- X-ray MuPIT

2VAG
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P49759
FrontTopSide
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 orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
     SGD
     Protein Sequence
     Alignment

-  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:0004715 non-membrane spanning 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:0008283 cell proliferation
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
GO:0018107 peptidyl-threonine phosphorylation
GO:0018108 peptidyl-tyrosine phosphorylation
GO:0043484 regulation of RNA splicing
GO:0046777 protein autophosphorylation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  LF383607 - JP 2014500723-A/191110: Polycomb-Associated Non-Coding RNAs.
AK025306 - Homo sapiens cDNA: FLJ21653 fis, clone COL08586, highly similar to HUMKINCDC Human protein kinase mRNA.
AK316127 - Homo sapiens cDNA, FLJ79026 complete cds, highly similar to Dual specificity protein kinase CLK1 (EC2.7.12.1).
M59287 - Human protein kinase mRNA.
BC028149 - Homo sapiens CDC-like kinase 1, mRNA (cDNA clone IMAGE:5217585), complete cds.
BC031549 - Homo sapiens CDC-like kinase 1, mRNA (cDNA clone MGC:21240 IMAGE:4387232), complete cds.
BC028573 - Homo sapiens CDC-like kinase 1, mRNA (cDNA clone IMAGE:4836776), with apparent retained intron.
L29219 - Homo sapiens clk1 mRNA, complete cds.
L29222 - Homo sapiens clk1 mRNA, complete cds.
AK294295 - Homo sapiens cDNA FLJ56064 complete cds, highly similar to Dual specificity protein kinase CLK1 (EC 2.7.12.1).
KJ890932 - Synthetic construct Homo sapiens clone ccsbBroadEn_00326 CLK1 gene, encodes complete protein.
KJ905177 - Synthetic construct Homo sapiens clone ccsbBroadEn_14589 CLK1 gene, encodes complete protein.
AB385095 - Synthetic construct DNA, clone: pF1KB5418, Homo sapiens CLK1 gene for dual specificity protein kinase CLK1, complete cds, without stop codon, in Flexi system.
AF212224 - Homo sapiens CLK4 mRNA, complete cds.
MA619184 - JP 2018138019-A/191110: Polycomb-Associated Non-Coding RNAs.
JD377234 - Sequence 358258 from Patent EP1572962.
LF317783 - JP 2014500723-A/125286: Polycomb-Associated Non-Coding RNAs.
JD372349 - Sequence 353373 from Patent EP1572962.
JD371642 - Sequence 352666 from Patent EP1572962.
JD509237 - Sequence 490261 from Patent EP1572962.
LF317784 - JP 2014500723-A/125287: Polycomb-Associated Non-Coding RNAs.
LF317785 - JP 2014500723-A/125288: Polycomb-Associated Non-Coding RNAs.
MA553360 - JP 2018138019-A/125286: Polycomb-Associated Non-Coding RNAs.
MA553361 - JP 2018138019-A/125287: Polycomb-Associated Non-Coding RNAs.
MA553362 - JP 2018138019-A/125288: Polycomb-Associated Non-Coding RNAs.
LF317786 - JP 2014500723-A/125289: Polycomb-Associated Non-Coding RNAs.
AK289365 - Homo sapiens cDNA FLJ77410 complete cds, highly similar to Homo sapiens CDC-like kinase 1 (CLK1), transcript variant 2, mRNA.
JD027278 - Sequence 8302 from Patent EP1572962.
LF317787 - JP 2014500723-A/125290: Polycomb-Associated Non-Coding RNAs.
JD028730 - Sequence 9754 from Patent EP1572962.
CU689170 - Synthetic construct Homo sapiens gateway clone IMAGE:100019619 5' read CLK1 mRNA.
AK297804 - Homo sapiens cDNA FLJ60725 complete cds, highly similar to Peptidyl-prolyl cis-trans isomerase-like 3(EC 5.2.1.8).
LF317788 - JP 2014500723-A/125291: Polycomb-Associated Non-Coding RNAs.
AK307301 - Homo sapiens cDNA, FLJ97249.
LF317790 - JP 2014500723-A/125293: Polycomb-Associated Non-Coding RNAs.
LF317792 - JP 2014500723-A/125295: Polycomb-Associated Non-Coding RNAs.
LF317793 - JP 2014500723-A/125296: Polycomb-Associated Non-Coding RNAs.
LF317794 - JP 2014500723-A/125297: Polycomb-Associated Non-Coding RNAs.
MA553363 - JP 2018138019-A/125289: Polycomb-Associated Non-Coding RNAs.
MA553364 - JP 2018138019-A/125290: Polycomb-Associated Non-Coding RNAs.
MA553365 - JP 2018138019-A/125291: Polycomb-Associated Non-Coding RNAs.
MA553367 - JP 2018138019-A/125293: Polycomb-Associated Non-Coding RNAs.
MA553369 - JP 2018138019-A/125295: Polycomb-Associated Non-Coding RNAs.
MA553370 - JP 2018138019-A/125296: Polycomb-Associated Non-Coding RNAs.
MA553371 - JP 2018138019-A/125297: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DFW7, CLK, CLK1_HUMAN, NM_004071, NP_004062, P49759, Q0P694, Q8N5V8
UCSC ID: uc002uwe.2
RefSeq Accession: NM_004071
Protein: P49759 (aka CLK1_HUMAN)
CCDS: CCDS2331.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004071.3
exon count: 13CDS single in 3' UTR: no RNA size: 1933
ORF size: 1455CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3364.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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