HsaEX0015695 @ hg38
Exon Skipping
Gene
ENSG00000013441 | CLK1
Description
CDC like kinase 1 [Source:HGNC Symbol;Acc:HGNC:2068]
Coordinates
chr2:200859680-200861466:-
Coord C1 exon
chr2:200861238-200861466
Coord A exon
chr2:200860125-200860215
Coord C2 exon
chr2:200859680-200859746
Length
91 bp
Sequences
Splice sites
3' ss Seq
CGCCCACTTGACGTTTCCAGAAG
3' ss Score
6.57
5' ss Seq
GATGTATAG
5' ss Score
-2.49
Exon sequences
Seq C1 exon
CCATTATTTGGAAAGCAGGTCTATAAATGAGAAAGATTATCATAGTCGACGCTACATTGATGAGTACAGAAATGACTACACTCAAGGATGTGAACCTGGACATCGCCAAAGAGACCATGAAAGCCGGTATCAGAACCATAGTAGCAAGTCTTCTGGTAGAAGTGGAAGAAGTAGTTATAAAAGCAAACACAGGATTCACCACAGTACTTCACATCGTCGTTCACATGGG
Seq A exon
AAGAGTCACCGAAGGAAAAGAACCAGGAGTGTAGAGGATGATGAGGAGGGTCACCTGATCTGTCAGAGTGGAGACGTACTAAGTGCAAGAT
Seq C2 exon
ATGAAATTGTTGATACTTTAGGTGAAGGAGCTTTTGGAAAAGTTGTGGAGTGCATCGATCATAAAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000013441_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion
Show PDB structure
Features
Disorder rate (Iupred):
C1=0.814 A=0.538 C2=0.077
Domain overlap (PFAM):
C1:
PF105774=UPF0560=FE(42.2=100)
A:
PF105774=UPF0560=FE(16.7=100),PF0006920=Pkinase=PU(0.1=0.0)
C2:
PF105774=UPF0560=FE(12.2=100),PF0006920=Pkinase=PU(11.3=95.7)
Associated events
Other assemblies
Conservation
Primers PCR
Suggestions for RT-PCR validation
F:
AAAGAGACCATGAAAGCCGGT
R:
TGATCGATGCACTCCACAACT
Band lengths:
183-274
Functional annotations
There are 2 annotated functions for this event
PMID: 7665564
Alternative splicing of the primary Sty (another name for CDC-like kinase 1 (CLK1)) transcript generates mRNAs encoding full-length catalytically active (STY) and truncated (via skipping of cassette exon HsaEX0015695), kinase-deficient polypeptides. Both STY and its truncated isoform, STYT, are localized in the nucleus and are capable of heterodimerizing.
PMID: 9315658
The Clk1 kinase, which phosphorylates SR proteins, is regulated through alternative splicing of the Clk1 pre-mRNA, yielding mRNAs encoding catalytically active (includes cassette exon HsaEX0015695) and truncated inactive polypeptides (skips HsaEX0015695) (Clk1 and Clk1T , respectively). The authors present evidence that Clk1 and Clk1T proteins regulate the splicing of Clk1 and adenovirus pre-mRNAs in vivo. The peptide domain encoded by the alternatively spliced exon of Clk1 is essential for the regulatory activity of the Clk1 kinase. This is the first direct demonstration of an in vivo link between alternative splicing and protein kinase activity. (Seems to be a case of auto-regulation of ratio of Clk1 transcripts with/without the cassette exon)
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development