MmuINT0037417 @ mm10
Intron Retention
Gene
ENSMUSG00000068917 | Clk2
Description
CDC-like kinase 2 [Source:MGI Symbol;Acc:MGI:1098669]
Coordinates
chr3:89170049-89170409:+
Coord C1 exon
chr3:89170049-89170115
Coord A exon
chr3:89170116-89170292
Coord C2 exon
chr3:89170293-89170409
Length
177 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACA
5' ss Score
8.88
3' ss Seq
CCTCCCCTATTACCTTACAGGGG
3' ss Score
9.87
Exon sequences
Seq C1 exon
ATGAAATTGTAAGCACCTTAGGAGAAGGGACCTTCGGCCGAGTTGTGCAGTGTGTGGACCATCGCAG
Seq A exon
GTAACAAATGTCCTGCCGCTTACTCCACATCTGTTAGGCAGAGACGATTGTCAGGGCATCGAATATGTTTAGAGATTAGACAGTCAGAAGTTCTTAGTCTGATCCATTAATCACTCACTGATCATTCAATCTGAGATGTTCTTGAACCCAACAAAAGCCTCCCCTATTACCTTACAG
Seq C2 exon
GGGCGGAACACAAGTTGCCCTGAAGATCATTAAGAATGTGGAGAAGTACAAGGAAGCAGCCCGACTAGAAATCAACGTGCTGGAGAAAATCAATGAGAAAGATCCTGACAACAAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000068917:ENSMUST00000121212:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.025 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=PU(14.7=95.7)
A:
NA
C2:
PF0006920=Pkinase=FE(12.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAATTGTAAGCACCTTAGGAGA
R:
TCTTGTTGTCAGGATCTTTCTCA
Band lengths:
182-359
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types