MmuINT0037413 @ mm9
Intron Retention
Gene
ENSMUSG00000068917 | Clk2
Description
CDC-like kinase 2 [Source:MGI Symbol;Acc:MGI:1098669]
Coordinates
chr3:88979314-88979657:+
Coord C1 exon
chr3:88979314-88979393
Coord A exon
chr3:88979394-88979566
Coord C2 exon
chr3:88979567-88979657
Length
173 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACT
5' ss Score
6.64
3' ss Seq
AACCTCCCCTTCCCCTCCAGAAA
3' ss Score
9.9
Exon sequences
Seq C1 exon
ACCCATGACAACAGAGAGCATCTAGCCATGATGGAAAGGATCCTGGGTCCTGTCCCTTCTCGGATGATCAGAAAGACAAG
Seq A exon
GTGACTCTCACGCGGGAGGCACTAGAGCGTCTCTCCTCGTGGAATTTGTCTGTTAGGCATCATTTTCTTGTTTTCATTGACATCTCCCTAGCCCCCACTTACTTGGGTAAACAAGGGAAAGGGTTTTATAGAAATGGAGCCTTCTGATGCACAAACCTCCCCTTCCCCTCCAG
Seq C2 exon
AAAACAGAAATATTTTTATCGGGGTCGCCTGGATTGGGATGAGAACACCTCAGCCGGGCGCTACGTTCGTGAGAACTGCAAACCTCTGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000068917-Clk2:NM_007712:11
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=FE(8.2=100)
A:
NA
C2:
PF0006920=Pkinase=FE(9.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCCATGACAACAGAGAGCAT
R:
CGCAGAGGTTTGCAGTTCTCA
Band lengths:
170-343
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: