MmuINT0037406 @ mm10
Intron Retention
Gene
ENSMUSG00000026034 | Clk1
Description
CDC-like kinase 1 [Source:MGI Symbol;Acc:MGI:107403]
Coordinates
chr1:58417013-58417383:-
Coord C1 exon
chr1:58417267-58417383
Coord A exon
chr1:58417180-58417266
Coord C2 exon
chr1:58417013-58417179
Length
87 bp
Sequences
Splice sites
5' ss Seq
TTTGTAAGT
5' ss Score
7.4
3' ss Seq
TTTTTTTAACGTGTTTATAGCCG
3' ss Score
6.41
Exon sequences
Seq C1 exon
GGGAGGTAGACGTGTAGCAGTAAAAATAGTTAAAAATGTGGATAGATACTGTGAAGCTGCTCAATCGGAAATACAAGTTTTGGAACACTTGAATACAACAGACCCCCATAGTACTTT
Seq A exon
GTAAGTATCACATTAAAACTTGAAATAGAGAGGTTTGAATTGTAAGCCCTATTATTGAGTTGTTTTGTTTTTTTAACGTGTTTATAG
Seq C2 exon
CCGTTGTGTCCAGATGTTGGAGTGGTTTGAGCATCGAGGTCACATTTGCATTGTGTTTGAACTTCTGGGGCTTAGTACTTATGATTTCATTAAGGAAAACAGTTTTCTGCCGTTTCGAATGGATCATATCAGGAAGATGGCATATCAAATATGCAAATCTGTAAACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026034:ENSMUST00000034868:6
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:
PF105774=UPF0560=PD(1.1=5.0),PF0006920=Pkinase=FE(12.3=100)
A:
NA
C2:
PF0006920=Pkinase=FE(17.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGAGGTAGACGTGTAGCAGT
R:
TGCAAATGTGACCTCGATGCT
Band lengths:
167-254
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