MmuINT0037400 @ mm10
Intron Retention
Gene
ENSMUSG00000026034 | Clk1
Description
CDC-like kinase 1 [Source:MGI Symbol;Acc:MGI:107403]
Coordinates
chr1:58412647-58413026:-
Coord C1 exon
chr1:58412947-58413026
Coord A exon
chr1:58412738-58412946
Coord C2 exon
chr1:58412647-58412737
Length
209 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
TGAACATTTAACTGTTTTAGGAA
3' ss Score
8.89
Exon sequences
Seq C1 exon
ACTCATGATAGCAGGGAACATTTAGCAATGATGGAAAGGATTCTTGGACCACTACCAAAGCACATGATACAGAAAACCAG
Seq A exon
GTATGTTTTACTTGAGCCACGGCATCTATAGTAGTACCACTGGATTTTGATTGGAACTTTTATTTATTTATTTTTTAAGCTATTTGTTCCTTTGCTCTAACTTTCTAGAAAAAGATTAGATAGTCTAATATCCTAATACAAATCTTTACCTTTGCTATTTTGACTTTGGGGAAGTCAGCATGGTAAATGTGAACATTTAACTGTTTTAG
Seq C2 exon
GAAACGCAGATATTTCCATCATGATCGATTAGATTGGGATGAACACAGTTCTGCTGGCAGATATGTTTCTCGGCGCTGTAAACCTCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026034:ENSMUST00000034868:11
Average complexity
IR
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
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCATGATAGCAGGGAACATTTAGCA
R:
GAGGTTTACAGCGCCGAGAAA
Band lengths:
164-373
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