MmuINT0037404 @ mm9
Intron Retention
Gene
ENSMUSG00000026034 | Clk1
Description
CDC-like kinase 1 [Source:MGI Symbol;Acc:MGI:107403]
Coordinates
chr1:58476511-58477055:-
Coord C1 exon
chr1:58476965-58477055
Coord A exon
chr1:58476578-58476964
Coord C2 exon
chr1:58476511-58476577
Length
387 bp
Sequences
Splice sites
5' ss Seq
GATGTATAG
5' ss Score
-2.49
3' ss Seq
TAATTATTCCTCTTTTTTAGATG
3' ss Score
9.68
Exon sequences
Seq C1 exon
AAGAGTCACCGAAGGAAAAGATCGAGGAGTGTAGAGGATGATGAGGAGGGTCACCTGATCTGTCAGAGTGGAGACGTACTAAGTGCAAGAT
Seq A exon
GTATAGAATATTTTTCAACACTTATTTACTTTTCAGATAACATAATCTATATGTATATATAGATTAAAGTTTCAGGGATTTGGAAATCTTTTTCTTTCTTTTTTTTCTTTTTTTTTTTGCTTTCATTTCTTTTGGTGGGAGGGGATTGTCTTTGCTTTCTTTGAAGTTTTAATATTAAATTCCACAGCAGTAAATCAAGTTAATGAAATTAGTCTGAGAATGAAATTAGATCTAAGAATAGTTGTATGTTTTTTGGATGGTGTTGGCTGATAAGTAATTAATGATAAGGAAATTTGCAGCATCACCTAGAATAATCTGCATTGATAATACTTATAAGTACATTGTTCTCATTTCCTGTTATGAATAATAATTATTCCTCTTTTTTAG
Seq C2 exon
ATGAAATTGTTGATACTTTAGGTGAAGGTGCTTTCGGAAAAGTGGTGGAATGCATCGATCATAAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026034-Clk1:NM_001042634:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.484 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF105774=UPF0560=FE(16.9=100),PF0006920=Pkinase=PU(0.1=0.0)
A:
NA
C2:
PF105774=UPF0560=FE(12.4=100),PF0006920=Pkinase=PU(6.9=95.7)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: