MmuINT0037428 @ mm9
Intron Retention
Gene
ENSMUSG00000032316 | Clk3
Description
CDC-like kinase 3 [Source:MGI Symbol;Acc:MGI:1098670]
Coordinates
chr9:57606091-57606530:-
Coord C1 exon
chr9:57606434-57606530
Coord A exon
chr9:57606158-57606433
Coord C2 exon
chr9:57606091-57606157
Length
276 bp
Sequences
Splice sites
5' ss Seq
GATGTACAG
5' ss Score
-3.25
3' ss Seq
CAGCTTCTTCTTTCTCACAGATG
3' ss Score
9.56
Exon sequences
Seq C1 exon
AGAAGCCAACAGAGCAGTAAGCGCAGCAGCCGGAGTGTGGAAGATGACAAGGAGGGCCACCTGGTGTGCCGGATCGGCGATTGGCTCCAAGAGCGAT
Seq A exon
GTACAGCCACCTTTCGTAAAACTTTACCTCTCTACTTTCTACCCCCCTTGTTAGATGAGACCTCTCCTGCGTGGAGGGGCCTCTAGTGCGCGTGGCGCCTTAGTGGGGCCACCAGTAATTGCCTGAATGACACAGACACTAGCAACTTCTGTTTTAAAGAGTGTAGCAGTGAGCAAGAACCTTTGTTGTTTTTGAGGATTTGAATGCTGTGAACTTGCAGGAGCTGCCACCCTCCTACCCTCCAGACTCTCATGCCCAGCTTCTTCTTTCTCACAG
Seq C2 exon
ATGAGATCGTGGGGAACCTGGGTGAAGGCACCTTTGGCAAGGTGGTGGAGTGCTTGGACCATGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032316-Clk3:NM_007713:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.424 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=PU(0.1=0.0)
A:
NA
C2:
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:
AGAAGCCAACAGAGCAGTAAGC
R:
CTGGCATGGTCCAAGCACTC
Band lengths:
164-440
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: