MmuINT0037442 @ mm10
Intron Retention
Gene
ENSMUSG00000020385 | Clk4
Description
CDC like kinase 4 [Source:MGI Symbol;Acc:MGI:1098551]
Coordinates
chr11:51275211-51275578:+
Coord C1 exon
chr11:51275211-51275327
Coord A exon
chr11:51275328-51275411
Coord C2 exon
chr11:51275412-51275578
Length
84 bp
Sequences
Splice sites
5' ss Seq
CTTGTAAGT
5' ss Score
8
3' ss Seq
ATTATTTTCATCTCTTTTAGCCG
3' ss Score
7.98
Exon sequences
Seq C1 exon
GGATGGCTTACATGTAGCAGTGAAAATTGTAAAAAATGTAGGCCGTTACCGGGAGGCAGCTCGTTCTGAAATCCAAGTATTGGAGCACTTGAACAGCACTGACCCCAACAGTGTCTT
Seq A exon
GTAAGTACACATTGAACCACAAGCTGTCAAACTGTGTGAGCTGCTCACTTCTGTGCACTCAATTATTATTTTCATCTCTTTTAG
Seq C2 exon
CCGATGCGTCCAGATGCTAGAGTGGTTTGATCATCATGGTCATGTTTGTATTGTGTTTGAGCTGCTGGGACTTAGTACCTATGATTTTATTAAAGAAAATAGTTTTCTGCCATTTCAAATTGATCACATCAGGCAAATGGCTTATCAGATCTGCCAGTCTATAAATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020385:ENSMUST00000093132:6
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=PU(13.2=97.5)
A:
NA
C2:
PF0006920=Pkinase=FE(17.7=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:
TTGAACAGCACTGACCCCAAC
R:
AGCCATTTGCCTGATGTGATCA
Band lengths:
171-255
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