MmuINT0037439 @ mm9
Intron Retention
Gene
ENSMUSG00000020385 | Clk4
Description
CDC like kinase 4 [Source:MGI Symbol;Acc:MGI:1098551]
Coordinates
chr11:51085302-51086670:+
Coord C1 exon
chr11:51085302-51085524
Coord A exon
chr11:51085525-51086579
Coord C2 exon
chr11:51086580-51086670
Length
1055 bp
Sequences
Splice sites
5' ss Seq
TCGGTATGA
5' ss Score
7.72
3' ss Seq
CTGCCCACTTGCCGTTCCAGAAG
3' ss Score
7.46
Exon sequences
Seq C1 exon
TCACTATTTAGAAGCAAGATGCTTGAATGAGAGAGATTATCGGGACCGGAGATACATTGATGAATACAGAAATGACTACTGCGAAGGATATGTTCCAAGACATTACCATAGAGACGTTGAAAGCACTTACCGGATCCATTGCAGTAAATCCTCAGTCAGGAGCAGGAGAAGCAGCCCTAAGAGAAAGCGTAATAGACCCTGTGCAAGTCATCAGTCGCATTCG
Seq A exon
GTATGAGTGGTTTGTTTTTATTTGGAATGGATTGATTGTAAAGCTCTGAAAGGGTGATAAGTTTCTAAGTTTCTTAATGCAATTTGGATATGCTGTAATTAAATTCATGTTACTGGAGTCCTTAAAGGAAGTGTATACATTCTCATAATTGACCACCTGTGTGTTAGTTAGTCTTCATTTTGCCCACACACTCATTCTGCAAAACAGATCATGCATGAGTTTGTTGGTTTTAATAGTAAGAACATCTTATTTTGTGGTTGTATAATATATTAAAAATGAGGCACCCATTTTTTTCTCCTTTGAATGTAAAGATTTTTTTATTTTGAAAGAAACTGCTTTACTGGTAGTTGGAAATAACTCAGGCAGGTCGCCTTGCTGAGGTGTTGAGCCATTGCTGACTCCTGTGTGGTCTAGCTCCTCGGACAGCACATCATTGTCTGCGTTAATTTCCTGAAGTTGTGAACCTGGGTGCTGAGGGGAAAATGTACTGAGAAAGCTAGACATCTTTTATTTGTAAATTTTGAGTTACCATGTCCCTCCCCCAAGTTTTTTTTCTATAGAACTAGCAGTTACTAGATGGAAGATTGAAATTAGTCTTTACTTCCCCTTCTTACTATGATGATGTCCACTTTTAAATGTTGCTAAAAGAGAACAATTTCAACTAATCTTGACATTTTCCTGACTAACTAGACAACCCAATTCACAGCATATGGTTATAGCAAAAATTAGTAAATCATGACAATGCATTCTTTAAACTTCAGACTTCAATTAAATCAGTATTTTAAAGAGACAATTGTGTTGTTTTTTTCTATTGCCACTTTAAGTATCTTATCTGAAAATCTGTTCCTTGCCATGTTTTTCTTCTGTAACATAAACTGTGCCCTGTGAATTTCTGGGGACTGAATTTGAAATTGCTCCTGCCAACTGTTCGTGGCCTGGTGCTTATCTGAATGCCTGAATATCTCCCCGCTGAATGAATTGCGTATTCTGCCCTGAATTCACTCTGATATATTGATTGGCTGGACGATCTTGGTGCTGCCCACTTGCCGTTCCAG
Seq C2 exon
AAGAGCCACCGAAGGAAAAGATCCAGGAGTATAGAGGATGATGAGGAGGGTCACCTGATCTGTCAAAGTGGAGACGTTCTAAGAGCAAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020385-Clk4:NM_007714:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.312 A=NA C2=0.323
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0006920=Pkinase=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAAGATGCTTGAATGAGAGAGA
R:
TGCTCTTAGAACGTCTCCACT
Band lengths:
297-1352
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: