MmuINT0037425 @ mm10
Intron Retention
Gene
ENSMUSG00000032316 | Clk3
Description
CDC-like kinase 3 [Source:MGI Symbol;Acc:MGI:1098670]
Coordinates
chr9:57750709-57751827:-
Coord C1 exon
chr9:57751737-57751827
Coord A exon
chr9:57751122-57751736
Coord C2 exon
chr9:57750709-57751121
Length
615 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
CACCTTGTGTCCTTGAGCAGAGT
3' ss Score
5.44
Exon sequences
Seq C1 exon
GAAGCAGAAATATTTCTACAAAGGGGGCCTGGTTTGGGATGAGAACAGCTCTGATGGGCGGTATGTGAAGGAGAACTGCAAACCTCTGAAG
Seq A exon
GTCAGTTTCTGGCTCCCCCAGCTCAGCCCATGCCAAGGAGACCCCAGGCATTGGGCAAACAAGCAGCAGAGGCAGGATGGGCAGCCAATAGCTGCCTGATCGTCTCAGTTCTCTGTGAGGCTTTCTGCGTGCTGGCCTTGAGGGGCTCTTAGCCCTGCCCCTGTCCACAGGGTGGCTGAGAATATAATGGGGGAAAAAACACAGAAGAGCCAACTGTCAGACTGCTATTTCCTGTCCCTCTCTCTTCTCTGAATTTTGGGAAGAATTAGGCAGGACTGAGGCAGGGGGAGGGAAGACCTAGATGTGACTAAGGAGGCCTGTCAACTGTAATTTGGTACCTGGACAAGTGCATTTTGCAGAGGTGATTTCTACCCACCCATCAGAACTTTGCATGTGGGGTAGAGGTACCAACCCAGCAAGATCCCACCCAGTAGCCTAAGTTCTGAGCATGAAAGGAAATGAGTGGCTGTTCTGTCCTGGAAGGCAGAAGTAGTCCTCCAAGGAGGCATCATTGCCTCCTCAACCCATCCCAGCAAGGCATCCCAGAGGCAAGGGGACTGCGGTGGCTTCCCACAACCCTGCCGTCCAACTGAGGCACCTTGTGTCCTTGAGCAG
Seq C2 exon
AGTTACATGCTGCAGGACTCCCTGGAGCATGTGCAGCTGTTTGACCTGATGAGGAGGATGTTAGAGTTCGACCCTGCTCAGCGCATCACATTGGCAGAAGCCTTGCTGCACCCCTTCTTTGCTGGCCTGACCCCTGAGGAGCGGTCCTTCCACAGCAGCCGTAACCCCAGCAGATGACAGGTGCAGGCCAGCACACGAAGAGTTGGAGAGCTGGACTGGGCTGCTGGCCCCTTTTCTCCAGCCTCTCCCACTGGCCTCAGAGCCAGAGCCACCGATGAACAGTGCAATGTGAAGGAAGGCAGGAGCCTGCAAGGGAAGGGGGAATGTGGTGCCCGGCTGCCAGAAAGCACAGATTGGACCCAAGCTATTTATATGTTGTAAAGTTATAATAAAGTGTTTCTTACTGTTTGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032316:ENSMUST00000065330:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.085 A=NA C2=0.155
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=FE(9.5=100)
A:
NA
C2:
PF0006920=Pkinase=PD(12.3=66.1)
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:
ATGGGCGGTATGTGAAGGAGA
R:
TCCTGCCTTCCTTCACATTGC
Band lengths:
342-957
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