MmuINT0028651 @ mm10
Intron Retention
Gene
ENSMUSG00000024942 | Capn1
Description
calpain 1 [Source:MGI Symbol;Acc:MGI:88263]
Coordinates
chr19:6011015-6011430:-
Coord C1 exon
chr19:6011297-6011430
Coord A exon
chr19:6011184-6011296
Coord C2 exon
chr19:6011015-6011183
Length
113 bp
Sequences
Splice sites
5' ss Seq
TAAGTGAGT
5' ss Score
6.43
3' ss Seq
CGACCTGGAGCTGCCCACAGAGT
3' ss Score
1.12
Exon sequences
Seq C1 exon
CTGTGGCAGTTCGGGGAGTGGGTCGACGTGGTCATAGATGACTTGCTGCCCACCAAGGACGGGAAGCTGGTGTTCGTGCACTCTGCCCAGGGCAACGAATTCTGGAGCGCACTGCTGGAGAAAGCCTATGCTAA
Seq A exon
GTGAGTAGGATCCCCAGGGCACATCTTCGGTCTCTGGGGGTGGAGAGGTTGTCCTGGCCCTCTTACCCGGTCCTCCTTGATGATGCTACTAACCGACCTGGAGCTGCCCACAG
Seq C2 exon
AGTGAATGGCAGCTATGAGGCTCTTTCGGGAGGCTGCACCTCAGAGGCCTTCGAGGACTTTACCGGTGGGGTCACTGAGTGGTACGACCTGCAGAAGGCCCCCAGCGACCTCTACCAGATCATTCTAAAGGCCCTGGAACGAGGCTCCTTGCTGGGCTGCTCCATTAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024942:ENSMUST00000025891:5
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:
PF0064816=Peptidase_C2=FE(14.7=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(18.7=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:
TAGATGACTTGCTGCCCACCA
R:
CCTCGTTCCAGGGCCTTTAGA
Band lengths:
244-357
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