MmuINT0028771 @ mm10
Intron Retention
Gene
ENSMUSG00000079110 | Capn3
Description
calpain 3 [Source:MGI Symbol;Acc:MGI:107437]
Coordinates
chr2:120485181-120486476:+
Coord C1 exon
chr2:120485181-120485349
Coord A exon
chr2:120485350-120486332
Coord C2 exon
chr2:120486333-120486476
Length
983 bp
Sequences
Splice sites
5' ss Seq
GACGTAAGT
5' ss Score
10.93
3' ss Seq
TCCTTCCCATTGGGCCTCAGGAT
3' ss Score
7.48
Exon sequences
Seq C1 exon
GCTCCATGGCTCCTATGAAGCTCTGAAAGGTGGGAATACCACAGAAGCCATGGAGGACTTCACAGGAGGGGTGACAGAGTTTTTTGAGATCAAGGATGCTCCGAGTGACATGTACAAGATTATGAGGAAAGCTATCGAGAGAGGCTCCCTCATGGGCTGCTCCATTGAC
Seq A exon
GTAAGTGTGATTCCAGGGAGGCCCTTCACTCAGCTAACAACAACACACAGCTTCCTCCTGAGATGGGGTGGATGCTGTAAAAGCAAGAGCCACATTGGTGAGATGGCTCGCTGGTAATGACACTTGTTACTAAACCTGAGGACCTAAGTTTGATCTGGAATCCACATGGTAGAAAGACAATGGACTCCCGAAACCTGTTGTCTGACTTCTGCATGCACTTCCTCCCCACACTAAATAAACAAAAATTTTTAAAAGAAACTACCAGTAGTTCCAGCAATTGAAAAGTTGAATCCAACCTGATTTGATTAGTGAGGTCCTGCTTCTAAAAACAAAGAACATGGATGATGGTTAACTTTAAAATTGACAGTTTTTCGGTGGGAATGTGTCCCTGAAGGTGGGGTGCTTTCCAAGAAAAAGAATGAGCCATGACACTCCAAACATTAGAATTCTGGTAGCAATAGACCAGAGGCCCCACTGATTGGCCTCTCTTGTCCAGACTGCTCAGCACAAGCGTGCCCCACAAGCCAACCACATCGCTGGCTATGGATCTTTGCCCTTAGAAAGTTCTGTAGTCGCTGAGTTTTGACATCACCTCAGTCCTTGGACTCTGTGCTGCAGTCTGGATGATCTCTCTGACCCTCTCTCAGGGTACCAAGATCATATGAACTGAGACAGGAACAAGGAGAGGACCCACCATGGCCTGGTTTCCCCAAGAGCTGCTTTGGGAATAGTAGTCTGGGGTGGGGCAAGCCACCTCCTGCCTCTTTCTCTCCCAGCACTCCCTGTGGGTAGGAAGGCTTGGTTGTCACCACATGGGAGAACTCTCCTGTCCTGTCATTGTCTTGTATCTTTTCTGCATTTACGCTCTGTTGATGTCTTTCTCCTCTTTTGCTTTGCCTGTCGCTCCCCCTTCCCTTCCCGCCCTCCCTTGTTTGCACTCTTTCTTTCCTGGGTTCTCTACTTTCCTTCCCATTGGGCCTCAG
Seq C2 exon
GATGGCACGAACATGACTTATGGAACCTCTCCTTCTGGTCTGAACATGGGGGAGTTGATTGCACGGATGGTGAGAAATATGGATAACTCGCTGCTCAGAGACTCAGACCTGGACCCCAGGGGCTCAGATGACAGACCGTCACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079110:ENSMUST00000028749:5
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=0.358
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(18.7=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(4.4=18.8),PF0064816=Peptidase_C2=PU(30.4=93.8)
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:
GCTCCATGGCTCCTATGAAGC
R:
GGTCTGTCATCTGAGCCCCT
Band lengths:
306-1289
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