MmuINT0028766 @ mm10
Intron Retention
Gene
ENSMUSG00000079110 | Capn3
Description
calpain 3 [Source:MGI Symbol;Acc:MGI:107437]
Coordinates
chr2:120503133-120503465:+
Coord C1 exon
chr2:120503133-120503211
Coord A exon
chr2:120503212-120503348
Coord C2 exon
chr2:120503349-120503465
Length
137 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCTG
5' ss Score
4.87
3' ss Seq
CCTCTCCCTGCCCCTCCAAGGCT
3' ss Score
6.16
Exon sequences
Seq C1 exon
AAAATCTTCAAGCACTATGACACAGACCATTCCGGTACCATCAATAGCTATGAGATGCGAAATGCAGTCAATGATGCAG
Seq A exon
GTGCTGGGGTGCAGGGGATGCTGGGGGGTTGAGAGGGTGACAACATGCAGACCTGAGAGCTGGGGGAAGCAGGAGGGGATGGGAAAGGAGACTGCAAGCCTGAGAACTTCATCCCTCCCTCTCCCTGCCCCTCCAAG
Seq C2 exon
GCTTCCATCTCAACAGCCAACTCTATGACATCATCACCATGCGCTATGCGGACAAACACATGAACATCGACTTTGACAGCTTCATCTGCTGCTTCGTCAGGCTGGAAGGGATGTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079110:ENSMUST00000028749:21
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:
PF134991=EF-hand_7=FE(28.3=100)
A:
NA
C2:
PF134991=EF-hand_7=FE(42.4=100)
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:
AATCTTCAAGCACTATGACACAGACC
R:
TGAACATCCCTTCCAGCCTGA
Band lengths:
194-331
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