MmuINT0028777 @ mm10
Intron Retention
Gene
ENSMUSG00000035547 | Capn5
Description
calpain 5 [Source:MGI Symbol;Acc:MGI:1100859]
Coordinates
chr7:98125829-98126442:-
Coord C1 exon
chr7:98126246-98126442
Coord A exon
chr7:98125945-98126245
Coord C2 exon
chr7:98125829-98125944
Length
301 bp
Sequences
Splice sites
5' ss Seq
CCGGTGTGT
5' ss Score
6.56
3' ss Seq
CCTATCCTGCCCTGTTTCAGGGA
3' ss Score
10.08
Exon sequences
Seq C1 exon
GTGGAAGAGAACCGCCAATACCGTATGCACAGCCTACAGCATAAGGCCGCCAGCTCCATCTACATCAATTCCCGCAGCGTTTTTTTGAGGACAGAGCTGCCCGAGGGCCGCTACGTTATCATCCCTACCACCTTTGAGCCAGGCCACACTGGCGAGTTCCTGCTCCGAGTCTTCACAGATGTCCCCTCCAACTGCCG
Seq A exon
GTGTGTGGGGGCTAGGGCTAGTGACCGCATGCATATATACCCCATGCTGGGCTGGATTTTAACATGGGTCTTACCATTACTACCACATGTCCCATCTGTCATCTGAGGATGAGAAATAGTATCTATAAGTGCTAAGTGCTCTGCCGTCCTGAGAGGAGGAGGTGGGGCAGAGAGGCTGGAGGCCTGTGGTAGTGGGTGTGGTTGAGTTTGCCATGAGGTTTGCTTAGCTCCTTGTTTTGAACCCCATCTGCACATTTGTCTTTATGCCGCCCATCCATTCCCCTATCCTGCCCTGTTTCAG
Seq C2 exon
GGAACTACGCCTGGATGAGCCCCCTCGGACCTGTTGGAGTTCCCTCTGTGGCTACCCTCAGCAGGTGGCCCAGGTACATGTCCTGGGGGCTGCTGGCCTCAAGGACTCCCCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035547:ENSMUST00000040971:10
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:
PF0106717=Calpain_III=FE(45.1=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0),PF0016825=C2=PU(20.5=40.0)
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:
GGAAGAGAACCGCCAATACCG
R:
CTGTTGGGGAGTCCTTGAGGC
Band lengths:
311-612
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