MmuINT0028784 @ mm9
Intron Retention
Gene
ENSMUSG00000035547 | Capn5
Description
calpain 5 [Source:MGI Symbol;Acc:MGI:1100859]
Coordinates
chr7:105279701-105280379:-
Coord C1 exon
chr7:105280186-105280379
Coord A exon
chr7:105279779-105280185
Coord C2 exon
chr7:105279701-105279778
Length
407 bp
Sequences
Splice sites
5' ss Seq
CACGTGAGG
5' ss Score
5.78
3' ss Seq
CCCTGATACTCACTCCCCAGGTC
3' ss Score
8.43
Exon sequences
Seq C1 exon
GCTGTGACAGCAGCTGACATGGAGGCCCGCCTGGCATGTGGCCTGGTGAAGGGCCATGCATACGCTGTCACCGATGTGCGCAAGGTGCGCCTGGGCCATGGCCTGCTGGCCTTCTTCAAGTCAGAGAAGCTTGATATGATCCGTCTGAGGAACCCCTGGGGCGAGCGGGAGTGGACGGGGCCCTGGAGTGACAC
Seq A exon
GTGAGGCTCACCAGGGTTGGGGCTGGGTATGGGCACAGAGGCAAGGACAAGCGGTGACACTGGACTGGGCCTTGCAGGGTCTGGGAGAGATGCTCTGAGGAAAAAATGGGAGACTTACTTTCCAGTGTAAGTGTGGTGCTTGGGGGGTAGGTTCATCAAGGACAGTGGCCAGAAGTGTGGCATGCTTTGTACGTGGACAATGGCGCCTCACCAGCTTTATTCCCTGACTTCATAGCCTTAGCATAAAGGAAGATCACAGTTCCTAGTGGGAGAGAACAGAGGCTTCTTAGCAGGGCTGGGCATGGCCTCCAGGTCTCTACCCACAGTGCTCTGCAGGCGGCTTGGTCCAGAGCTCTCCCTTGGGCCACTCCTCTTATCCCGTTCCCTCCCTGATACTCACTCCCCAG
Seq C2 exon
GTCAGAGGAATGGCAGAAAGTGAGCAAGAGTGAGAGGGAGAAGATGGGCGTGACCGTGCAGGATGATGGGGAATTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035547-Capn5:NM_007602:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.046 A=NA C2=0.296
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(20.1=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(8.2=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:
CTGTGACAGCAGCTGACATGG
R:
AGAATTCCCCATCATCCTGCAC
Band lengths:
270-677
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: