MmuINT0028687 @ mm10
Intron Retention
Gene
ENSMUSG00000058626 | Capn11
Description
calpain 11 [Source:MGI Symbol;Acc:MGI:1352490]
Coordinates
chr17:45639069-45639484:-
Coord C1 exon
chr17:45639410-45639484
Coord A exon
chr17:45639233-45639409
Coord C2 exon
chr17:45639069-45639232
Length
177 bp
Sequences
Splice sites
5' ss Seq
CTGGTCAGT
5' ss Score
6.6
3' ss Seq
GTCCGTCCTCCCCTTCCCAGGAT
3' ss Score
10.74
Exon sequences
Seq C1 exon
AGCCACAGAGTGGGAAGAGGTGAGCCCAGATGTTCGGGTACAGCTGCTACACAAGAAGGATGATGGCGATTTCTG
Seq A exon
GTCAGTGTGGCTTGGAGGAGCCTCAGACTCCCCACAGGCATCCCTCATCTCCCTACAATCGCCTCTGTGTGGTGTGCCTCGGGTGAGGAGGTCCTAGGGTCCCTTCACAGTCAGGTCAGGGCCCGTAGGTGTGGCTGTGGAGTGTACTGACAGCGCTGTCCGTCCTCCCCTTCCCAG
Seq C2 exon
GATGTCCTATGAAGACTTCATGAGCAACTTTACACTGCTGGAGATCTGCAACCTCACCCCGGATGCCCTCAACACCTGGGATTACAAGAGCCGCTGGCACTCCACCTTCTATGAGGGCAGCTGGCGAAGGGGAAGCACTGCAGGGGGCTGCAGAAACCACCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058626:ENSMUST00000120717:9
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=0.018
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(8.3=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(6.3=33.9),PF0106717=Calpain_III=PU(15.2=42.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGAGTGGGAAGAGGTGAGC
R:
CGGGTGGTTTCTGCAGCC
Band lengths:
234-411
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