MmuINT0028668 @ mm10
Intron Retention
Gene
ENSMUSG00000058626 | Capn11
Description
calpain 11 [Source:MGI Symbol;Acc:MGI:1352490]
Coordinates
chr17:45638695-45639232:-
Coord C1 exon
chr17:45639069-45639232
Coord A exon
chr17:45638871-45639068
Coord C2 exon
chr17:45638695-45638870
Length
198 bp
Sequences
Splice sites
5' ss Seq
CGGGTAGGC
5' ss Score
7.5
3' ss Seq
TTGACCTGGATCTTCCACAGAGA
3' ss Score
7.34
Exon sequences
Seq C1 exon
GATGTCCTATGAAGACTTCATGAGCAACTTTACACTGCTGGAGATCTGCAACCTCACCCCGGATGCCCTCAACACCTGGGATTACAAGAGCCGCTGGCACTCCACCTTCTATGAGGGCAGCTGGCGAAGGGGAAGCACTGCAGGGGGCTGCAGAAACCACCCGG
Seq A exon
GTAGGCGAGGGCAACCTGAAAACTAGGCCTGGGCAGGAAGTCACAGAGGCAGGGTGGATGAGGGCACAGTTTGTGGAATGCCACGGCCCTCAGGAACCCAGGCAGGAATGGCTGGAATCTCAGGGCACCCAACAAGGGCCCAGTCAAAGACAGAAGGCCCTGCCCCAGCACAACCACCTTGACCTGGATCTTCCACAG
Seq C2 exon
AGACGTTCTGGAGCAACCCCCAGTTCAAGATCTCTCTCCCGGAAGTGGATGACCCAGAGGATGACTCTGAGAAAAACGAAATGGTTTGCACCTGTCTGGTGGCACTGATGCAGAAGAACTGGAGACATGCTCGAGAGGGACCCCAGCTCCTCACCATAGGCTTTGTCATCTTCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058626:ENSMUST00000120717:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=0.068
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(6.3=33.9),PF0106717=Calpain_III=PU(15.2=42.9)
A:
NA
C2:
PF0106717=Calpain_III=FE(36.7=100)
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:
CTGGGATTACAAGAGCCGCTG
R:
AAGCCTATGGTGAGGAGCTGG
Band lengths:
252-450
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