MmuINT0028683 @ mm10
Intron Retention
Gene
ENSMUSG00000058626 | Capn11
Description
calpain 11 [Source:MGI Symbol;Acc:MGI:1352490]
Coordinates
chr17:45642468-45642962:-
Coord C1 exon
chr17:45642829-45642962
Coord A exon
chr17:45642637-45642828
Coord C2 exon
chr17:45642468-45642636
Length
192 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
AGCGCCCTATCTGCCTGCAGGCT
3' ss Score
8.84
Exon sequences
Seq C1 exon
CTTTGGCAGTTTGGGCACTGGTTGAACGTGGTCGTGGACGACCGGCTGCCCACTAGGAACAACAAGCTGGTATTCGTGCACGCCTCCCATCGCCAGGATTTCTGGAGCGCCCTGCTGGAGAAGGCCTACGCCAA
Seq A exon
GTGAGTTGCCCAGGCCAGGAACCAGGCTGGCCTTGAGCTGCCTGGCTTTGGCTGCCAAGGAAGGTGGGCTAGGACACTAACTGAACCAGGGGAGGAGACAGGCCACGATAAGGCATGCCTCATTTCCCTCACAATTCTGCCTGACTGTTCACCCCAACTGACATCTCCTAACAGCGCCCTATCTGCCTGCAG
Seq C2 exon
GCTGATCGGATCCTACGGAGCGCTGTCTGGAGGCAGCACTTTGGAGGGTTTGGAAGATTTCACAGGCGGCGTAGCACAGTGCATTCCGCTCCAGAAGCCCCCTGGCAACATGCTAAGGCTCCTCAAGAAAGCCCTGGAGAAGTCTTCCCTCATGGGCTGTTCCATTGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058626:ENSMUST00000120717:5
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:
PF0064816=Peptidase_C2=FE(14.7=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(18.7=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:
GCTGCCCACTAGGAACAACAA
R:
TGAGGGAAGACTTCTCCAGGG
Band lengths:
242-434
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