MmuINT0028707 @ mm10
Intron Retention
Gene
ENSMUSG00000054083 | Capn12
Description
calpain 12 [Source:MGI Symbol;Acc:MGI:1891369]
Coordinates
chr7:28887573-28888055:+
Coord C1 exon
chr7:28887573-28887736
Coord A exon
chr7:28887737-28887819
Coord C2 exon
chr7:28887820-28888055
Length
83 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
ACCTCCTTCTTTTCTGTCAGAAA
3' ss Score
8.89
Exon sequences
Seq C1 exon
GATGGAGCTTCAAGACTTTCTCACGCACTTCAACACAGTGCAGATTTGTTCACTGAGTCCTGAGGTGTTGGGCCCCAGCCCTGCTGGCGGCGGCTGGCATATCCACATCTTCCAGGGCCGCTGGGTGCGAGGCTTCAACTCCGGTGGGAGTCAGCCCAGCGCTG
Seq A exon
GTGAGGCCTTGGGGACCCCTGAGAAGCAAACTTGGGTGAGGCTTGTGGCAGGATGGGAACTCCACCTCCTTCTTTTCTGTCAG
Seq C2 exon
AAAACTTCTGGACCAACCCCCAGTTCCGGCTGACACTGCTGGAGCCTGATGAGGAAGAGGATGACGATGATGAAGAGGGACCCTGGGGAGGCTGGGGAGCGGCAGGGGCCCGGGGCCCGGCGAGAGGAGGCCGAGTCCCCAAGTGCACGGTCCTGTTGTCACTCATCCAGCGCAACCGCCGGTGTCTGAGGGCCAAGGGCCTCACTTACCTCACTGTGGGCTTCCACGTGTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054083:ENSMUST00000066880:9
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=0.278
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(6.4=33.9),PF0106717=Calpain_III=PU(13.6=42.9)
A:
NA
C2:
PF0106717=Calpain_III=FE(44.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGAGTCCTGAGGTGTTGGG
R:
CCTCTTCCTCATCAGGCTCCA
Band lengths:
173-256
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