MmuINT0028772 @ mm10
Intron Retention
Gene
ENSMUSG00000079110 | Capn3
Description
calpain 3 [Source:MGI Symbol;Acc:MGI:107437]
Coordinates
chr2:120486333-120488157:+
Coord C1 exon
chr2:120486333-120486476
Coord A exon
chr2:120486477-120488073
Coord C2 exon
chr2:120488074-120488157
Length
1597 bp
Sequences
Splice sites
5' ss Seq
CGGGTGTGT
5' ss Score
5.31
3' ss Seq
GTCTGGTTATTTCTCTACAGACA
3' ss Score
7.84
Exon sequences
Seq C1 exon
GATGGCACGAACATGACTTATGGAACCTCTCCTTCTGGTCTGAACATGGGGGAGTTGATTGCACGGATGGTGAGAAATATGGATAACTCGCTGCTCAGAGACTCAGACCTGGACCCCAGGGGCTCAGATGACAGACCGTCACGG
Seq A exon
GTGTGTACATCTCCAAATGTCGAGACTGACTAGCGCCCCCAGATCTGCATGGCCCATCCTTCTGAAGTCAGTGCCAACAGAATAGATTCCCTCCATTTTGGTAACTCTCCTCTAAGGAACACAGGGCTTCAGTGCTATGTAGTGCTTGCATCCTCCTGTTTGAACGGCCCATGTGCTTCCTGAAGGACTGAGCCAGACAGAAAAGCACAGAGGAAAAGTTAGTCTATATTTTCTCATCTAAAGATAACTGCCCAGGGTTTGGTATATGGTCCTTCTGGGCACAAGCTTAAACTATATATTTTTTAAAATTGTATCTTAGTATATGTTACATCTTTACAGCCTGTTTTTTGTTGTTGTTGAGTTTTTTGGTCCTCCCCCCCCCCCACCAGCAAGACAGGGTTTTTCTGTGTAGCCCTGGCTGTCCTGGAACTTACTCTGTAGACCAGGCTGTCCTCGAACTCAGAAATTCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGTGTGTGCCACCACTGCCCGGCAAGGTTCATATTTTTAAAATGCAACTAAGTATTCTTTTTATATCATTTTAGTAGCTGTACAATATTCTAGTGTACAAATATATTATAATTTACTTACTAACACTCTATTATTGAAGAGTTAGAGGGTTTTTTTAAAGTCTGTTTTTCAAAAGTGCTGTAATAAGCATAAAGACAGTTTTGTATACACCCATAATGGTTTCTATAGGAGAGTCTCAAGAAGAAAACTGCTGGTCAAAATGATAGGCCGTGTAGCGCGCCAAAAGCCATCTCAGGCAGCCTCTGAGCTATAGCTGAGCGGATTAGTGAGTGCCCTGCCCTAATCTGAGTCAGATGAATGAAATCGAAGACACTAAGATGAAAAAAGTTCCAGACTCACCTACACCTGTCACCCTGAAGGCGGCTTCAGGAATTCACCTCCATGTGGCTCCCAGAAGCTTCCCCAAAGCTGTTGTTACTGGGCCAGCGGATGCTGAGATGCCTGTCGAGAGCTCAGAGGGCGTTGGTGGTCTATCTACCCTTGTGCCGAGGAACCCTCAAGAACTAGAACTTGAACATCTTTGCCCCTGAATTCAGGCATAGTCCTGTCACAGCAGGGAACCGCCCCGTATGTATTGCCAGCATTGGGAGTCTTGACTTCCATGTTCTAGTAAGTGTGAGAGAGGTGAAGTGACAGCAAGAGAACTCTCTTTCTCAAATCCTTCTTTGGGGAATAGTCAACTCTAGATGGGCTCAGAGGAAGGCACAGACCCCAGATGTCCCCCTCTCCTCTGCTGAGGAAGTCTAGAATGGAGGGGAAATTCTTTTACTTACCTCCTATTCCAGGACTCACCTTGATCTCTGGCCATCAGGGCAGCAAGATCAGCTAGGAGGAGTAGGGCAGCATCTTCCTGTTGCTCTTGAAAAACCAGCGAGGGTCTGACCCTGGCCATAAGGCATAAGGTCAAGGAAGAGAGTCATCTTTAGTCTGAGATAACTCAGAAAAGGACCAGCATGAACCCTTGTCTCCAATCAGCAGAACTTCTGCCCTCCTTCACCCCAACTCCTGACAAGCTGTCTGGTTATTTCTCTACAG
Seq C2 exon
ACAATTGTTCCAGTGCAGTATGAAACAAGAATGGCCTGTGGGTTGGTGAAAGGGCATGCCTATTCAGTCACTGGGCTGGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079110:ENSMUST00000028749:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.358 A=NA C2=0.041
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(4.4=18.8),PF0064816=Peptidase_C2=PU(30.4=93.8)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(18.2=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:
TGGCACGAACATGACTTATGGA
R:
CCTCCAGCCCAGTGACTGAAT
Band lengths:
224-1821
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