MmuINT0028775 @ mm10
Intron Retention
Gene
ENSMUSG00000079110 | Capn3
Description
calpain 3 [Source:MGI Symbol;Acc:MGI:107437]
Coordinates
chr2:120490954-120491954:+
Coord C1 exon
chr2:120490954-120491031
Coord A exon
chr2:120491032-120491793
Coord C2 exon
chr2:120491794-120491954
Length
762 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
CTCCTCTCTCAACCTCTCAGGAT
3' ss Score
8.64
Exon sequences
Seq C1 exon
TTGGAAGGACTGGAGCTTTGTAGACAAAGATGAGAAGGCCCGTCTACAGCACCAGGTTACTGAGGATGGAGAGTTCTG
Seq A exon
GTAAGTTCATGACCCAGGCAGGGAGCCACCAGGGTGCATCTTTGGCATATCTGGGCCCTGTTTTCCTATGGGTGCTCAAGGCCCAGCAAAGGTGAGGTTCTGAAAAGAGAGTGCCAGTATGGCAGTGACTGAGCTCAGACCCTGGCCATCCCATGGCAGCTCTCGTTCCAGAAGCTACCCTTGCGCACTGGCCCTGATGTGGCTCTCTTCTGAACCAAGGGGCTTTTCTTACCTGATATCCAGTGCCAGCCTTATTCTGATCATGTCAGCCTTCTGAGTCTCAGCTGACAATAGTGTCTCCTATGACGCCTTTGGTTCCCTCAGGACCCAGAGGCATTTATCTATGATGTCACTGGCCTTAAAACTATCTTTTCCCAAGTGACATCTCTTTTTCCATGCTGAAAATGTGCCTGGCAATAATGAAACATACAGTGAGTAACATTTTGGAGAACTGATTTCCAGCACACTCTTTTCAAAGACAAATGAGGAGTCATGAACATAAGACATGGTGATAGTTTGGGGTAGATAGGTCAGAAATGACAGTGCCAGGCACACACCTGTAAGTCCATCATTTGGGAGACAGAGGAAGGAGGGTCAAAAGGTCAAGGCCAACCAAGACCACAGGATGAAATCCTGTCTCTCAAAAGCAATTGAACAAGCCAAGTGACATCAGGGTCTTCTGGGGGACTTTGCTGTGCTGTATTAGCCCTTGAATCTTCCCTTCCTCAGCCTGTGTGAGTGTCTCCTCTCTCAACCTCTCAG
Seq C2 exon
GATGTCATATGATGACTTCGTCTACCATTTCACGAAGCTGGAGATCTGCAACCTCACAGCTGACGCCCTGGAGTCCGATAAGCTTCAGACCTGGACGGTGTCTGTAAACGAGGGCCGCTGGGTGAGGGGCTGTTCTGCTGGAGGCTGCCGAAACTTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079110:ENSMUST00000028749:9
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=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(17.6=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(12.8=34.5),PF0106717=Calpain_III=PU(15.5=43.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGGAAGGACTGGAGCTTTGT
R:
CTGGGAAGTTTCGGCAGCC
Band lengths:
239-1001
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