MmuINT0028760 @ mm9
Intron Retention
Gene
ENSMUSG00000079110 | Capn3
Description
calpain 3 [Source:MGI Symbol;Acc:MGI:107437]
Coordinates
chr2:120326947-120327916:+
Coord C1 exon
chr2:120326947-120327060
Coord A exon
chr2:120327061-120327838
Coord C2 exon
chr2:120327839-120327916
Length
778 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTCT
5' ss Score
-0.33
3' ss Seq
TTTCCTTTGTGTCCCTATAGCCA
3' ss Score
10.74
Exon sequences
Seq C1 exon
CCCATCATCTTCGTTTCTGACAGAGCAAACAGCAACAAGGAGCTGGGTGTGGACCAGGAGGCAGAGGAGGGCAAAGACAAAGCAGGGCCCGAGAAACGAGGGGAAACCCCACAG
Seq A exon
GTTTCTGAGCATGCGGCATGGATGGGGAGTTTAGCTCGTAGTGGCGGCTCTGCTATGCTCTTGGGGTCCTTAGGGGTTATGGTAGCTCTCAGGGGAGGGTCTCTTCAGCACTGTGGGGTTTGGAATTGTCTGCTGACTTTTCCTCCCGGCAAGTTCCTCTGAACTTTGCAGGTATTTCTTGGGTAAGTGTCTTTTAAGGTCGCTGCCACACCAAACCAGTCCCAGGGTGGGAAGGATAGGCCAAGAACAGCCCACTGACGCCTCTCCAGTCAGGACAATGGAGCATGGGGAGACAAAGGCTGAGTGAGGCGAGCCAGCTGCAGAGAACGAAGCTGAACTGTCTTTGAGTTGTTGCAAAGGGAGGAAAAGGGGATGGTAGCAGAAAGTGGGGTCTGACAGCAGCCCTGAAGTCCTGCAGAACTCCAGGGCCACGCCCTCCATCCCAGAGAACCTACCAGGTGGGGAGGGAGGGGTCCTTTGAGGACTTAGCTACAGAGACAGTAGCGGTTGGAGGACCTGGCCTCTGGTCAGGCTCAAAAGAGCAGAGAAAGTTCTATCTGGAAGAGAGTCGGGAGAGTCAAGGATGCTGTCTGCATGTTAGCATGGCAAATTTGTCCTTTGGCCTGAGGTTCCGGGACTGCAGAGCCTCTAGAATCCTCACTGAGTTTGCAGGTAGACTGAAAACTTGAACCTTGTGCCACCTGCTGCTGCTTTATGGGGCTGTTTGGGATACTGACGCCTGGGTTCCCATAAACCAGTTTCCTTTGTGTCCCTATAG
Seq C2 exon
CCAAGGCCTGGCCACACAGACCAGGAAAGTGAGGAGCAGCAGCAATTCCGGAACATCTTCAGGCAGATCGCAGGCGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079110-Capn3:NM_007601:16
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.763 A=NA C2=0.731
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF138331=EF-hand_8=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCATCATCTTCGTTTCTGACAGA
R:
CGCCTGCGATCTGCCTGA
Band lengths:
190-968
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: