MmuINT0028757 @ mm10
Intron Retention
Gene
ENSMUSG00000079110 | Capn3
Description
calpain 3 [Source:MGI Symbol;Acc:MGI:107437]
Coordinates
chr2:120495865-120497014:+
Coord C1 exon
chr2:120495865-120496073
Coord A exon
chr2:120496074-120496977
Coord C2 exon
chr2:120496978-120497014
Length
904 bp
Sequences
Splice sites
5' ss Seq
TGAGTGAGT
5' ss Score
6.51
3' ss Seq
ACCCTTTGTGTTTTTCGCAGGGA
3' ss Score
11.01
Exon sequences
Seq C1 exon
ATGCACGGGAATAAGCAACACCTGCAGAAGGACTTCTTCTTGTACAACGCCTCCAAGGCCAGAAGCAAAACCTACATCAACATGCGGGAGGTGTCCCAGCGCTTCCGCCTGCCACCCAGCGAGTATGTCATCGTACCCTCCACCTACGAGCCCCACCAGGAGGGGGAATTCATCCTCCGAGTCTTCTCCGAAAAGAGGAATCTCTCTGA
Seq A exon
GTGAGTGGCAGCCTGGCTTTCCCCACCTACCGCTAAGAGGTCACTCATGTGGCCCATCCTATAGCCAGGAGGCAGCTGGACCAATTTCCTTCAGGTCTTTTGGGACACAGCCACAGGCTTTTGCCATTCTGTACTCTAGGACCTTTACTCAAGTTCCTTCAGTCCTTTCTTTGATTGCTTTTTACAGCACTGGAGTGCAATCCCGGGGCGCCACAGGTTTAACTAAACCTCCCAGGCTAGCCTTGAACTCACTCAGATTGGCCTCGAACCTTTGATCCTCCTACCCCAGCCTCCAGAGGAGTTGCAAGTATAGCCCTGTGGCACTAGAGCAGCTCACAAATACTCACTCCATTCATCCTGCAGATATGTTTTGAGCAGCCATTCTACCCCAGGACTCTTCCAGGCACTGGGGATCATGAAGTAAACAGGATCACAGAAACAGAAACAGAAGGGGCTCGGTGACTTCATGAAGGTTAACACTCAAGGGACAAGGGACGAAGAAACACACATTGCTTTATAGACACATTAGATTTATAGAAATGATAAGCAAGTGAGTGTAGTTGGAATGCACGGGAAGCCAGCCAGGCTTCATTTCAGCAGATGTACTGACAGACCCTGCCTCTCTGAGTTCTGTCCCTGGAAGAGGTGCTAGGCCTGTTGCTAGGTAGCTGGGCCATGCTTTGAGGGAGCTCTGGGCAACACCAAGGAGTAGCTGTGTGCCTGGGCTTTTTTGGGAATGGCATCTACATGAGGCTGGCTCCTGGGGTGGGTGTTTAGTCCCAGGCTCTTTTAGATTTAATCTCAAATCTTTGACCACAAAGAAGCCATGTGACCTGGACAAATTTGTGGGGGTGACTCCTGTTTGTTCCGGGGGATATTGAGATACCCTTTGTGTTTTTCGCAG
Seq C2 exon
GGAAGCTGAAAATACAATCTCTGTGGATCGGCCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079110:ENSMUST00000028749:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.833
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(44.5=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0)
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:
ATGCACGGGAATAAGCAACAC
R:
CACTGGCCGATCCACAGAGAT
Band lengths:
246-1150
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