MmuINT0028764 @ mm10
Intron Retention
Gene
ENSMUSG00000079110 | Capn3
Description
calpain 3 [Source:MGI Symbol;Acc:MGI:107437]
Coordinates
chr2:120480683-120482228:+
Coord C1 exon
chr2:120480683-120480752
Coord A exon
chr2:120480753-120482109
Coord C2 exon
chr2:120482110-120482228
Length
1357 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGA
5' ss Score
7
3' ss Seq
GGGTCTGTTTTTGCTTGCAGGGG
3' ss Score
8.98
Exon sequences
Seq C1 exon
GAAATTTGTGAGAATCCCCGGTTTATCATTGGTGGAGCCAACAGGACTGACATCTGCCAAGGAGATCTAG
Seq A exon
GTAGGAAAAATCCTCTATGTCCTACCAGGTGACCCAGGGTTAGTTAACCTGAGAGATCTCTATTCAGGATGGGAAGGGATAAATTCTGGTTTCTCTTTTAGTGCATCTCCTAATATTTTAAAATAATTTTTATTTATTTATTTAGTGAGTGAGTGTGTCTGTCTGTCTGTCTGTCTGTGTGCACATACCATGGCCTATACCTGTGAAGGTCAAAGGACACCTTGTGGGGGCCAGGTTTTTCCTTCTTCCGTGTGGCATCTGGAGGTCAGTCTCAGGTCCTCAGATCAGGCATCTCCACACTAAAGGAAGTCTTTTGGCAGAGGCGGCGTCTGCCATGTAGAGGAGAGGACAAGGTTCTGTCACCTTGTCGTCTGGACTGTTCTGAGTCCCTTCCTCTCCTCCACCTTTTGTTCTGGAAGCATCCTCCCTAGGCAGACTGTAGGAGAGCTCTGTGAAGAGAAACTGGAGAGAACATTAAAGGACTATTTAAAACTTGACCCAAAAAAAGCAGGAACAACTGAAAAATACCTATCACTTTGTTCCAGAAAGGGAGGCTGAGAACACCTCAGGTACAGTGGCTTCTGGCATCTGAGGGACACTGCCTGGAGGGTGTGGACAAATTAATCCCTGAGCCCTCAAACCAATACACTGCTTCTGAGCTGAGTCAAGGCAGGGAGATAGGGGGTTTGGGTGGTTACAAGCCTCTCTTCCCACCAGCAGTGTGGCAGCTAGCCTGTGCCCCCAGTAGAGCTATGGAATTGTCAGGGTACCAGGCATGTCCCTTTGGCAGCCTTAGTGACCTGTGTAGAATGGTTCTGTGGCAGCTAGCTGCCCAACACCCCTGCCTTCTGACACACGTCTGCTTAGCTGATGGTTCTCTAATACTGTTTTCCGTGATGCCAGAAGGGGAAATGGGCTCACCCTACAAAGACAGAGGACAGCCATAATTACCACTGTTGTCTCTACTGAGACCATAGAAGGAAGTGACTTATTTATTTATTTATTTACAATGTAAAAAGCAAGAGGAATTTATTGTTCCAACATGTTGCGGTTGCCCTGCACATGGAGAGAGAGAATGACCAGGAAGTGTTTTATTAAAGGAGGAATCCATTGCCTAACTTAGGAAAGCCTGTCTTGAGAGAATGAGTTACCCGGTCCTCGTGCTGCTCGTGCCGTTGAGGAGCTCCTGTCCCTGACAGTCTCCTTGCTTGAGCTCACACCTACTTGAGGGCAGGCAGGAAGCAGGGCAGTGGGCATCCCGAGTCATTAGCTATGGGGAGCTTCTTACTGGGGCTGGCAGGGCTCTTCTGAGAGGGGAAGCCCCCATCTGACTACCTGGGTCTGTTTTTGCTTGCAG
Seq C2 exon
GGGACTGCTGGTTTCTTGCAGCCATCGCCTGCCTGACCCTGAATGAGCGGCTGCTTTTCCGAGTTATACCCCATGATCAAAGTTTCACTGAAAACTACGCAGGGATCTTCCACTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079110:ENSMUST00000028749:2
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(11.3=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(13.0=100)
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:
TGTGAGAATCCCCGGTTTATCA
R:
CTGGAAGTGGAAGATCCCTGC
Band lengths:
183-1540
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