MmuINT0028748 @ mm9
Intron Retention
Gene
ENSMUSG00000026509 | Capn2
Description
calpain 2 [Source:MGI Symbol;Acc:MGI:88264]
Coordinates
chr1:184416675-184417920:-
Coord C1 exon
chr1:184417846-184417920
Coord A exon
chr1:184416836-184417845
Coord C2 exon
chr1:184416675-184416835
Length
1010 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
CCCTGTCTGTGCTTTGCTAGGAT
3' ss Score
8.97
Exon sequences
Seq C1 exon
TTGCCCCAGCTGGAACACGGTTGACCCAGAAGTAAGGGCAAATCTAACCGAACGGCAGGAGGACGGAGAATTCTG
Seq A exon
GTAAGGCAGCAGGGGCGGCAGGGACATTCCTAACCAGGGCACCAGTCAGCAATGCGTTCAGCACGCTGAGGACGTGTGGTAGGGCAACCTGGCTTTGCTGCTCTTTATGCATCTAAGTCCCAAGCAGGTGGCGCACCTCTGTAATCTTAGCTCTCTAAAAATTGAGGAAGAGGGCTCTCAAACTGGAGACCAAGCTGCATAGCCTTGGCTATCCAGAAAGAACCTGTTTCCAACAAAGAAAAAAAAAAAACTCTATATGATCCTAAACAGCTTTTAAATCTCTTCAATTTGTCCATCTCAGCTGTGGGGTTAACACCCGGCAATTTCACAAGGGCTGAGAGGAATTCCTTCAGAAATGTTTAGACCCCAAGAGAAAACACAGAGAAAGATGAGACCTTTCCTTCCATCAGTCTCTAAAGAGAGATCCTTGGCTCATTAAGAAACCAACTCTAAGCCAGGCGGTGGTGGTGCACGCCTTTAATCCCAGCACTCGGGAGGCAGAGGCAGGCAGATTTGAGTTTGAGGCCAGCCTGGTCTACAGAGTGAGTTTCAGGACAGCCAGGGCTACACAGTGAAACCCTGTCTCGAAAGAAAAAAAAAAGAAAAGAAAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAAGGAAGAAAGAAAGAAAGAAACCAGTTCGTTAGTGAGCCGAGAGGGTCCTCTGTGTGTGCACTGCCCCCACAGAACACCTCGAGTGGATATTGTTCCAAGAGTCCATATGTTGTTTCGGTTCGTACTTATTCATGGCTTTCATTCCACCACTGAGAACTCTGGGGTGCAAAGAGAACTCATCAATTTGCCCCAAATCACCCCTGAGAAAGTGGCTGCTACAGAACTAGATTTGGAGCCTCCGAGTCTGGCCATAGCGTCCATCACTGAGTCTTAGACAGCCCCACCCCACCCCTGTCAACCAGGTAGAAGATTAAGGTGAAGCCAGTGTCTTCTATAACTCGGGACACCCTGTCTGTGCTTTGCTAG
Seq C2 exon
GATGTCCTTCAGTGACTTCCTGAGACACTACTCTCGCCTGGAGATCTGCAACCTGACCCCGGACACCCTCACCTGTGACTCCTATAAGAAGTGGAAACTCACCAAGATGGATGGGAACTGGAGGCGAGGCTCCACCGCAGGGGGCTGCAGGAATTACCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026509-Capn2:NM_009794:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.077 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(8.3=100),PF0106717=Calpain_III=PU(23.0=65.4)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(6.3=34.5),PF0106717=Calpain_III=PU(15.4=43.6)
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:
CAGCTGGAACACGGTTGACC
R:
TTGGGTAATTCCTGCAGCCC
Band lengths:
230-1240
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: