MmuINT0028733 @ mm9
Intron Retention
Gene
ENSMUSG00000026509 | Capn2
Description
calpain 2 [Source:MGI Symbol;Acc:MGI:88264]
Coordinates
chr1:184409837-184411789:-
Coord C1 exon
chr1:184411578-184411789
Coord A exon
chr1:184409874-184411577
Coord C2 exon
chr1:184409837-184409873
Length
1704 bp
Sequences
Splice sites
5' ss Seq
CCAGTAGGT
5' ss Score
5.41
3' ss Seq
AAATATCCCTCTGTTTCCAGAGC
3' ss Score
7.76
Exon sequences
Seq C1 exon
CTAACAGGGCAGACCAACATCCACCTCGGCAAAAACTTTTTCCTCACAACCCGAGCCAGGGAGCGGTCAGATACCTTCATTAACCTCCGCGAGGTCCTCAACCGCTTCAAGCTGCCCCCGGGAGAGTATGTCCTCGTTCCCTCCACCTTCGAACCCCACAAGGATGGCGATTTCTGCATCCGAGTCTTCTCGGAGAAGAAGGCTGACTACCA
Seq A exon
GTAGGTTCTACTACCTCTCCCTGTTCCCAGCCTTGGTCTGCCCTTCACCTTTCTTTTGCTTTAATACCAGCAGCACTTGACAGGTCAGTGTAGAGCTGGAGAGCCCTGAAGTTTCTACTCAAGGAAAAAGCCACTCAGGACATCTTAAGTTGGAACAGGGCAGCTGGGGAAGGGAGTGGCTTGCAGTCCAGTTTCACAGTCTGTCTATGAATTACCAATCATTAATATCATCCTAATGGCCCGTGTACACCTGGCATAACCCTTGCTTTCCCAGGTCACGTGTAATGGATAATGTCAATGTCCAAAACCTTCCCAGTTTTAGTCAGAAAGTGTCTGGTGGAGCCTTTTAAGTAGATATGACAAGTTCCCACCATTGTCCCTGTGGCTTCGGCTCATAGTAGTGTCTGCTACCCTATCACCCTGTCAGTCATTTAGCCAACAGACAGAACCACCCCTGGGCAGTGTAAGCCCAGGAGAATCACTGAAAGGCTGGAGGGACCCCAGCACTGATGGGGCACCAGGGACAAAATGGGGAGGACAGGTCAAGGGCATTCTGGAGAACCATAGTTGGGACAGCCTTTGCCAAGGACCTAGAGGTCCCATAGATTGTGTCTGATGGAGTGGGTACAGGCCAGTCTCTACCCATCACCTCCTGTGAAAGGAAGAGGCGGAAGGAGAGAGACCAGGGTACCTTTGCTTCAAGATAATACAGGACACTGAAAGAGCTTCAGTTCCCAACAGCTGTGAACCAATAAATGCCACTAGAGCATGACGGTGCTCCCTGCCATGACAGGTCCTCCTGTTTGATTGAAGTTTGCTACAGGGAAAGGGCCGAGTCATTTCACTGGGGGAGTCCCAGTGTGTCCAGCTTCGTCTCCACTGATGAGATGGAGTCAGGCCCTAATATCACTGTGAAGGCTCTGCTCTTGGTCAAACCCTATCCTGCCCTTCTCCCAGGGAAGGGTTAGTCCCCAAGGTAAGCTCTCTGCCACTCAAAGCTGCTTCCCTGACCTAGGATAGCCAACCTACTGCAGATCCCAGTTAGCAGCACTTAGAAGTCCCTTTACTCTCTCGTGACAATTCAGGCCTGCAGGTGGGACTCTTAGTAACCTAGTTTAACATTACAGGCTCCCAAAGAAAGCCTTCCCAGGCTTAAATATCCTCACCAAAGGACCCAACGTATGTAAGGGACTGTGTGAGAATAAGCTAACTTTGCCATCAGGTTCCATATGGCTTACTCCAGCCCAATGTGGGACAGAGTCGGAGGCTCATACAAGCACGAATGATAGCTTTCTCATGGCAAAAAATGTTTTAGATGGAACTTCAAAGTTGTCCTTTGAGACCAGGGATGTAACTCAGTGGTAGGGTGCTTGCTCAGCCTTACAAGGCACCAGCACTTAAAAACAAACAAACAAACAAACAAACAAAACCCAAAGCTAAGAAACAGATGCCAAGAAACTGTCTAGCCAGAAGCTAAGTGAGTCTCTAGAGCCCTTGCTCTATTCCACACGGGAAGCTGTTTGATAAAGACTCAAAGCAAAAAAGTATCTCTGCCCTGGCTACTGTTGCCAAGGGGCTGTGTTATCACAGAAACTCCCTGTGCCACAGCATGCTGGATGTAAACACTGCTGTTCCATCTCAACTTCTGCAGTAATGGTTCACACTCTCCAGTCCTCTAGTAACAAAATATCCCTCTGTTTCCAG
Seq C2 exon
AGCTGTTGATGACGAGATCGAGGCCAACATTGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026509-Capn2:NM_009794:12
Average complexity
IR-S
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:
PF0106717=Calpain_III=FE(44.9=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0)
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:
CTAACAGGGCAGACCAACATCC
R:
TTCAATGTTGGCCTCGATCTCG
Band lengths:
246-1950
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: