MmuINT0028644 @ mm9
Intron Retention
Gene
ENSMUSG00000024942 | Capn1
Description
calpain 1 [Source:MGI Symbol;Acc:MGI:88263]
Coordinates
chr19:5991539-5991924:-
Coord C1 exon
chr19:5991856-5991924
Coord A exon
chr19:5991618-5991855
Coord C2 exon
chr19:5991539-5991617
Length
238 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
CCCTTTATCCTTCCACACAGACC
3' ss Score
10.17
Exon sequences
Seq C1 exon
CGAGATGGCAACGGGAAGCTGGGTCTGGTGGAGTTCAACATCCTGTGGAACCGCATCCGAAATTACCTG
Seq A exon
GTAGGTGGCAGGAGGTTCCCTGGCTGGGTTCTACTGGCCCTCTGTGGCCTCAGTCATGGCATGGCCGGGCCTGGTTGCAGAGCCCAGGCTAGCTACATAGCCAGCCTTCCCAACAGAGCTTCCTTTCCGCATGTGACTCCTTTCCCATCCAAGCCTACGGGTCTCAGCAAATGGCCATTCCCCATGCCGCTGAGCAGCAGCTGACTCACTCGGCCCCACCCTTTATCCTTCCACACAG
Seq C2 exon
ACCATCTTCCGGAAGTTTGACCTGGACAAGTCTGGCAGCATGAGTGCCTATGAGATGAGGATGGCCATCGAGGCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024942-Capn1:NM_001110504:18
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:
PF138331=EF-hand_8=PD(29.5=78.3),PF134991=EF-hand_7=PU(3.4=13.0)
A:
NA
C2:
PF134991=EF-hand_7=FE(29.2=100)
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:
GAGATGGCAACGGGAAGCTG
R:
CCTCGATGGCCATCCTCATCT
Band lengths:
141-379
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: