MmuINT0028858 @ mm9
Intron Retention
Gene
ENSMUSG00000031981 | Capn9
Description
calpain 9 [Source:MGI Symbol;Acc:MGI:1920897]
Coordinates
chr8:127127786-127128250:+
Coord C1 exon
chr8:127127786-127127863
Coord A exon
chr8:127127864-127128089
Coord C2 exon
chr8:127128090-127128250
Length
226 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGTG
5' ss Score
0.67
3' ss Seq
CACCCTTCCCTCTGTCGCAGGAT
3' ss Score
10.87
Exon sequences
Seq C1 exon
CTCTCCTGAGTGGCGCTCTGTGGACCTGGAGGAGCAGAAGCGCCTGGGCCACACTGCCCTTGATGACGGGGAGTTCTG
Seq A exon
GTAGTGCCATCCTTTCCATTTTTGTTTGAAATTGGGGTGCATGGGGCAGCACCCACCATCCTTTTCCCCTTTCCTTCCTCATCCCCTTCCCTCCTCCTTTCTCTTTCTCCCTGTCTCCCTCCTCCTGGGAGGGACCCCTGGCTCTCCTCCCCATGAAGGGGGTTAGATGGTTGTCTAGTGCCATCACCATGACACTGCAGCGCACCCACCCTTCCCTCTGTCGCAG
Seq C2 exon
GATGGCATTCAAAGACTTCAAGATCCATTTTGACAAAGTGGAGATCTGCAACCTCACACCTGATGCCCTGGAGGACAGCGCCCTCCACAGGTGGGAGGTGACCATCCACCAAGGAAGCTGGGTCCGTGGCTCCACTGCTGGTGGCTGTCGCAACTTCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031981-Capn9:NM_023709:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.074 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(8.8=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(6.4=34.5),PF0106717=Calpain_III=PU(16.3=43.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTCCTGAGTGGCGCTCT
R:
CAGGAAGTTGCGACAGCCAC
Band lengths:
238-464
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: