MmuINT0028646 @ mm9
Intron Retention
Gene
ENSMUSG00000024942 | Capn1
Description
calpain 1 [Source:MGI Symbol;Acc:MGI:88263]
Coordinates
chr19:6013996-6014468:-
Coord C1 exon
chr19:6014201-6014468
Coord A exon
chr19:6014066-6014200
Coord C2 exon
chr19:6013996-6014065
Length
135 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGA
5' ss Score
10.65
3' ss Seq
CATGACCGTGGGTCTTGTAGGAA
3' ss Score
7.72
Exon sequences
Seq C1 exon
GATGACAGAGGAGTTAATCACCCCTGTGTACTGCACCGGGGTGTCAGCCCAAGTACAGAAGAAGCGGGACAAGGAGCTGGGCTTGGGCCGCCATGAAAACGCCATCAAGTACCTGGGCCAGGATTATGAAACGCTTCGGGCAAGATGCCTGCAGAGTGGGGTCCTCTTCCAAGACGAGGCCTTCCCTCCGGTTTCTCATAGCCTGGGCTTCAAGGAACTGGGTCCTCATTCCTCTAAAACCTATGGCATCAAATGGAAGCGGCCTACG
Seq A exon
GTAAGAGGGCCACTCTGGGTGGAACTTGGTTCTGATGGTGGTGGGCAATGGGACTGGGCCCCCCCATTATTCGTGGTGTCTGGGTACCAGTTTCTAGGAGGGACTGGCCCAGGAACATGACCGTGGGTCTTGTAG
Seq C2 exon
GAACTGATGTCAAACCCCCAGTTCATCGTGGATGGAGCCACCCGGACAGACATCTGCCAGGGAGCACTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024942-Capn1:NM_001110504:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PU(11.3=38.2)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(7.7=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:
CAGAAGAAGCGGGACAAGGAG
R:
GCTCCATCCACGATGAACTGG
Band lengths:
251-386
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: