MmuINT0028656 @ mm9
Intron Retention
Gene
ENSMUSG00000024942 | Capn1
Description
calpain 1 [Source:MGI Symbol;Acc:MGI:88263]
Coordinates
chr19:6014201-6015247:-
Coord C1 exon
chr19:6015106-6015247
Coord A exon
chr19:6014469-6015105
Coord C2 exon
chr19:6014201-6014468
Length
637 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CAGGCCCATGTGTTCCCCAGGAT
3' ss Score
6.86
Exon sequences
Seq C1 exon
GAGGGGCGGTGGAGGAGGGCGGGGAGGAGGGCAGGGAGGAGGGCAGGGAGGAGCGCTCTTCCTGGTTGGGCCCTGCCCTGAGCTGCCACCAAGGAAGCCAGCCCCAGGGACCGCAGCAATCTCCCAAACTCCCCTTCCCCAG
Seq A exon
GTAAGAAGTTGGGTGTCCAGACTACGACTGTTTGACCCAGGCCACTGCTTCTGGGGTTAGGGGGCTGTCGCTGATCAGCCCCTGCTTCAGGTCTTCTGTGTGTTTGCCTGAGGGTTAAGGGTCCGGAAGCAGCTCAACCCAGGCGCTCAGCTCAACCTGTCCGCTGTAGCTGGGCCAGTGTCCAGTGCTCTGATGTTCAGCTTGTGGAAAGGCATCAGTGCGTGGAGTTTTCAGTTCCTAAGCCGAGGAAAGGGGCAAATGAACTAGATGCTTGGCAGCTTTGTGGAGGGGAAGTTACAGGCAGGCAAATGGTGTCAGGGATCGTACCTGGAGTACCTCTGCTCTGCTGCTGTGGCTGGCCTCCACCCTATCCTACCTGCCTGGATGGCTGATACCAAACTGTCACCTCTGGGCGGTAAGAATAGGGAAAAGAGAGGTGGTGACCAGGATACCTAGAAACTGGACACCCCTTTCCAGATTCTGAGAGCCTAACAACAAGGTGGCTGAGAGTCCCAGGCACTGTAAAGGGAGCAGTGACCCATGTTTGGGGAGGAATGAGTCCAGGAGAATGTCGGCAGGCAGTTGTGTTTTATCCCTGGGAAGGCCTGCATCTCTACCAGGCCCATGTGTTCCCCAG
Seq C2 exon
GATGACAGAGGAGTTAATCACCCCTGTGTACTGCACCGGGGTGTCAGCCCAAGTACAGAAGAAGCGGGACAAGGAGCTGGGCTTGGGCCGCCATGAAAACGCCATCAAGTACCTGGGCCAGGATTATGAAACGCTTCGGGCAAGATGCCTGCAGAGTGGGGTCCTCTTCCAAGACGAGGCCTTCCCTCCGGTTTCTCATAGCCTGGGCTTCAAGGAACTGGGTCCTCATTCCTCTAAAACCTATGGCATCAAATGGAAGCGGCCTACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024942-Capn1:NM_007600:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.011
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0064816=Peptidase_C2=PU(11.3=38.2)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTTCCTGGTTGGGCCCT
R:
CGTAGGCCGCTTCCATTTGAT
Band lengths:
355-992
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: