MmuINT0028635 @ mm9
Intron Retention
Gene
ENSMUSG00000024942 | Capn1
Description
calpain 1 [Source:MGI Symbol;Acc:MGI:88263]
Coordinates
chr19:6014201-6015825:-
Coord C1 exon
chr19:6015736-6015825
Coord A exon
chr19:6014469-6015735
Coord C2 exon
chr19:6014201-6014468
Length
1267 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATC
5' ss Score
7.05
3' ss Seq
CAGGCCCATGTGTTCCCCAGGAT
3' ss Score
6.86
Exon sequences
Seq C1 exon
GGGGTGGGGCTACCGTTTGTCTAGCGTCCGGCAGAAGTCAGCTCTCATCCAGCCAGGGGCAGCTCCAGCAAGCAGTTGCAGCCACCAGAG
Seq A exon
GTAATCCCTGCTTCGCCGAGCGCCGGCTGGGCTGGAAGACAGCTGCAACCCAGAGGCACGCGGGGGCGCAGGAGGCGGGTGGAGGACTGTGTTGGCGGCGTCACTGAGCCGGATCGTCCCCAGTACCTTCCCGGAGGGCGACATAGGGTGGGGCCGGCGGCTCTGCAACTCGAGCTGCGGCCCTAGTTAAAAATACCCCTTGCCCTACCCTCTCTCTGGCCGGCGGTGCCCTTCTGTCCCAGTCCAACCCTTCTCACCCGGACCGGCGACCGGCTCCTCCCGGGAGACAACTCTGCCATTTACCAATTTGTCCTCTCGCAGAGCTGGCTTAGAGTCTGCAGAGGAAGGGGGCGGGGGGAGGGGACTGAAAGACACCCTAAGTAAGAGATAGTAAAAAAGTGTTGCGGGGGAGATAAGGGAGAGCCTAGAGGGAGCGGGGTAAGAGCCTCGGGCGTAGGTGGAGGACCAGGGAGGGAGGGACCAGGGCCGAGGGGCGGTGGAGGAGGGCGGGGAGGAGGGCAGGGAGGAGGGCAGGGAGGAGCGCTCTTCCTGGTTGGGCCCTGCCCTGAGCTGCCACCAAGGAAGCCAGCCCCAGGGACCGCAGCAATCTCCCAAACTCCCCTTCCCCAGGTAAGAAGTTGGGTGTCCAGACTACGACTGTTTGACCCAGGCCACTGCTTCTGGGGTTAGGGGGCTGTCGCTGATCAGCCCCTGCTTCAGGTCTTCTGTGTGTTTGCCTGAGGGTTAAGGGTCCGGAAGCAGCTCAACCCAGGCGCTCAGCTCAACCTGTCCGCTGTAGCTGGGCCAGTGTCCAGTGCTCTGATGTTCAGCTTGTGGAAAGGCATCAGTGCGTGGAGTTTTCAGTTCCTAAGCCGAGGAAAGGGGCAAATGAACTAGATGCTTGGCAGCTTTGTGGAGGGGAAGTTACAGGCAGGCAAATGGTGTCAGGGATCGTACCTGGAGTACCTCTGCTCTGCTGCTGTGGCTGGCCTCCACCCTATCCTACCTGCCTGGATGGCTGATACCAAACTGTCACCTCTGGGCGGTAAGAATAGGGAAAAGAGAGGTGGTGACCAGGATACCTAGAAACTGGACACCCCTTTCCAGATTCTGAGAGCCTAACAACAAGGTGGCTGAGAGTCCCAGGCACTGTAAAGGGAGCAGTGACCCATGTTTGGGGAGGAATGAGTCCAGGAGAATGTCGGCAGGCAGTTGTGTTTTATCCCTGGGAAGGCCTGCATCTCTACCAGGCCCATGTGTTCCCCAG
Seq C2 exon
GATGACAGAGGAGTTAATCACCCCTGTGTACTGCACCGGGGTGTCAGCCCAAGTACAGAAGAAGCGGGACAAGGAGCTGGGCTTGGGCCGCCATGAAAACGCCATCAAGTACCTGGGCCAGGATTATGAAACGCTTCGGGCAAGATGCCTGCAGAGTGGGGTCCTCTTCCAAGACGAGGCCTTCCCTCCGGTTTCTCATAGCCTGGGCTTCAAGGAACTGGGTCCTCATTCCTCTAAAACCTATGGCATCAAATGGAAGCGGCCTACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024942-Capn1:NM_001110504:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
5' UTR
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
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTACCGTTTGTCTAGCGTCC
R:
CGTAGGCCGCTTCCATTTGAT
Band lengths:
350-1617
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: