MmuINT0028645 @ mm9
Intron Retention
Gene
ENSMUSG00000024942 | Capn1
Description
calpain 1 [Source:MGI Symbol;Acc:MGI:88263]
Coordinates
chr19:5990338-5991617:-
Coord C1 exon
chr19:5991539-5991617
Coord A exon
chr19:5990455-5991538
Coord C2 exon
chr19:5990338-5990454
Length
1084 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CCCATCCCCTCTCTGCTCAGGCT
3' ss Score
9.22
Exon sequences
Seq C1 exon
ACCATCTTCCGGAAGTTTGACCTGGACAAGTCTGGCAGCATGAGTGCCTATGAGATGAGGATGGCCATCGAGGCTGCAG
Seq A exon
GTGAGGCCTGAGGCTGATGGCCCCACTGCTCCTGAACCCCAGGCAGCCTCCCTGCCAGTGGAGCACCCACCTGGCTGGCCCTTGTCCCTGGGAGATGGTAGTACTAAAGGTGCTGTGGTTGCTAAGCTACGGACTTTATCTGGGCTCTTCCCTTTCCTCTCCTTGTAGCTTACCAAGAACAAGGGCCTTTTCATTCATTTCTGCATGTGTGTGTATGTGTGTGTGTGGTGTGTGCATGTATGTACCTATGTTCATATGTGTGTGGACACACATAAAAGCCAGAGGGTGATATCATCTGTCTTCCTTCATTACTGTTGCTGAGACAGGGCCTCTCACTGAACCTGGATCTCACAGATTAGCCTAGTTTGGCTATCCAGTTTCCCCAGGGAATCCTGTCTGCCTCCCCAGTGAAGGCTGGGATTACTGGCAAACTACCAAGTTTCCTTGGCTTTTATGTGGATTCTAGGAACCCAGTCTTGGTCCTCAAGCTTTCGTGAGGGATGCTTTATCCACTGAGCCATCAAACAGAGCCCTTTGTTATTGCTAATGTGAAGAAGAGAAAAGTAATTCTTAGGAGAGTGACTGAGTCTGGGTCACATGACTGGAGCAGGCAGGGTGAGGATGGGCCGGTACAGGCTCCAAGCTCCAGTTAGGCAGGTGTAGGACTCTCCCACACTGGCCTGCGTAAAAACAAGTATGGCCAGATGTCTAGATCCTCTGCAGCCAGCGTGTGATTTTCTGGGGTGTTCTTGGGGTGATGTTCCCATGTTCCCCTTGGGCCTGGCCCTCACTTGCCTAGCCCCTCCTAGCTTCTTTTGTTTTGTTGTTGCTGTTATTTATTTTATGTAATCCCATTACAGATGGCTGTGAGCTACTATGTGGTTGCTGGGAATTGAACTCATGACCTCTTAACCTCTGAGCCATCTCCTCCAGCCTGGCCCCCATGCAGCCCCCACCCTGCCCTCCATCCCCACCCCAGCTCTACCCAAGAGGTCTTGCAGCACATCTTCTCAGAGCAGCTCCTCCCGGCCCAAGCTGGCTGCCCCTGCTCCAGCCCTCACTTGCCCATCCCCTCTCTGCTCAG
Seq C2 exon
GCTTCAAGCTTAACAAGAAGCTGCATGAACTCATAATCACCCGCTACTCGGAGCCCGACCTGGCCGTGGACTTTGACAACTTTGTGTGCTGTCTTGTGCGGCTGGAGACCATGTTCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024942-Capn1:NM_001110504:19
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:
PF134991=EF-hand_7=FE(29.2=100)
A:
NA
C2:
PF134991=EF-hand_7=FE(43.8=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:
CTTCCGGAAGTTTGACCTGGA
R:
GAACATGGTCTCCAGCCGC
Band lengths:
190-1274
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: