MmuINT0028652 @ mm9
Intron Retention
Gene
ENSMUSG00000024942 | Capn1
Description
calpain 1 [Source:MGI Symbol;Acc:MGI:88263]
Coordinates
chr19:6009087-6011183:-
Coord C1 exon
chr19:6011015-6011183
Coord A exon
chr19:6009171-6011014
Coord C2 exon
chr19:6009087-6009170
Length
1844 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGT
5' ss Score
7.8
3' ss Seq
GTGCACGTTTCTTTCCGTAGATC
3' ss Score
10.36
Exon sequences
Seq C1 exon
AGTGAATGGCAGCTATGAGGCTCTTTCGGGAGGCTGCACCTCAGAGGCCTTCGAGGACTTTACCGGTGGGGTCACTGAGTGGTACGACCTGCAGAAGGCCCCCAGCGACCTCTACCAGATCATTCTAAAGGCCCTGGAACGAGGCTCCTTGCTGGGCTGCTCCATTAAT
Seq A exon
GTGAGTGATGTCTAAGTTCCTCTGACAAACCCTAATCTCATCTTCAGCGCACCACTCGCCCCCTCCTCAGCTCATTTCCGGCTGGGGATGAGCCCCGCCCATCACCTCCTCGAATACTCCATGTTCCTCACTTCTTCCTTCAAATCTCAGCGGTGCCCCAGCTCCTCAGCTCCCTCCTGCTCCCTCCCTTCTCATTCTTGTCTGTTTGTCTGTTTGTTTGTTTTTATTTACTGTGCATTGGTGCTTTTCCTGTATGTATGTCTGTGTGAAGGTGTCAAGTCCCTGGAACTGGAATTACAGACAGCTGTGTGCTGCCGTGTGGGTGCTGGGTATTGAACCTGGGACCTCTGGGAGAGCAGCCAGTGCACTTAACATTGAGCCATTTCTTTAGGCAGCACATATACTACAATTGGAACAATATGGAGTAGATTAGCCAGGCCTTCATTCTTATGACCTTCCCGTGTTCCAAGGCTCTCCCAGTCCAGTGCTTCAGCCTTCTGATGCAATCTCTTTCCTATTCTTGACTTCACCCACGCCTGGCTCCTTCTCCTTTCCTTTCTCCTTGCTTACCGTTGTCTGGCCCACAATTCCCACAGTCACTTCTAGCCCTCCCTAGCCCCGTGCTTGGTCATTCCACACCAGCATCCTGGCTATCCTTGGCCACACAATGCTATGGAGCCCAACACAAAATCTCAGAATCTTACTTAAAACATGAGATCTTAAAATCTGTGAATTGACTGAGCCATCCCCAAGTGTGAACTCTGTGAATGGCAGTGCCTTGCTACAATGTCTCAGGGTTGGAGAGATGGCTTAGTGGTTAAGAGCTTGTACTGCTCTTAAAGAAAACCCAAGTTCGGTTCTCAGCTCCCGCCCACATCAGGTAACTCAGGACGTGCCTGGGATTCCCACCCCAGGAGGATCTGATGCCTCTGGCTGCTAAGGGTATCTGTACTCGCATGCACACAGCAATACAGAGAGAGTTAGAGTTAGAGTCGCATACAGAGAGAGTTAGAGCCAACTAGAAAAGAAGCTTTTAAAATAACTTCCTTATTTTTATTTTATGAGCATTTGATTGGCATTTCACCTGCACACATGTCTGTGTGTGGGTATTGAATCCTCTGAAACTGGAGTTACAGACAGTTGTGAGCTGCCATGTGGGTGCTGGGAATTGAACCTAGGTCCTCTGGAAGAACAGCCAATGTTCTTTTTTTTTTTTTTTTTTTAAGATTTATTTATTTATTATATGTAAGTACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGAGTCAGATCTTATTACGGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCCGGACCTTCGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCTGCAGCCAATGTTCTTAACGTAGCCATCTCTCCAGCCCCTAAACTAAACTTTTTTTAAAAGGGCTATTTGACCCCGCAAGTTTAGCCCCACTGGATCTGTCCTTCTCTTTCCCCTGTTTGTCCCCTGGCTGAGTCCCCCTTGGAGGGTTTGCTTGATTATAAGTGTGTGTATATATGCACACTCACAGTCTGGCCAGCCCTTGCCAGCAGCAGTATAGCGAGAGCATTGATTGGGGAGGTATCTAGGCTCTGCCCTGCTCCCCAGAAGGAACGGCATTTGTGTAACAATGGAGTGGTTAGGTGAGGAGTGTCTAAAAGTTTCTTCGATCAGCTTTTGTGGGGGTTGTGTGTGCAAGGGGACAAGGGGTACGGCCTGAGCCTCATATATGCTCCAAGCAGGGATGGCACCTCATCTTCTGACCACAGTGCACGTTTCTTTCCGTAG
Seq C2 exon
ATCTCCGATATCCGTGATTTAGAGGCTATTACTTTTAAGAACCTGGTGAGGGGCCATGCGTACTCTGTGACGGGCGCCAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024942-Capn1:NM_001110504:6
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:
PF0064816=Peptidase_C2=FE(18.7=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(9.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGAATGGCAGCTATGAGGC
R:
GCGCCCGTCACAGAGTAC
Band lengths:
246-2090
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: