MmuINT0028712 @ mm10
Intron Retention
Gene
ENSMUSG00000043705 | Capn13
Description
calpain 13 [Source:MGI Symbol;Acc:MGI:2685789]
Coordinates
chr17:73330056-73331179:-
Coord C1 exon
chr17:73330977-73331179
Coord A exon
chr17:73330093-73330976
Coord C2 exon
chr17:73330056-73330092
Length
884 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAG
5' ss Score
8.73
3' ss Seq
CTGTCCCTCTGGTTTTCTAGGGA
3' ss Score
10.56
Exon sequences
Seq C1 exon
TTCCAGAATGTCCAGGGAAGATTGCCTCCTGCATTTTTCTCCCCATTTAGAAGTGCTGCCCAAGGCACAAAGTATGTGTCCAAGTGCAACTTCACAAAGTCCTTCCACCTGAATCCTGGTACCTATGTAGTGGTTACCACAGCAAACGGAAAAGAAGTGGAATTCCTACTCCGAATATTCCTCAAAATGCCAGACAAGCACAG
Seq A exon
GTATAGAAGCACTGGGGTCTTGAGTGATTTGTCTACTTCAGTGTGCCTTTGTGAGCAGTGCTCTGTGCATTGTGTGTTAGCACACAGTATGCCAGGGACACAAGATGAGTCTTGCTCTTGAGATGCCAACCAAAATGGGAAATGAGAAAGCCCATGAACTAAAAACTTGACCTCAACAGCAATGTAAAAATCATACAAAAGGACTGAGTCAAGGGATGGCTTCTGACCACAGGGATTAGGAATGGCTTCTCGGAGTAAACAGCACTTGAGCTGGTCCTTGAAGGCAAACAGAAATTATTAACTTCAAGGAGAAGACCATACATGTGGGAAAAAAGAGCCTAAGAAGAAACAAGGACATAGTGCAGCCTTGGGCTTACTGAATAAGCGCTGTCAGTTGTGTGTACAGAAAAATCATACTGTGTGTTACATTCATTCATTTGAAATATGGCCAGAATGCAGGGTAGACCAGGAAGATGGCCTGACCTGAAAACAGGCCTCGATTCTAGAGGACCTTGAATAATGTTAAGTCATAGGTTATATCTACAGATCCTGTCCCTCTGAGCCTGAGGTAGGTGTTACTATAGTCATAGAGATCTATATAAATACAGTGGATATGTAAGGGTCTGCCAATTCAAGACAGACCATGAGTCAAAGGTCATCTGTATCCTGGCACCCATGTGCATCTCAGTATGAACAAGTCAATGGTGAGAATCCCAGACTATGCCCACCCCAAGTGAGCATATGATCATTGGGCGTCTGTTGCCATGGCGACCTTCTTCTCATCCTTGTGGGAGATGTTATTTGTTATTGAGTGTCCTTCACAGGTAGACCTCTGGGAATACAGTGTGGGTCATTTTCGTCATGCTGTCCCTCTGGTTTTCTAG
Seq C2 exon
GGATCCAAGCAGCAATTTCAACCTCAGAGCCCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043705:ENSMUST00000095208:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.615
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(48.9=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
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:
CCAGAATGTCCAGGGAAGATTGC
R:
CTTGAGGGCTCTGAGGTTGAA
Band lengths:
238-1122
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types