MmuINT0028712 @ mm9
Intron Retention
Gene
ENSMUSG00000043705 | Capn13
Description
calpain 13 [Source:MGI Symbol;Acc:MGI:2685789]
Coordinates
chr17:73679396-73680521:-
Coord C1 exon
chr17:73680317-73680521
Coord A exon
chr17:73679433-73680316
Coord C2 exon
chr17:73679396-73679432
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
AGTTCCAGAATGTCCAGGGAAGATTGCCTCCTGCATTTTTCTCCCCATTTAGAAGTGCTGCCCAAGGCACAAAGTATGTGTCCAAGTGCAACTTCACAAAGTCCTTCCACCTGAATCCTGGTACCTATGTAGTGGTTACCACAGCAAACGGAAAAGAAGTGGAATTCCTACTCCGAATATTCCTCAAAATGCCAGACAAGCACAG
Seq A exon
GTATAGAAGCACTGGGGTCTTGAGTGATTTGTCTACTTCAGTGTGCCTTTGTGAGCAGTGCTCTGTGCATTGTGTGTTAGCACACAGTATGCCAGGGACACAAGATGAGTCTTGCTCTTGAGATGCCAACCAAAATGGGAAATGAGAAAGCCCATGAACTAAAAACTTGACCTCAACAGCAATGTAAAAATCATACAAAAGGACTGAGTCAAGGGATGGCTTCTGACCACAGGGATTAGGAATGGCTTCTCGGAGTAAACAGCACTTGAGCTGGTCCTTGAAGGCAAACAGAAATTATTAACTTCAAGGAGAAGACCATACATGTGGGAAAAAAGAGCCTAAGAAGAAACAAGGACATAGTGCAGCCTTGGGCTTACTGAATAAGCGCTGTCAGTTGTGTGTACAGAAAAATCATACTGTGTGTTACATTCATTCATTTGAAATATGGCCAGAATGCAGGGTAGACCAGGAAGATGGCCTGACCTGAAAACAGGCCTCGATTCTAGAGGACCTTGAATAATGTTAAGTCATAGGTTATATCTACAGATCCTGTCCCTCTGAGCCTGAGGTAGGTGTTACTATAGTCATAGAGATCTATATAAATACAGTGGATATGTAAGGGTCTGCCAATTCAAGACAGACCATGAGTCAAAGGTCATCTGTATCCTGGCACCCATGTGCATCTCAGTATGAACAAGTCAATGGTGAGAATCCCAGACTATGCCCACCCCAAGTGAGCATATGATCATTGGGCGTCTGTTGCCATGGCGACCTTCTTCTCATCCTTGTGGGAGATGTTATTTGTTATTGAGTGTCCTTCACAGGTAGACCTCTGGGAATACAGTGTGGGTCATTTTCGTCATGCTGTCCCTCTGGTTTTCTAG
Seq C2 exon
GGATCCAAGCAGCAATTTCAACCTCAGAGCCCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043705-Capn13:NM_001033444:13
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=0.615
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:
AGTTCCAGAATGTCCAGGGAAGA
R:
AGGGCTCTGAGGTTGAAATTGC
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: