MmuINT0028726 @ mm10
Intron Retention
Gene
ENSMUSG00000043705 | Capn13
Description
calpain 13 [Source:MGI Symbol;Acc:MGI:2685789]
Coordinates
chr17:73350476-73351553:-
Coord C1 exon
chr17:73351379-73351553
Coord A exon
chr17:73350551-73351378
Coord C2 exon
chr17:73350476-73350550
Length
828 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TCTGCTCTACCTTTCTGCAGCTG
3' ss Score
10.15
Exon sequences
Seq C1 exon
GCTACTTGGCTCCTATTCCCAATTACACTATGGCTACCTTCCTGATGCCCTGGTGGACCTCACAGGAGGAGTGGTCACCATCATCAACCTGCACTCCTCTCCATTTGACCTACTGACGACAGTGAAGACCGCAATCCAAGCAGGCTCAATGGTGGCCTGTGCCACCGAAAATGGG
Seq A exon
GTGAGTAGATGGGGGCTTCCTTGGTACCCAACAGGTTTTTCTTCCTAGAAGTGTCCATATGTATCTTCTCTCTGAGGCAGGGATTCCAAACACATATCATAGACAAGGAAATGAGAACTAAGCGAAGTTTCCGAGTCACACAGTTCAGGGTACTGTGCACAATCCGAATGCAGCTAACCACCAAATCCTCAGATATTGCTCCCTCCTGACCAGGAGCAGCATGTGTCCCTGGGTGACCAGAAGGATTGACAGGTGTTAGAGAAAGCAACCATAGCTACTAGTAGTTCTATTGTGTTTTCTTTATATTTATAAAGAGCTCTGATTCTCACCAGTCATAGAAGTAGCAGGTCTCATAGGTCATGTAAGGTCCAAATTACTTGAGTCTATTCTAAAACATCTGGTTCCCCATCTACATGATACTTCCTGTACCCTTAAACATTGTGGCCAAGTCACACCGTTCCTTGCAGAGGGAGGTCGTTGGGGCGGGGAGATCCTGCTGACATGGGTTATGTCATGAGCAAGACAGCATATGTCCTCAGAGACTGTGAGTTTCATAGTCAGTGGGGTAGGAAACTCCTGAGCATGAACTATTGAGACCTCTCACCTAATAGCCTCCACTCATAACTCACAAGAAGTGTTATACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCACACACACACACACACACACACACACACACACACACACACACACACACCTTTCCTCCTGGGTGGCGACTCACTAATTCAGCTGTGCTACTGTCTGAATGGATTTTTTAAAATGTCTCCAAAGAACTCTGTCTGCTCTACCTTTCTGCAG
Seq C2 exon
CTGACAGAAGAGGCCAAAGTGATGGAGAATGGACTGGTGAGCCAGCACGCATACACAGTGACTGGAGCTGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043705:ENSMUST00000095208:6
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=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(19.3=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(8.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTACTTGGCTCCTATTCCCA
R:
TCTCAGCTCCAGTCACTGTGT
Band lengths:
248-1076
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