MmuINT0028859 @ mm10
Intron Retention
Gene
ENSMUSG00000031981 | Capn9
Description
calpain 9 [Source:MGI Symbol;Acc:MGI:1920897]
Coordinates
chr8:124604190-124605563:+
Coord C1 exon
chr8:124604190-124604350
Coord A exon
chr8:124604351-124605405
Coord C2 exon
chr8:124605406-124605563
Length
1055 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGT
5' ss Score
6.86
3' ss Seq
CACCCCCTTTCAAACGGCAGACA
3' ss Score
5.22
Exon sequences
Seq C1 exon
GATGGCATTCAAAGACTTCAAGATCCATTTTGACAAAGTGGAGATCTGCAACCTCACACCTGATGCCCTGGAGGACAGCGCCCTCCACAGGTGGGAGGTGACCATCCACCAAGGAAGCTGGGTCCGTGGCTCCACTGCTGGTGGCTGTCGCAACTTCCTGG
Seq A exon
GTAGGTGGCCTCTCTGTCCTTCTCTGTCCTATTCTCATATTCAATCTGTCTGGGGACATGGAAGGGGCAGTGTGTGTGGAGCTGGACAGCAAAGTTGGGATGAACAGGGAGACAACAGCTGAGCCTTAGGCAGGAAGCTGGCATGAGATGCCTGGGAACTGCTCTGTTGTAAGGTTCAGGTGACATACATAAGGTGAATGACAAGTCACACCAGGTGAGTGGGAAAGAGGATCTGTTGCTCAACAGCACCTCAGAGGGGTGCGGCAGGCATCGAAGCCTTTGAAGGCTGCATAGGTGGTGGCCAAAAAGTTGGAGGAAGAGTGAGGCAGGAGCTTGGAGTGTTGCTCAGGGTTAGAGTGAGAGGGCTGATGGGAAAGGGGAGGGAAGAGATCACCTTTTCAGGAATAGAAGCAACCTGTGGAGGTGCCAGGGGCAGTGTGTGTATCCTAAAAAGTTTGGCTCTTGTAATGTTTTTCTTTGTGTTGGTGTTAAATAGCTGTGCTCATACATTTTATTTTGATTTTGTCATTTTTTTTCTGTGTTCATATGAATCTAGAGACAAACAAAAACTTTGGCTGCCATTCCTCAAATGTCACCCACCTTGTTTTTGAGACCAGGGCTCTTGCTGGCCAGGAGCCTGCTAAGTAGGCTAGGCTGGCTGGCCCTCGAGCACCAGGTTGCCTGATTCCACCTCCCTGGCACTAAATACATGCTGCGACACCTTGTGTTTCCATTTACCCAGTTTATTTAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCATTCTACCTTGCACCAGTGGAGATTAGGGGACAGCTGTTTGGAGTAGGCTTTCTGCCTCTACCTTATAGGTCCCAGGTCATCAGCCTTGACAGAAAATGCCTTTCTCGGCTGAGCCGTCTTGCTGAGCTTTTTGTTTTGTTGGTTGTGGGGTTTGGAGGTAGATTCTGGGGAATCGAACTCATGTGCCTGCACAGCAAGCACTTTGCCATCTGAGCTCTGATTTGGTATTTTTAAGGACATGATAGTAATCCACCCCCTTTCAAACGGCAG
Seq C2 exon
ACACCTTCTGGACCAACCCTCAGATAAAGCTGTCCCTGACCGAGAGGGACGAGGGCCAGGAGGGCTGCACTTTCCTAGCAGCCTTGATGCAGAAAGACCGCAGGAGGCTCAAGAGGTTTGGCGCCAACATGCTGACCATTGGCTACGCCATTTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031981:ENSMUST00000093033:9
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=PD(6.4=34.5),PF0106717=Calpain_III=PU(16.3=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(35.4=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:
TGGCATTCAAAGACTTCAAGATCCA
R:
CGTAGCCAATGGTCAGCATGT
Band lengths:
306-1361
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