MmuINT0028831 @ mm9
Intron Retention
Gene
ENSMUSG00000038599 | Capn8
Description
calpain 8 [Source:MGI Symbol;Acc:MGI:2181366]
Coordinates
chr1:184543457-184544956:+
Coord C1 exon
chr1:184543457-184543668
Coord A exon
chr1:184543669-184544919
Coord C2 exon
chr1:184544920-184544956
Length
1251 bp
Sequences
Splice sites
5' ss Seq
TCTGTGCGT
5' ss Score
2.77
3' ss Seq
CATTTCTGTCTGGATTTCAGAGA
3' ss Score
7.15
Exon sequences
Seq C1 exon
CTGGAGAATCACACCGATGAGCACCTGGGCCGGGATTTCTTCCAGGGCCGCCAGCCCTCCACCTGCTCCAGCACCTACATGAACCTTCGAGAGGTGTCCAGCAGGGTCCAACTCCCCCCAGGACAGTACCTGGTGGTGCCATCCACCTTTGAGCCCTTCAAGGACGGTGACTTCTGCCTGAGGGTGTTCTCGGAGAAGAAGGCCCAGGCTCT
Seq A exon
GTGCGTCTACTTGGTCAATCGTGGCTGGAGGGGGTGGTTTTCTGAGTTAGGCCCCAGATGGAGGTGCAGGATCTGGAGGAACTCATTGCTAAATGACCTGCCTGCCCCAGGAGCGTAGTGGGTGCTTCTAAAGGAAGTTTGGAAAGCATGACATCTCCCTGGGTGTGCCTCCTGCTGCCTCCACTTTTCTCTATAGGACTGGGAATTTCCTCATCCAGAAAGTGAAGGCTGGGGAGAAAGGGCGCCAACAACAGACTATTGACCAACTGTTCTACCATCTGGCAGAGGCTGATGGGATCTGGGATAGGGCTGTGCACACAGTACACACATACTTTGTATACATACCATGTACATCAATTATGTACACTACGCACAACCTACTTACTATATATATCTGTCATATACACTAGACATATATATGACACATGTACTAATTGTGTACTATCTATACATCCCACATTATATACGTATATGTACTATGTACACACTACAGACAAACATATACATACGCACAGTGTGCATACCATGTCTATTATGTACACACACAGCAATGCATCAAATACATAACACAAACATGCAACATACAAACCACACATACATATTATATATACCATATCATATACATGCAACATATGACATGCACATATGCCATACATTAGATACACAACACACTATACATTTCAAGTACCACATACCACACTATGTACACATACCACTAATGCATAACTCAAATATACTATGTTTATTCACTACAGAGCACACACAGAATATTCACATAGATTCATAGAAACTATATGCATAAGTACCACATACCATGTGCACCATCCACACATCCCATGCCATAGATCCTGAGCACATGGCACACACATAGGGCATATCCCATGCCCTATAGCCATTTCTCAGACTTCAGGCTCTCCACAAGGCCAGCAGAGCCTTCAGCAGTGAACTTTTCAGGAGAAAGAAGAGTAGCCATCACTGAGGTAAACAGGGACGCGTCTCAGAATGTTCAGTATTCTAGAATCCACAGGAGACCCAGGAGCCCCTTATCTTATGAAACTTCAGGCTGGGTGGTGGGCTGGGGCAGTGAAGGGGAAGCATTTCTTTTAGGGATTCAGCTATACAGTTTCTTTAAAAACAGGAACTGAAAATCCTGAGTGTGAAATTCCCATAAGAGGAAATTCTCCCTGAAAGGGCCCAGCCATTATCTGAACTTGCTTTTTGATGTTTAATTCATTTCTGTCTGGATTTCAG
Seq C2 exon
AGAAATTGGGGACGCTGTTGCTGGAGACCCACATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038599-Capn8:NM_130890:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.141 A=NA C2=0.769
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(44.3=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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGAATCACACCGATGAGCA
R:
CTCATGTGGGTCTCCAGCAAC
Band lengths:
247-1498
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: