MmuINT0028677 @ mm9
Intron Retention
Gene
ENSMUSG00000058626 | Capn11
Description
calpain 11 [Source:MGI Symbol;Acc:MGI:1352490]
Coordinates
chr17:45768737-45769036:-
Coord C1 exon
chr17:45768958-45769036
Coord A exon
chr17:45768851-45768957
Coord C2 exon
chr17:45768737-45768850
Length
107 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGCG
5' ss Score
2.99
3' ss Seq
CACACACATCTGTTCCCTAGGCA
3' ss Score
8.07
Exon sequences
Seq C1 exon
GAAATCTTCAAAGAGTGTGATGAGGACCGCTCAGGGAACTTGAACTCCTATGAGATGCGCCTGGCAATAGAGAAAGCAG
Seq A exon
GTGGCGCCCTGCAGGGGCCAGGAGCCGGGAGGTTGTGTCCAGACCTGAACTCTGCCCTTACTGTCCCCCCCCCCCCAACCCCTCACACACACACATCTGTTCCCTAG
Seq C2 exon
GCATCAAGATGAACAACAGAGTGACCGAGGTAGTCGTTGCCAGGTACTCGGATAACATGATTGTGGACTTTGACAGCTTCCTCAACTGTTTCCTGAGGCTCAAGGCCATGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058626-Capn11:NM_001013767:19
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=0.000
Domain overlap (PFAM):
C1:
PF0175117=Toprim=FE(24.8=100),PF0003627=EF-hand_1=PD(86.2=92.6)
A:
NA
C2:
PF0175117=Toprim=PD(13.3=35.9)
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:
TCAAAGAGTGTGATGAGGACCG
R:
GCCTTGAGCCTCAGGAAACAG
Band lengths:
178-285
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: