MmuINT0036292 @ mm9
Intron Retention
Gene
ENSMUSG00000014609 | Chrne
Description
cholinergic receptor, nicotinic, epsilon polypeptide [Source:MGI Symbol;Acc:MGI:87894]
Coordinates
chr11:70428710-70429088:-
Coord C1 exon
chr11:70428902-70429088
Coord A exon
chr11:70428817-70428901
Coord C2 exon
chr11:70428710-70428816
Length
85 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGC
5' ss Score
8.8
3' ss Seq
GCTTGCTGTTGCCTTAGCAGCAG
3' ss Score
4.14
Exon sequences
Seq C1 exon
ATTTTATTAGAGCTGCTGCCGCGTCTCCTGGGCTCGAGCCCACCCCCAGAGGATCCCCGAACTGCCTCACCAGCGAGGCGTGCCTCGTCTGTGGGCATTCTGCTCAGAGCGGAGGAGCTCATCTTGAAAAAGCCGCGGAGCGAACTCGTGTTTGAGGGTCAGAGGCATCGGCACGGAACTTGGACCG
Seq A exon
GTAAGCACTGCTCTTGGGTCAAAGGCATACACTCGCCGTTAGGGACGCTCTTTTAATGACCTAGCGCTTGCTGTTGCCTTAGCAG
Seq C2 exon
CAGCCCTCTGCCAGAACCTGGGTGCTGCAGCCCCAGAAATCCGCTGCTGTGTGGATGCTGTGAACTTTGTGGCTGAGAGCACAAGAGACCAGGAAGCCACTGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000014609-Chrne:NM_009603:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.175 A=NA C2=0.055
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(27.1=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(15.7=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:
GCTCATCTTGAAAAAGCCGCG
R:
AGTGGCTTCCTGGTCTCTTGT
Band lengths:
172-257
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: