MmuINT0036299 @ mm9
Intron Retention
Gene
ENSMUSG00000014609 | Chrne
Description
cholinergic receptor, nicotinic, epsilon polypeptide [Source:MGI Symbol;Acc:MGI:87894]
Coordinates
chr11:70430457-70430849:-
Coord C1 exon
chr11:70430649-70430849
Coord A exon
chr11:70430572-70430648
Coord C2 exon
chr11:70430457-70430571
Length
77 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
TCACAGCTTGCTCCCTCTAGCTG
3' ss Score
5.8
Exon sequences
Seq C1 exon
AGAATGGAGAATGGGCCATAGACTACTGCCCAGGCATGATTCGCCGCTATGAGGGAGGTTCCACAGAAGGTCCTGGAGAAACTGACGTCATCTATACGCTCATCATCCGCCGGAAGCCGCTTTTTTACGTCATTAACATCATTGTGCCTTGCGTGCTCATTTCTGGCTTGGTGCTGCTCGCTTACTTCCTGCCTGCGCAGG
Seq A exon
GTAAGGGGTGACCCTGACTCCTGAACCCCAGGCTGGGCTTGCTCCCTGGCTTGCCTCTCACAGCTTGCTCCCTCTAG
Seq C2 exon
CTGGTGGCCAGAAATGCACGGTCTCTATCAACGTCCTGCTAGCCCAGACTGTCTTCTTGTTTCTAATTGCCCAGAAAATTCCAGAGACTTCTCTGAGCGTGCCACTGCTGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000014609-Chrne:NM_009603:7
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:
PF0293118=Neur_chan_LBD=PD(18.0=57.4),PF0293211=Neur_chan_memb=PU(9.2=30.9)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(16.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGTCCTGGAGAAACTGACGT
R:
TGGGCTAGCAGGACGTTGATA
Band lengths:
180-257
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: