HsaINT0035257 @ hg19
Intron Retention
Gene
ENSG00000108556 | CHRNE
Description
cholinergic receptor, nicotinic, epsilon (muscle) [Source:HGNC Symbol;Acc:1966]
Coordinates
chr17:4804088-4804485:-
Coord C1 exon
chr17:4804285-4804485
Coord A exon
chr17:4804203-4804284
Coord C2 exon
chr17:4804088-4804202
Length
82 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGC
5' ss Score
9.04
3' ss Seq
CTCACTGGCTCTCCCTCCAGCCG
3' ss Score
9.53
Exon sequences
Seq C1 exon
AGAACGGCGAGTGGGCCATCGACTTCTGCCCGGGGGTGATCCGCCGCCACCACGGTGGCGCCACCGACGGCCCAGGGGAGACTGACGTCATCTACTCGCTCATCATCCGCCGGAAGCCGCTCTTCTACGTCATTAACATCATCGTGCCCTGTGTGCTCATCTCGGGCCTGGTGCTGCTCGCCTACTTCCTGCCGGCGCAGG
Seq A exon
GTAAGCAGTGGCCCCGAACCTACCCCCAAACCCGGGCTCGCTCCCGGGAGGCGGGGCCCGCTCTCACTGGCTCTCCCTCCAG
Seq C2 exon
CCGGCGGCCAGAAATGCACGGTCTCCATCAACGTCCTGCTCGCCCAGACCGTCTTCTTGTTCCTCATTGCCCAGAAAATCCCAGAGACTTCTCTGAGCGTGCCGCTCCTGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108556-CHRNE:NM_000080:7
Average complexity
IR-C
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(16.7=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:
CAGGGGAGACTGACGTCATCT
R:
GAGCAGGACGTTGATGGAGAC
Band lengths:
170-252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)