HsaINT0035250 @ hg19
Intron Retention
Gene
ENSG00000108556 | CHRNE
Description
cholinergic receptor, nicotinic, epsilon (muscle) [Source:HGNC Symbol;Acc:1966]
Coordinates
chr17:4802296-4802679:-
Coord C1 exon
chr17:4802493-4802679
Coord A exon
chr17:4802403-4802492
Coord C2 exon
chr17:4802296-4802402
Length
90 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGC
5' ss Score
8.19
3' ss Seq
CCCGGTGTTTTCCCCGCCAGCTG
3' ss Score
9.23
Exon sequences
Seq C1 exon
GTTCTCCTGGAGCTGCTGCCGCGCCTCCTGGGCTCCCCGCCGCCGCCCGAGGCCCCCCGGGCCGCCTCGCCCCCAAGGCGGGCGTCGTCGGTGGGCTTATTGCTCCGCGCGGAGGAGCTGATACTGAAAAAGCCACGGAGCGAGCTCGTGTTTGAGGGGCAGAGGCACCGGCAGGGGACCTGGACGG
Seq A exon
GTGAGCACAGTGGCCCTGGCCCGGGGGGCCGCGCGGGGTGCCTGCCAGGGGGGAGGCTCCTAAGGCCCACCCCGGTGTTTTCCCCGCCAG
Seq C2 exon
CTGCCTTCTGCCAGAGCCTGGGCGCCGCCGCCCCCGAGGTCCGCTGCTGTGTGGATGCCGTGAACTTCGTGGCCGAGAGCACGAGAGATCAGGAGGCCACCGGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108556-CHRNE:NM_000080:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.175 A=NA C2=0.056
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(27.2=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(15.4=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:
CGCGGAGGAGCTGATACTGAA
R:
TCCTGATCTCTCGTGCTCTCG
Band lengths:
174-264
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)