HsaINT0035253 @ hg38
Intron Retention
Gene
ENSG00000108556 | CHRNE
Description
cholinergic receptor nicotinic epsilon subunit [Source:HGNC Symbol;Acc:HGNC:1966]
Coordinates
chr17:4902217-4902494:-
Coord C1 exon
chr17:4902450-4902494
Coord A exon
chr17:4902327-4902449
Coord C2 exon
chr17:4902217-4902326
Length
123 bp
Sequences
Splice sites
5' ss Seq
ATCGTGAGT
5' ss Score
8.88
3' ss Seq
TTCCATCCCCCACCCCTTAGGAT
3' ss Score
9.31
Exon sequences
Seq C1 exon
AATGAAAAAGAGGAGACTCTCACCACTAGCGTCTGGATTGGAATC
Seq A exon
GTGAGTCAAATCTGGGGAATGGTGTGAGGTCTTGTCCAGGGCACCCCTTTTCCCCCAAACCCCTCCCAGGCAGCGCCAGGTGGGAGATGCAGGGCACGCGGCCTTCCATCCCCCACCCCTTAG
Seq C2 exon
GATTGGCAGGATTACCGACTCAACTACAGCAAGGACGACTTTGGGGGTATAGAAACCCTGCGAGTCCCTTCAGAACTCGTGTGGCTGCCAGAGATTGTGCTGGAAAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108556:ENST00000293780:3
Average complexity
IR
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=FE(6.5=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(16.6=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:
GGAGACTCTCACCACTAGCGT
R:
TTCCAGCACAATCTCTGGCAG
Band lengths:
139-262
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