HsaINT1007694 @ hg38
Intron Retention
Gene
ENSG00000108556 | CHRNE
Description
cholinergic receptor nicotinic epsilon subunit [Source:HGNC Symbol;Acc:HGNC:1966]
Coordinates
chr17:4902621-4903074:-
Coord C1 exon
chr17:4903018-4903074
Coord A exon
chr17:4902764-4903017
Coord C2 exon
chr17:4902621-4902763
Length
254 bp
Sequences
Splice sites
5' ss Seq
TCGGTACGG
5' ss Score
8.77
3' ss Seq
CCTTCTTGACCCCATCGCAGGCA
3' ss Score
6.22
Exon sequences
Seq C1 exon
CACGCAGCAGGATGGCAAGGGCTCCGCTTGGGGTCCTGCTCCTCTTGGGGCTTCTCG
Seq A exon
GTACGGACAGGGGCTAGAGGGGCAATTGGACACACACAGATACTGACATGAAGGGACTGGGAAGACAAAGACAGAGACCAAGATGGAGACTTAGACACAGTATTTCGTTCCCAGGCACAGCATAATTGGTTTAGGAGACAGATACTGATAGTACACAGCCTCAGAGGCCTGTGAGGACCCAGGGGAGGCAGAGGGGAGAGAGGTGCTCCAGCCTCTTCATTGCCAATGACCCTTCCTTCTTGACCCCATCGCAG
Seq C2 exon
GCAGGGGTGTGGGGAAGAACGAGGAACTGCGTCTTTATCACCATCTCTTCAACAACTATGACCCAGGAAGCCGGCCAGTGCGGGAGCCTGAGGATACTGTCACCATCAGCCTCAAGGTCACCCTGACGAATCTCATCTCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108556:ENST00000293780:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.042
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.0=81.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACGCAGCAGGATGGCAAG
R:
AGTGAGATGAGATTCGTCAGGGT
Band lengths:
199-453
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains