HsaINT0035236 @ hg19
Intron Retention
Gene
ENSG00000117971 | CHRNB4
Description
cholinergic receptor, nicotinic, beta 4 (neuronal) [Source:HGNC Symbol;Acc:1964]
Coordinates
chr15:78923418-78923674:-
Coord C1 exon
chr15:78923630-78923674
Coord A exon
chr15:78923528-78923629
Coord C2 exon
chr15:78923418-78923527
Length
102 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
GGCCTTGCCTGTCTGTCCAGGAA
3' ss Score
7.72
Exon sequences
Seq C1 exon
AATGAGCGAGAGCAGATCATGACCACCAATGTCTGGCTGAAACAG
Seq A exon
GTAAGTGCCCTGAAGGGCCCTGAGCCCCAGAGATCTTTTCTTTAGGGCTGCCCTTTGGTGGCAGTGGACCTGCAAGTGACAGGGCCTTGCCTGTCTGTCCAG
Seq C2 exon
GAATGGACTGATTACCGCCTGACCTGGAACAGCTCCCGCTACGAGGGTGTGAACATCCTGAGGATCCCTGCAAAGCGCATCTGGTTGCCTGACATCGTGCTTTACAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000117971-CHRNB4:NM_000750:3
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=FE(13.9=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(17.5=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:
CGAGAGCAGATCATGACCACC
R:
TTGTAAAGCACGATGTCAGGCA
Band lengths:
146-248
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)