HsaINT0035225 @ hg19
Intron Retention
Gene
ENSG00000160716 | CHRNB2
Description
cholinergic receptor, nicotinic, beta 2 (neuronal) [Source:HGNC Symbol;Acc:1962]
Coordinates
chr1:154541938-154542312:+
Coord C1 exon
chr1:154541938-154542083
Coord A exon
chr1:154542084-154542267
Coord C2 exon
chr1:154542268-154542312
Length
184 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
GCCTCTCTTCCTCCCTGCAGCAT
3' ss Score
11.95
Exon sequences
Seq C1 exon
GGGTGTGGGGTACGGATACAGAGGAGCGGCTGGTGGAGCATCTCCTGGATCCTTCCCGCTACAACAAGCTTATCCGCCCAGCCACCAATGGCTCTGAGCTGGTGACAGTACAGCTTATGGTGTCACTGGCCCAGCTCATCAGTGTG
Seq A exon
GTGAGTAGAGGTCCCAGGCTCTCTGCCCAGCTACTGAAATCAGCCCCGCCAAAATGTGTTAATGCTTGTGTGCTTCCTCCCCTGGTGTTTCCAAGGCTTGGGGAGGTGTGAGAGGGACCCTGGGTGGTGGCAGTGACCCCACAGGCTTAGGGGCCTTCTCGGCAGCCTCTCTTCCTCCCTGCAG
Seq C2 exon
CATGAGCGGGAGCAGATCATGACCACCAATGTCTGGCTGACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000160716-CHRNB2:NM_000748:2
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=PU(19.9=83.7)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(6.8=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:
GGTGTGGGGTACGGATACAGA
R:
GACATTGGTGGTCATGATCTGCT
Band lengths:
178-362
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)