HsaEX0015305 @ hg38
Exon Skipping
Gene
ENSG00000138435 | CHRNA1
Description
cholinergic receptor nicotinic alpha 1 subunit [Source:HGNC Symbol;Acc:HGNC:1955]
Coordinates
chr2:174757566-174759375:-
Coord C1 exon
chr2:174759331-174759375
Coord A exon
chr2:174757946-174758020
Coord C2 exon
chr2:174757566-174757675
Length
75 bp
Sequences
Splice sites
3' ss Seq
CCTTTTCTGTGGGTGGACAGGGT
3' ss Score
6.18
5' ss Seq
GAGGTCAGT
5' ss Score
7.7
Exon sequences
Seq C1 exon
GATGAAGTAAATCAGATCGTGACAACCAATGTGCGTCTGAAACAG
Seq A exon
GGTGACATGGTAGATCTGCCACGCCCCAGCTGCGTGACTTTGGGAGTTCCTTTGTTTTCTCATCTGCAGAATGAG
Seq C2 exon
CAATGGGTGGATTACAACCTAAAATGGAATCCAGATGACTATGGCGGTGTGAAAAAAATTCACATTCCTTCAGAAAAGATCTGGCGCCCAGACCTTGTTCTCTATAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138435_MULTIEX1-1/2=C1-2
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (No Ref)
Show structural model
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(25.0=100),PF0293118=Neur_chan_LBD=PU(1.4=6.7)
A:
PF0293118=Neur_chan_LBD=PD(0.1=0.0),PF0293118=Neur_chan_LBD=PU(3.8=24.0)
C2:
PF0293118=Neur_chan_LBD=FE(22.5=100)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAGTAAATCAGATCGTGACAACCA
R:
GTTATAGAGAACAAGGTCTGGGCG
Band lengths:
151-226
Functional annotations
There are 1 annotated functions for this event
PMID: 8788941
CHRNA1 undergoes alternative splicing to produce two splice variants: P3A(-), without exon P3A, and P3A(+), with the exon P3A. Only P3A(- ) forms functional nAChR. Aberrant alternative splicing caused by intronic or exonic point mutations in patients leads to an extraordinary increase in P3A(+) and a concomitant decrease in P3A(-). Consequently this resulted in a shortage of functional receptors.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development