HsaALTA0001868-2/2 @ hg38
Alternative 3'ss
Gene
ENSG00000120903 | CHRNA2
Description
cholinergic receptor nicotinic alpha 2 subunit [Source:HGNC Symbol;Acc:HGNC:1956]
Coordinates
chr8:27469905-27471194:-
Coord C1 exon
chr8:27470986-27471194
Coord A exon
chr8:27469982-27470031
Coord C2 exon
chr8:27469905-27469981
Length
50 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TAAGCATCTCCATTTTACAGATG
3' ss Score
7.46
Exon sequences
Seq C1 exon
GTTCGGTGGTGAGAGGAAGCCTCGCAGAATCCAGCAGAATCCTCACAGAATCCAGCAGCAGCTCTGCTGGGGACATGGTCCATGGTGCAACCCACAGCAAAGCCCTGACCTGACCTCCTGATGCTCAGGAGAAGCCATGGGCCCCTCCTGTCCTGTGTTCCTGTCCTTCACAAAGCTCAGCCTGTGGTGGCTCCTTCTGACCCCAGCAG
Seq A exon
ATGAGCAAACTGAGGCTCAGTGAGGCTGAGTGGCTCTGATTTGATGGCAG
Seq C2 exon
GTGGAGAGGAAGCTAAGCGCCCACCTCCCAGGGCTCCTGGAGACCCACTCTCCTCTCCCAGTCCCACGGCATTGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120903-8-17,8-16-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.495
Domain overlap (PFAM):
C1:
PF0315410=Atrophin-1=PU(5.4=12.0)
A:
NA
C2:
PF0315410=Atrophin-1=PD(92.9=88.1),PF0293118=Neur_chan_LBD=PU(12.5=40.7)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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:
GATGCTCAGGAGAAGCCATGG
R:
GAGAGTGGGTCTCCAGGAGC
Band lengths:
142-192
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Autistic and control brains
- Pre-implantation embryo development