HsaALTA0001868-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000120903 | CHRNA2
Description
cholinergic receptor, nicotinic, alpha 2 (neuronal) [Source:HGNC Symbol;Acc:1956]
Coordinates
chr8:27327422-27328711:-
Coord C1 exon
chr8:27328503-27328711
Coord A exon
chr8:27327499-27327548
Coord C2 exon
chr8:27327422-27327498
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
ENSG00000120903-5-13,5-12-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.479
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)
Main Inclusion Isoform:
NA
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
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
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)