HsaALTD0001434-2/2 @ hg19
Alternative 5'ss
Gene
ENSG00000101204 | CHRNA4
Description
cholinergic receptor, nicotinic, alpha 4 (neuronal) [Source:HGNC Symbol;Acc:1958]
Coordinates
chr20:61981005-61987436:-
Coord C1 exon
chr20:61987327-61987436
Coord A exon
chr20:61987309-61987326
Coord C2 exon
chr20:61981005-61982379
Length
18 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
TTCGCTCTCTTCCTGCCCAGTGC
3' ss Score
8.55
Exon sequences
Seq C1 exon
GAGTGGCACGACTACAAGCTGCGCTGGGACCCAGCTGACTATGAGAATGTCACCTCCATCCGCATCCCCTCCGAGCTCATCTGGCGGCCGGACATCGTCCTCTACAACAA
Seq A exon
GTGAGTCCTCTACAACAA
Seq C2 exon
TGCTGACGGGGACTTCGCGGTCACCCACCTGACCAAGGCCCACCTGTTCCATGACGGGCGGGTGCAGTGGACTCCCCCGGCCATTTACAAGAGCTCCTGCAGCATCGACGTCACCTTCTTCCCCTTCGACCAGCAGAACTGCACCATGAAATTCGGCTCCTGGACCTACGACAAGGCCAAGATCGACCTGGTGAACATGCACAGCCGCGTGGACCAGCTGGACTTCTGGGAGAGTGGCGAGTGGGTCATCGTGGATGCCGTGGGCACCTACAACACCAGGAAGTACGAGTGCTGTGCCGAGATCTACCCGGACATCACCTATGCCTTCGTCATCCGGCGGCTGCCGCTCTTCTACACCATCAACCTCATCATCCCCTGCCTGCTCATCTCCTGCCTCACCGTGCTGGTCTTCTACCTGCCCTCCGAGTGTGGCGAGAAGATCACGCTGTGCATCTCCGTGCTGCTGTCGCTCACCGTCTTCCTGCTGCTCATCACCGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101204-11-13,12-13-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.232 A=NA C2=0.348
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.4=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=25.1),PF0293211=Neur_chan_memb=PU(91.1=73.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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:
GAGAATGTCACCTCCATCCGC
R:
GAACAGGTGGGCCTTGGTCA
Band lengths:
117-135
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)