HsaINT0035184 @ hg19
Intron Retention
Gene
ENSG00000080644 | CHRNA3
Description
cholinergic receptor, nicotinic, alpha 3 (neuronal) [Source:HGNC Symbol;Acc:1957]
Coordinates
chr15:78910959-78911257:-
Coord C1 exon
chr15:78911118-78911257
Coord A exon
chr15:78911004-78911117
Coord C2 exon
chr15:78910959-78911003
Length
114 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
ACTTTAATTCCTCTTTCTAGGAT
3' ss Score
11.13
Exon sequences
Seq C1 exon
TGGCCAGGGCCTCAGAGGCTGAGCACCGTCTATTTGAGCGGCTGTTTGAAGATTACAATGAGATCATCCGGCCTGTAGCCAACGTGTCTGACCCAGTCATCATCCATTTCGAGGTGTCCATGTCTCAGCTGGTGAAGGTG
Seq A exon
GTGAGTGCTGGAAGCCACGAGCCGTGGCCATGGGGACCGGGGCTTCTGGAGGAGCCTTTCCCAGAATTAGTCTTGTTTTGTAATTCTCCTGTCAACTTTAATTCCTCTTTCTAG
Seq C2 exon
GATGAAGTAAACCAGATCATGGAGACCAACCTGTGGCTCAAGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080644-CHRNA3:NM_001166694:2
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(18.8=83.0)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(6.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAGGCTGAGCACCGTCTATT
R:
TTGCTTGAGCCACAGGTTG
Band lengths:
172-286
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)