HsaINT0035184 @ hg38
Intron Retention
Gene
ENSG00000080644 | CHRNA3
Description
cholinergic receptor nicotinic alpha 3 subunit [Source:HGNC Symbol;Acc:HGNC:1957]
Coordinates
chr15:78618617-78618915:-
Coord C1 exon
chr15:78618776-78618915
Coord A exon
chr15:78618662-78618775
Coord C2 exon
chr15:78618617-78618661
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:ENST00000326828:2
Average complexity
IR
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