HsaINT0035210 @ hg38
Intron Retention
Gene
ENSG00000174343 | CHRNA9
Description
cholinergic receptor nicotinic alpha 9 subunit [Source:HGNC Symbol;Acc:HGNC:14079]
Coordinates
chr4:40335329-40335972:+
Coord C1 exon
chr4:40335329-40335531
Coord A exon
chr4:40335532-40335826
Coord C2 exon
chr4:40335827-40335972
Length
295 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
AGATCCCTCTTGTTGAGTAGCTG
3' ss Score
0.72
Exon sequences
Seq C1 exon
ATGCAATGCAAGCCTGAGCTCTCCCGCCATAAGGCTGCAGCGGTGTGGGCTCCTTGTGCCCAGATCCTTTGTATTCATAGGGGGAAGTGGAAGACCACGCTGCCTGACTGAGACTTTATTATAGAGGCTCAGGAAAAAGATGAACTGGTCCCATTCCTGCATCTCCTTTTGCTGGATCTACTTTGCTGCTTCCAGACTGAGAG
Seq A exon
GTGAGAGGCTGGTGACACGTAACCTATCTTGTCTCATCTGGGGCTATTGCTTTGGTGGGAGGTGGGGCAGGACAGGGAAGACAAAACAGATGATTCAACCGCATGGAAGTGTTCTGTGCTTCCTACTGACTCTGATCTTGGTAGGGCATGCCAGAAAAACAACTCATCCATCCACCCAAAGCTTGTCCCTCGCCAGTGTTGGGCCATCCCCCATTTTAGACCTCAGTCTTGTGTTGTTTGTCTTGAAATACACACAACACTCTGAATGTTAATCCAGATCCCTCTTGTTGAGTAG
Seq C2 exon
CTGCAGAGACGGCAGATGGAAAATATGCTCAGAAGTTGTTTAATGACCTTTTTGAAGATTATTCTAATGCTCTTCGTCCAGTGGAAGATACAGATAAAGTCCTGAATGTGACCCTGCAGATTACGCTCTCTCAGATTAAGGATATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000174343:ENST00000310169:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.8=79.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGCTCTCCCGCCATAAGG
R:
CTGCAGGGTCACATTCAGGAC
Band lengths:
308-603
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