HsaINT1007696 @ hg38
Intron Retention
Gene
ENSG00000196811 | CHRNG
Description
cholinergic receptor nicotinic gamma subunit [Source:HGNC Symbol;Acc:HGNC:1967]
Coordinates
chr2:232539727-232540131:+
Coord C1 exon
chr2:232539727-232539802
Coord A exon
chr2:232539803-232539991
Coord C2 exon
chr2:232539992-232540131
Length
189 bp
Sequences
Splice sites
5' ss Seq
TGGGTGGGA
5' ss Score
0.72
3' ss Seq
CTCACGCCTGTCTATTGCAGGGG
3' ss Score
9.67
Exon sequences
Seq C1 exon
ACTGCAGAGAGCTGAGGCACCATGCATGGGGGCCAGGGGCCGCTGCTCCTCCTGCTGCTGCTGGCTGTCTGCCTGG
Seq A exon
GTGGGACACAAAGGAATCTCAGCCTGGGGAGTCCCAGAGCTGGGGTCCACAGCCTCAGGGGATGGAGGGTCTGAGGGGTATTGGGGCCTGCCCTGGACCCAGTTCCCTGAGTCCCCACTTCACACCCCCAGGGCCTCCCCGCTCTTTCCACCTCCAAGCTCCTGCTAGGCTCACGCCTGTCTATTGCAG
Seq C2 exon
GGGCCCAGGGCCGGAACCAGGAGGAGCGCCTGCTCGCAGACCTGATGCAAAACTACGACCCCAACCTGCGGCCCGCGGAACGAGACTCGGATGTGGTCAATGTCAGCCTGAAGCTAACCCTCACCAACCTCATCTCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196811:ENST00000389494:1
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(41.1=83.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAGAGCTGAGGCACCATG
R:
AGGGAGATGAGGTTGGTGAGG
Band lengths:
211-400
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains