HsaINT0035236 @ hg38
Intron Retention
Gene
ENSG00000117971 | CHRNB4
Description
cholinergic receptor nicotinic beta 4 subunit [Source:HGNC Symbol;Acc:HGNC:1964]
Coordinates
chr15:78631076-78631332:-
Coord C1 exon
chr15:78631288-78631332
Coord A exon
chr15:78631186-78631287
Coord C2 exon
chr15:78631076-78631185
Length
102 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
GGCCTTGCCTGTCTGTCCAGGAA
3' ss Score
7.72
Exon sequences
Seq C1 exon
AATGAGCGAGAGCAGATCATGACCACCAATGTCTGGCTGAAACAG
Seq A exon
GTAAGTGCCCTGAAGGGCCCTGAGCCCCAGAGATCTTTTCTTTAGGGCTGCCCTTTGGTGGCAGTGGACCTGCAAGTGACAGGGCCTTGCCTGTCTGTCCAG
Seq C2 exon
GAATGGACTGATTACCGCCTGACCTGGAACAGCTCCCGCTACGAGGGTGTGAACATCCTGAGGATCCCTGCAAAGCGCATCTGGTTGCCTGACATCGTGCTTTACAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000117971:ENST00000261751:3
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=FE(13.0=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(17.5=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:
CGAGAGCAGATCATGACCACC
R:
TTGTAAAGCACGATGTCAGGCA
Band lengths:
146-248
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