HsaINT0035218 @ hg19
Intron Retention
Gene
ENSG00000170175 | CHRNB1
Description
cholinergic receptor, nicotinic, beta 1 (muscle) [Source:HGNC Symbol;Acc:1961]
Coordinates
chr17:7350152-7350470:+
Coord C1 exon
chr17:7350152-7350261
Coord A exon
chr17:7350262-7350361
Coord C2 exon
chr17:7350362-7350470
Length
100 bp
Sequences
Splice sites
5' ss Seq
CAAGTAGGA
5' ss Score
4.46
3' ss Seq
ATGAGATCCCTTCTCTGCAGCAA
3' ss Score
5.92
Exon sequences
Seq C1 exon
GAGTGGACTGACTACAGGCTGAGCTGGGACCCTGCGGAGCACGACGGCATCGATTCGCTCCGCATCACGGCGGAATCCGTGTGGCTCCCTGACGTGGTGCTACTGAACAA
Seq A exon
GTAGGAGAACTTCCAAAGCCCGGGAGGTGGCGCGGGGCCTCGGGGGGCGGGGGGCCTCCGGGCGCGGGGCCTGATCCCTGATGAGATCCCTTCTCTGCAG
Seq C2 exon
CAATGATGGGAATTTTGACGTGGCTCTGGACATTAGCGTCGTGGTGTCCTCCGACGGCTCCGTGCGTTGGCAACCCCCGGGCATCTATCGCAGCAGCTGCAGCATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170175-CHRNB1:NM_000747:4
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=FE(16.4=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(23.4=88.2)
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:
GACTACAGGCTGAGCTGGGA
R:
CTGGATGCTGCAGCTGCTG
Band lengths:
210-310
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)