HsaINT0035214 @ hg19
Intron Retention
Gene
ENSG00000170175 | CHRNB1
Description
cholinergic receptor, nicotinic, beta 1 (muscle) [Source:HGNC Symbol;Acc:1961]
Coordinates
chr17:7348406-7348728:+
Coord C1 exon
chr17:7348406-7348504
Coord A exon
chr17:7348505-7348588
Coord C2 exon
chr17:7348589-7348728
Length
84 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
CTTATTCTCTCCTCCCCCAGGCG
3' ss Score
11.05
Exon sequences
Seq C1 exon
AGCGGCTCTCTGAGCGAAGTCACTGAGCGAGCCGCCAGGCTATGACCCCAGGGGCTCTGCTGATGCTGCTGGGGGCGCTGGGGGCGCCGCTCGCCCCAG
Seq A exon
GTAAGTGTAGGCCCCGAAGGGGCAGTGACGGGGCCAGCGGTCGTGGCCAGGCACCAGGGCTGCACTTATTCTCTCCTCCCCCAG
Seq C2 exon
GCGTCCGCGGCTCGGAGGCGGAGGGTCGACTCCGGGAGAAACTTTTCTCTGGCTATGATAGCTCCGTGCGGCCAGCGCGGGAGGTGGGAGACCGTGTCAGGGTCAGCGTTGGTCTCATCCTGGCGCAACTCATCAGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170175-CHRNB1:NM_000747:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
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(17.8=83.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCTCTGAGCGAAGTCACTG
R:
GCCGCACGGAGCTATCATAG
Band lengths:
167-251
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)