HsaINT0035214 @ hg38
Intron Retention
Gene
ENSG00000170175 | CHRNB1
Description
cholinergic receptor nicotinic beta 1 subunit [Source:HGNC Symbol;Acc:HGNC:1961]
Coordinates
chr17:7445061-7445409:+
Coord C1 exon
chr17:7445061-7445185
Coord A exon
chr17:7445186-7445269
Coord C2 exon
chr17:7445270-7445409
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
GTCACTTCCCCTGTGCTGGCGGTCCCAGCGGCTCTCTGAGCGAAGTCACTGAGCGAGCCGCCAGGCTATGACCCCAGGGGCTCTGCTGATGCTGCTGGGGGCGCTGGGGGCGCCGCTCGCCCCAG
Seq A exon
GTAAGTGTAGGCCCCGAAGGGGCAGTGACGGGGCCAGCGGTCGTGGCCAGGCACCAGGGCTGCACTTATTCTCTCCTCCCCCAG
Seq C2 exon
GCGTCCGCGGCTCGGAGGCGGAGGGTCGACTCCGGGAGAAACTTTTCTCTGGCTATGATAGCTCCGTGCGGCCAGCGCGGGAGGTGGGAGACCGTGTCAGGGTCAGCGTTGGTCTCATCCTGGCGCAACTCATCAGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170175:ENST00000306071:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.023
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