HsaINT0035219 @ hg38
Intron Retention
Gene
ENSG00000170175 | CHRNB1
Description
cholinergic receptor nicotinic beta 1 subunit [Source:HGNC Symbol;Acc:HGNC:1961]
Coordinates
chr17:7447043-7447650:+
Coord C1 exon
chr17:7447043-7447151
Coord A exon
chr17:7447152-7447502
Coord C2 exon
chr17:7447503-7447650
Length
351 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTCC
5' ss Score
-1.9
3' ss Seq
TGACTCTCTCCTCCATCCAGGTC
3' ss Score
11.4
Exon sequences
Seq C1 exon
CAATGATGGGAATTTTGACGTGGCTCTGGACATTAGCGTCGTGGTGTCCTCCGACGGCTCCGTGCGTTGGCAACCCCCGGGCATCTATCGCAGCAGCTGCAGCATCCAG
Seq A exon
GTTTCCGGCCTCCACATTGGAAGCTGAAGGAGCTCTTACAAATCCTCCCTTTCCTTAGACATCCTGACTCCCCGGCGACTCCCATCCTTCATCCTTCCCCCATTATCTAATCCCCATGACCCTCACCTCGTCTACCCTCCTGGTTTTCCATTGAGTGTTCTGTACACTTTCTTTGACTTCTAGTCTTACTCAGTGACCGCCCTCCCCATCCCTCCCCCATTAATGGCTTCCCTTCATAACCCTCCAATTCCTCCATGATTTCCCTTCTCTGTGCCCTCCCCAAAGACCTCCCAAACTCCACCAGCGCTGACTGGTTCTCTGGCAGCTCTAGTGACTCTCTCCTCCATCCAG
Seq C2 exon
GTCACCTACTTCCCCTTCGACTGGCAGAATTGCACTATGGTGTTCAGCTCCTACAGCTACGACAGCTCGGAGGTCAGCCTGCAGACAGGCCTGGGTCCTGACGGGCAAGGGCATCAGGAAATCCACATTCATGAAGGGACTTTCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170175:ENST00000306071:5
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=0.030
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(23.4=88.2)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(29.5=100),PF0293211=Neur_chan_memb=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGATGGGAATTTTGACGTGGCT
R:
CAATGAAAGTCCCTTCATGAATGTGG
Band lengths:
254-605
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development