HsaINT0035223 @ hg38
Intron Retention
Gene
ENSG00000170175 | CHRNB1
Description
cholinergic receptor nicotinic beta 1 subunit [Source:HGNC Symbol;Acc:HGNC:1961]
Coordinates
chr17:7455284-7455941:+
Coord C1 exon
chr17:7455284-7455456
Coord A exon
chr17:7455457-7455793
Coord C2 exon
chr17:7455794-7455941
Length
337 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGA
5' ss Score
7
3' ss Seq
GCCAGTCACTCCTCTTCCAGGTT
3' ss Score
8.02
Exon sequences
Seq C1 exon
ATCTTCATTCACAAACTTCCGCTGTACCTGCGTCTAAAAAGGCCCAAACCCGAGAGAGACCTGATGCCGGAGCCCCCTCACTGTTCTTCTCCAGGAAGTGGCTGGGGTCGGGGAACAGATGAATATTTCATCCGGAAGCCGCCAAGTGATTTTCTCTTCCCCAAACCCAATAG
Seq A exon
GTAGGACTACGCCCGTTACCCACATAAGAGGGAGAGGGAGAACTACAGTTCCCAGAAGAGTGTGCGGAAGAAGCGGCCCATGCTCTCGGAAGACGCTGTGGTTGAGCATCATGGGAGTTGTAGTACTCCTGCTGCTCACTTTGAGGGGAGGTGGGAACTAAAACAGAGGCGGTGGAAGAAGTTGCACAAGGCTAGAGAGATCACTGCTGGAGGGAAAAGCATGATGGGCTCTCGGGTTTTGAGAACTGGCAAGTTGTTGGAGGCAGCTGGAGCGGGGCCTGGGTCGCCGGCACTGGCTGTCTTTGCGTTTGGGCGTGGCCAGTCACTCCTCTTCCAG
Seq C2 exon
GTTCCAGCCTGAACTGTCTGCCCCTGATCTGCGGCGATTTATCGATGGTCCAAACCGGGCTGTGGCCCTGCTTCCGGAGCTACGGGAGGTCGTCTCCTCTATCAGCTACATCGCTCGACAGCTGCAGGAACAGGAGGACCACGATGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170175:ENST00000306071:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.223 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=PD(41.1=89.8)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(20.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTTCATTCACAAACTTCCGCTGT
R:
CATCGTGGTCCTCCTGTTCCT
Band lengths:
318-655
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