HsaINT0035227 @ hg19
Intron Retention
Gene
ENSG00000160716 | CHRNB2
Description
cholinergic receptor, nicotinic, beta 2 (neuronal) [Source:HGNC Symbol;Acc:1962]
Coordinates
chr1:154542734-154544637:+
Coord C1 exon
chr1:154542734-154542843
Coord A exon
chr1:154542844-154543664
Coord C2 exon
chr1:154543665-154544637
Length
821 bp
Sequences
Splice sites
5' ss Seq
CAAGTAGGT
5' ss Score
7.33
3' ss Seq
CTGTGCCCATCCTTTGGCAGTGC
3' ss Score
8.3
Exon sequences
Seq C1 exon
GAGTGGGAAGATTATCGCCTCACCTGGAAGCCTGAAGAGTTTGACAACATGAAGAAAGTTCGGCTCCCTTCCAAACACATCTGGCTCCCAGATGTGGTCCTGTACAACAA
Seq A exon
GTAGGTGCAATGGGAAGGTTGGGGGAGACCATTGGAGGGCTCAGGGAGGGAAGGGGTTCTGGGGAAAATAAGAGAAATTACTTATGCTGTGGGAGGGGAGGGACTTATAATAGATATGTAGTCACTACCTAGACAGACAGACCCAGACCAGTGAGGTACAGCGTGGACAGCCAAGGTGACCTGGGCAATGACCAGCCCACTCCCAGCCGGTTAGGACTCCCAGTATGTATTTGATGATGTGGTGGGGATACAAACAAGTATTGACAGCCCCCAGCGCCTCAACTGATTCAGGAACAGGCTTTCCTGGAAGCCTGGGAAGGATCAAAGAACTTTAAGGTCCCAGTTTCTCCTCCAGGTTCTATCCTGTCTCCTGCAATAATCCATCTTATCTCTAGGGTACAAAGCCACCTTCCTCAACTGATGGGACCATGCCCTGTCCCCTTCCATTGCTTGGGGCTCCTCACTCTGGCCTCCTGGCTCCCCTGACTTCTCCACCCTCATGAGGATCAACCAGCTTATACAATGTGTGACAAGTAGCAGATGTGTCCCCTTCCTCCACCCACCACCCCCTTCTACCTGCAAGGTGTCACACAGGCCTTCTGACCAGGACACTTCTTCTGGTCACTAACCTTCCCCCCCCTCCCCATATCCCCTTCTTGCTCAATTCCACCTCTCTATACTCCTGGATGGTTACTCTCAGATCTGGGTGTCCCCTCCCCATGTCTCCCTCTGGTTTTGCTCTCCTCCCATTAGGGGCTGGGTTGATGGGTAAGGAGGAAGGAACGCTTAGGCCAGGGCTGACTGTGCCCATCCTTTGGCAG
Seq C2 exon
TGCTGACGGCATGTACGAGGTGTCCTTCTATTCCAATGCCGTGGTCTCCTATGATGGCAGCATCTTCTGGCTGCCGCCTGCCATCTACAAGAGCGCATGCAAGATTGAAGTAAAGCACTTCCCATTTGACCAGCAGAACTGCACCATGAAGTTCCGTTCGTGGACCTACGACCGCACAGAGATCGACTTGGTGCTGAAGAGTGAGGTGGCCAGCCTGGACGACTTCACACCTAGTGGTGAGTGGGACATCGTGGCGCTGCCGGGCCGGCGCAACGAGAACCCCGACGACTCTACGTACGTGGACATCACGTATGACTTCATCATTCGCCGCAAGCCGCTCTTCTACACCATCAACCTCATCATCCCCTGTGTGCTCATCACCTCGCTAGCCATCCTTGTCTTCTACCTGCCATCCGACTGTGGCGAGAAGATGACGTTGTGCATCTCAGTGCTGCTGGCGCTCACGGTCTTCCTGCTGCTCATCTCCAAGATCGTGCCTCCCACCTCCCTCGACGTGCCGCTCGTCGGCAAGTACCTCATGTTCACCATGGTGCTTGTCACCTTCTCCATCGTCACCAGCGTGTGCGTGCTCAACGTGCACCACCGCTCGCCCACCACGCACACCATGGCGCCCTGGGTGAAGGTCGTCTTCCTGGAGAAGCTGCCCGCGCTGCTCTTCATGCAGCAGCCACGCCATCATTGCGCCCGTCAGCGCCTGCGCCTGCGGCGACGCCAGCGTGAGCGCGAGGGCGCTGGAGCCCTCTTCTTCCGCGAAGCCCCAGGGGCCGACTCCTGCACGTGCTTCGTCAACCGCGCGTCGGTGCAGGGGTTGGCCGGGGCCTTCGGGGCTGAGCCTGCACCAGTGGCGGGCCCCGGGCGCTCAGGGGAGCCGTGTGGCTGTGGCCTCCGGGAGGCGGTGGACGGCGTGCGCTTCATCGCAGACCACATGCGGAGCGAGGACGATGACCAGAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000160716-CHRNB2:NM_000748:4
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=0.006
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.5=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(54.4=34.5),PF0293211=Neur_chan_memb=PU(86.1=63.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGTTCGGCTCCCTTCCAAAC
R:
TACGTAGAGTCGTCGGGGTTC
Band lengths:
352-1173
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)