HsaINT0035178 @ hg19
Intron Retention
Gene
ENSG00000120903 | CHRNA2
Description
cholinergic receptor, nicotinic, alpha 2 (neuronal) [Source:HGNC Symbol;Acc:1956]
Coordinates
chr8:27326852-27327498:-
Coord C1 exon
chr8:27327278-27327498
Coord A exon
chr8:27326897-27327277
Coord C2 exon
chr8:27326852-27326896
Length
381 bp
Sequences
Splice sites
5' ss Seq
GTGGTGCGC
5' ss Score
4.59
3' ss Seq
TCTGTCTCTCTCTGGGCCAGGAT
3' ss Score
8.87
Exon sequences
Seq C1 exon
GTGGAGAGGAAGCTAAGCGCCCACCTCCCAGGGCTCCTGGAGACCCACTCTCCTCTCCCAGTCCCACGGCATTGCCGCAGGGAGGCTCGCATACCGAGACTGAGGACCGGCTCTTCAAACACCTCTTCCGGGGCTACAACCGCTGGGCGCGCCCGGTGCCCAACACTTCAGACGTGGTGATTGTGCGCTTTGGACTGTCCATCGCTCAGCTCATCGATGTG
Seq A exon
GTGCGCCTGTCTTCCCACCGCTGGCCCGAGGAAGGAGATCCCAGACCACCCACCGCTTTCCCCCTGCTCCTTCCTCTACCCCAGCCCTGCCCTCACGCACAGCAGTGACTTGGGGTGGGGTTGGGGATGGCTCTTCCCAGGGCGGCTACGCTCTCCCCTCTCCCAGCTCTGGAGCTCCCTCCTAGGAGGGCATTGATTGGCAGCAGTGCCTGTGTGACCCTGGAGAATCTGAGTAAGGGTGGCAGGTTTCAGAGTGGGTGGCGGGCGGGCTGGGCTTGGGGTGTCCTATCAGAGGGTCTGAAAACAGCCCATCCCACTCCACCCTGTCTTCTGGGGCTGGGCCCACCCCTTTAATTGCTCCTCTGTCTCTCTCTGGGCCAG
Seq C2 exon
GATGAGAAGAACCAAATGATGACCACCAACGTCTGGCTAAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120903-CHRNA2:NM_000742:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.429 A=NA C2=0.095
Domain overlap (PFAM):
C1:
PF0315410=Atrophin-1=PD(93.2=74.3),PF0293118=Neur_chan_LBD=PU(18.8=52.7)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(14.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGAGAGGAAGCTAAGCGC
R:
CCAGACGTTGGTGGTCATCAT
Band lengths:
257-638
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
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)