HsaINT0035166 @ hg19
Intron Retention
Gene
ENSG00000138435 | CHRNA1
Description
cholinergic receptor, nicotinic, alpha 1 (muscle) [Source:HGNC Symbol;Acc:1955]
Coordinates
chr2:175618231-175619142:-
Coord C1 exon
chr2:175618947-175619142
Coord A exon
chr2:175618469-175618946
Coord C2 exon
chr2:175618231-175618468
Length
478 bp
Sequences
Splice sites
5' ss Seq
CCGGTAGGT
5' ss Score
9.39
3' ss Seq
AACCTCACTTCCTTTCTCAGGAA
3' ss Score
8.72
Exon sequences
Seq C1 exon
TGCAGATGGTGACTTTGCTATTGTCAAGTTCACCAAAGTGCTCCTGCAGTACACTGGCCACATCACGTGGACACCTCCAGCCATCTTTAAAAGCTACTGTGAGATCATCGTCACCCACTTTCCCTTTGATGAACAGAACTGCAGCATGAAGCTGGGCACCTGGACCTACGACGGCTCTGTCGTGGCCATCAACCCG
Seq A exon
GTAGGTGGTGGCCACATATGATAAGGGTGGTTTCAGGAAAATTGTGATTCGGGTCTCCAACTTTTCCTTGGACAATCATAGGCTCTCAGTACCAGTTAGAACTTAGGAATCATCTAGTTTGATGGTTCAAGTTGATTGGGAAGGGAGAACTAAATGGGAGCTTAAATTAATTTGCTACACCCAGGCTCAGTCTCAAGAATTCTGATGTAATGGGCCTGGGGTGGCGGTAGGGCATCAATATGTTTTAAAGCTCCCAGGTGACTTGAATGTGTAGCCAAAATGGAGAATGCTACTAGTCCAAACCCCCTTATGTCATAGGAAAGGCATCTAAGACCCCAAAGCAGTAGTGTCCCACAGTCCCTCCTGGGTGTGTGACCCACAGAGCTGGAATCTGTGGCCTTGTCACTGCTGATTACAAAACGCTGCCCCTCATCAGGGTGACCTGCCTGGGATTTCCAAACCTCACTTCCTTTCTCAG
Seq C2 exon
GAAAGCGACCAGCCAGACCTGAGCAACTTCATGGAGAGCGGGGAGTGGGTGATCAAGGAGTCCCGGGGCTGGAAGCACTCCGTGACCTATTCCTGCTGCCCCGACACCCCCTACCTGGACATCACCTACCACTTCGTCATGCAGCGCCTGCCCCTCTACTTCATCGTCAACGTCATCATCCCCTGCCTGCTCTTCTCCTTCTTAACTGGCCTGGTATTCTACCTGCCCACAGACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138435-CHRNA1:NM_000079:5
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=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(0.1=0.0),PF0293118=Neur_chan_LBD=FE(26.0=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(31.2=62.5),PF0293211=Neur_chan_memb=PU(15.3=27.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTTCACCAAAGTGCTCCTGC
R:
CAGGGGATGATGACGTTGACG
Band lengths:
355-833
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)