HsaINT0035165 @ hg19
Intron Retention
Gene
ENSG00000138435 | CHRNA1
Description
cholinergic receptor, nicotinic, alpha 1 (muscle) [Source:HGNC Symbol;Acc:1955]
Coordinates
chr2:175618947-175622403:-
Coord C1 exon
chr2:175622294-175622403
Coord A exon
chr2:175619143-175622293
Coord C2 exon
chr2:175618947-175619142
Length
3151 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGC
5' ss Score
6.39
3' ss Seq
CTCTTTTATCCCAATTGTAGTGC
3' ss Score
7.44
Exon sequences
Seq C1 exon
CAATGGGTGGATTACAACCTAAAATGGAATCCAGATGACTATGGCGGTGTGAAAAAAATTCACATTCCTTCAGAAAAGATCTGGCGCCCAGACCTTGTTCTCTATAACAA
Seq A exon
GTGAGCAAACTGCATGGGTGGCGGAGGGTGCTCCTGGGGCAGGTGGAATAAAGTGCCCTAATAGAAGGGCTGCGCGCTCGGAATGCTTCTCACCACTGCTAATGTTAAATCACCCAGGATGGTGGCTCACACCTGTAAACTCAGCACTTTGGGAGGCCAAGGTGGGAGGATTGCTTGAGGCCAGGAGTTTGAGATCAGCCTGGGCAACATAGCAAGACAACATCTCTACAAAATTAAAAAAAAAAATCACTCTAAACCAAGAGCCAAGTTGACGGGCTAGGGGTGCCATATGGTGTCTCATGACTTAAAGAGAAGGGATTACTGCGGCCAAATTGAATCCAGGCTGAGGGTGGGGGACATTTGATCCCTGAGAGCCCCTGAAGCATGTGTGGCAACTTTCCAAGGCACCCAAACGTCCTATCGCTGAATTCCTTGCAATCTAGTGTCTTCCCTACCAAATATTTCTGAGCCTCCTAGGGTTGTCACTCATCACATCCTGAACACCTTCTCGACATCCACTGCTGCTGTTGGCCTGGGATGCCTTCACTGCCCATCCACTGGGCCCCACGACAGACTGCATGTTGTGAAATTATAATATTATTCAAGACGTTCTGGTCTAATGACACGTTCATTAGCATACGCCCTTCATTTGTCAGGAAATGCTCGTTTCAAAAAGCATCCTTCCCAGGCAGGAGCATGCAACACCGGCCGGGAGGATTTATGGTCTGACATTATACAACATGTGTCGGGGGTCCACAAGCTGTGTGTCCTAGCAGACTTAGGGAAGGTGACAGGGCTAGTGGATGAAAACGATACCTTTTAAGGCGGGCCTTTTCAAGCTTTGATTTTCTGCCACACGTCATCCAATTATACCTGGGGTTCAAGCTTGAGCCAAATTATCCGATCATTTGTGTAATCTTTTTGGACAAATGGGCTGATGAAGTATCTTTCAGTTTCTCTTCCAGTAGGAATCTGAGAAGAGCAATTAAAATCCTTTGGTTCTTTTGCCAAACTCACTCAGGATCACCCTGGTGAGGAGAGAACACTGTTTTGTTGCTTATTGGGAGAGACTAAGACAACCCTATGACTCTCTGCCCTTTGGGGCTGCTTTGGGTGGGTCCAATGCCACATAGTTTTCCAGGTAAAGAGCCCACTTCAGGCCCAAGGAAAAATCAATGGGAAGAAAACCTCTTGATTTATGACATGAGGGACCAACATATGCCATGATGTCCCTGAAATCCCACTGAGACAGACCTCATCCTGCCCATTCAACACTTATTCTAACACCCTGCCCTCTGCTAAATCCCTTGAACAGACTGCTGTTTACGGGAAGAGTAAGTAGTCCACTGAATAAGGCCGGCAGAAATGGCTTATTTTGTTTTTTTAGAACCTCCCATGGTTTCTGTCTTTTTAAAAATAATAAATCATTGCCAACATTTGAAAACCAAGAAACATCACATTAAAATCTATTTTTTAGCCTCTCTAGAAAAATCCAACATTTAAACTTCCAGATTTTTTTTTTTTTTTTTGAGACAAGGTCTCTGCTCCATTGCTCAGGCTGGAGTGTTGTGGTGTGATCATAGCTCATTGCAACCTTGAACTCTGGGGCTTGAGCAATCCTCTGCCTCAACCTCCCAGGTAGCTGGTACTACTGGTGTGTACCACCATGCCTCGCTAATTTTTAAAGAAAATTTAGTAGAGATGAGGTCTCGCTGTTGGCCAGGCTGGTCTCAAACTCATGGACTCAAGCGATCTTCCTGCCTTAGTCTTCCAAAGTGCTGGGATTACAGGCATGAGCCACTGTACCTGGCAAAGTCTGGCAATTTTTGATTTAAAAAAATCTACGTTTCACTGGGCGCAATGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCAGATCACAAGGTCAGGAGATCAAGACCATCCTGGCTAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCTGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGCTGAGGCAGGAGAATGGTGGGAACCCAGGAGACAGAGCTTGCAGTGAGCCGATATCACGCCACTGCACTCCAGCCTGGGCAACAGAGGGAGACTCCATCTCAAAAAAAAAAAAGAAAAAAAATCTAAGTTTCCAGCTTCCGAGGAAGAATCCAAATCTGGCAAGATTGGGCCTTCATTCCCACATGGGCGCCTCAGGGGACACTGCAAGGTGGCACCTTCCTGACAGGAGAGAGGGGCGCTCTGTTCAGCAGTGTCAGCCTGCACTCATTCCTCACCTGCCTGGCCCTGGAGATATCTGAGTTTGTGAGTCCACCCCAATGAGTTCTAAATCGTTCTTTAAAAAGTAGTAGGCCAGTCAGGCACGGTGGCTCACTCCTGTAATCCTAGCACTTTGAGAGGCCAAGGCAGGCGGATCACTTGAGGTCAGGAATTCAGGGCCAGCCTGGTCAACATGGTGAAACCTAGTTTCTATTAAAAATACAAAAATTAGCTGGGTGTTTGGTGGGTGCCTGTAATCTCAGCTACCTGGGAGGCTGAGGCAGGAGAATTGCTTGAGCCCGGGAGGTGGAGGTTGCTGTGAGCCAAGATTGCACCATTGCACTCCAGCCTGGGTGACAAAGCGAGATTCCATCTCAAAAAAAAAAAAAAAAAAAAAGAGTAGTAGGCCCCTTCCCTAACCTGCTTGTCGCAGTAATGAGTCGCTGGAGGTGTTTTATGTAAAATTCCTGTGTTTTTTTTCCCCAACATAGTACATCAGGGAGGTGATAGATGAAGATTAACATTACAAATACTTGTGAGGGCTGGAAAAATAATCTGGGATGCAGTGGACCCATGTTACCTGTTATTTCTTTAAAACTGTGGGTTCCCACATTCTTTCCCAGATACTCAGATTCAGGGTTTACTTAGAGGGTGTGCAGAACTCTGTATTTTTAACAAGCACCCCAGTGATTCTTATTATCAAATATGGGGAACATTGCAATAGATAAAAAGTGACGCTGCCCGAAACAGAGCTTCTATAATTAGCACCTGAATAATTAACAGCTGTCTCCTGTTAACGTCCCCAAGCAGAATGGAAGGCTCATCTGTCACTTGGAGCCATTTTCCTCTTTTATCCCAATTGTAG
Seq C2 exon
TGCAGATGGTGACTTTGCTATTGTCAAGTTCACCAAAGTGCTCCTGCAGTACACTGGCCACATCACGTGGACACCTCCAGCCATCTTTAAAAGCTACTGTGAGATCATCGTCACCCACTTTCCCTTTGATGAACAGAACTGCAGCATGAAGCTGGGCACCTGGACCTACGACGGCTCTGTCGTGGCCATCAACCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138435-CHRNA1:NM_000079:4
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=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(22.5=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(0.1=0.0),PF0293118=Neur_chan_LBD=FE(26.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)