HsaINT0035162 @ hg19
Intron Retention
Gene
ENSG00000138435 | CHRNA1
Description
cholinergic receptor, nicotinic, alpha 1 (muscle) [Source:HGNC Symbol;Acc:1955]
Coordinates
chr2:175624216-175629200:-
Coord C1 exon
chr2:175629080-175629200
Coord A exon
chr2:175624362-175629079
Coord C2 exon
chr2:175624216-175624361
Length
4718 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
GGTGTCATCTGCTGTCTCAGCTG
3' ss Score
4.3
Exon sequences
Seq C1 exon
AGACAAGCACCCAGCCAGAGTGCCAGTGAGAAGCACAGGCCACCACTCTGCCCTGGTCCACACAAGCTCCGGTAGCCCATGGAGCCCTGGCCTCTCCTCCTGCTCTTTAGCCTTTGCTCAG
Seq A exon
GTAAGTGCTGGGGTCAGGGGTGGGGAGAGGGCTCTCCTTTGAGGCTAAAGTGCTGGAGGCCCCCAAATCAAAGTCTTGCTTCTTTGATGAGACCACAGAATGGCAGAGCCTCCCCAACCAGGGGCTGCTCTGTCAGTTTCTTCCTGATGTTAGCTTGATTGAGTTTTTGGATAAAGATTTTTAGTTTGCCTTATCTAATTAAAATAGAAACTGCCTGGTCAAAGACTTCAAGATAGACACGCATGTCTCTCCCTCCATCATGCCTGGCAGCCGACTCATCCCTCTGAACACTCGGCACCATTTGTAGGACCTGGACCACTTGTGGATCATGGTAGTGTCCGGGGGTTCATATTTAAACAACTATGGATACTTAGAACAGTGCCTTATAATCACATACAATGGAGTTAACAAGTCCCTTTACTGCTCCAGGAGAATTCTAATAATAAAGAGGACTGATTGACAGCTACATGTGCTGGAGATAGAAACCAGTTAATAATCATAACTAAACTCTCTCCACAGAGACAAATATTTTTTAATTTTTTCAAAATTTCTGAAGTTAAAAAAAATTCCATATGAATACATTCCTACCTACTTTTTTTTTTTAAGATGTTACTATATATAGGTTTGGGTTTGAATTGAAACTATAAAACCTTGCACAGCATTTGACCTGCATTCTACTCTGGAATGTGTCCTAACACAGCAGCTGAAACACCATCCTGAATCCCAGACTTCCGCTAGAGGGAAACAGGAGATGTTTGCTGATTGCTTCACATAAAAGTTTACTGGTGATATCATCCCAACTGAGAAACAAGGTGGCTGACATCCTGTGATTTTTCATTTCCAATATTGCTCTGAAAAACACAGGCCTTCTGGTCAAGAGGCAAAAAGCTTTATTATTAATTTTTTTCAATATCAGAGTTGAGTGAAAGAGCCTAAACTCAGATAAATTATATCATGTGGGATTTGGACTCTGTCCAGCCAAAGCTGGCCTGATGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCGCGCGTGCACACACATGCGTGCACGCAAAACCACAGTCACAGGAAAATTCTTAAATGATATGCTTTAATGTAAACATCCTTAAGAGATCTCTTAGGATTTTGGTTATTGCTAACCAAAAATGCATGATTAGCTATTAAAGAAGTATGTGATATGTATTTAGGTCAAATCTCGAGTTTGCTGGCATTGATTTCCATGGGTGTTTTATAGAAATTTAGAGCTAGATCAGGCAGTCCAACATCCTCAATTTTTTATTACAAGGAAACTAAAGCTGACCTGCCCAAGGTCACTTAATTTATACATTTTGGAATGTGGTCAGTTGGAGACTTGGTTTATTACATGCACAGTCAGAAAACACAGCCTGAACTAGCCAAAGGTAGCAAGAGATACAGAATCAGGTTAAGATAATAATGATCCATGGGACTAGTAACAGTTCAAAATTTCTTTTGCCCAGCCCAGGGAGCTATTTCCTACATACAAATACAAATGGAACCAGTGTGGTACAAAAGGAACACTTTGAAACTGTGGTTGAGTTTCCCTTCTTAGAATCAGTCCTTTGTAGACAAAATTGTCATTTATATCAGGGACTCTTTTCCTGTGTTAGCTTAACACAGCGTGATCTCTGTTCTATTTATACAGCACTTTTCATTTCAACTTTTTCTTTTCTTTGCCTCTGGAATCTCAAGCACTTCATTGCCGTCTTTCTTACGGCATATCACTTTCCAACTTGTTCACAGTTATTTACGTAAATGACAAATGTCAATCTCCATGAGGGTAGGAAGAAGGATTCAGTTTTGAATATCTCGAAGCTCCCAAAACAATGCTTTGCTTACAGTAAATGCTCAACAAATATTTCATGAATAAATTAATGTTACCATCATCTGAATAAAGATTACAAATATAATCTTGCTAAAAAGGGGAATTTGACATTATTTAATTTTTTATTTGCATATTTGTTTATTTACACCCTACCTTTTTACAAAAGTATTTACTGTGATTCGTTGAATCCATGAAGAACTAATCCAACTCTCCAGGCCATATGGGAGTTGGGAAGAGAATCATAGAGTTCTGACTTTGAGCCCTGTGAGTTTTCTATCACTCTACCCTGTGCTGGGGAGGAAAAAAGAAAAGAATACCAGTGAACCAATCTAAGAAATGAAGCCCTCCTTCCTTAGAAATTCCTTATGGAAGGAACAGGCACCTTGTTATTGGCTAGGGTGGGAAAGGAGGAGGTGACTGTCTCTGAAATGCTGATTATGTCTGCTTCTGTCATCCTCCCCTTCCTCTTAGTGGGCCATAGGGTTGGTCTGCATAGTTCTCCTGCTACATAATGCTGACCATCTGCTCTGCCCTCTGCTTTCTAATATGTTCTTCCTGTCAAACTGGAGTGAACAGTCATTTAAAAATAAGCAGCCCAAGGCAAGGCCAAAGCAACAGCTTCAAATTCAATGGCCAAGGTGCTCAGTAATCCATTCCAGTCTGCAACTCCACCATGGGATGGATGAGGCCCAGGATAGAAAATGCATAGAGGACAGAAGGATTATCAAGTCCCAGGGGCTCAATGGGGTGGTTGCAAAAACGGAATATTCAAACAACATATTCCCTTCAAGAGTCCTCAAATGCAGGTGGCTTTAGGGAAATGTCATGTGAAATCTCTGCGTGGTTGGGCACTGAGTGCCCTTGGAACATTTTGGGTTCAGAAAACGTGTGAAACTAGCCGGGTGAGGTGGCTCTTGCCTGTAATCCCAGCACTTTGGGAGGATGAGGTGGGTGGATGGCTTGAGCTCAGGAGTTTGAGACCAGCCTGAACAATGTGGCAAAACCCCATCTGTACAAAAAATACAAAAATTAGCTGGGTGTGGTGGTGCGCACCCAGGTAATTTTTGTATTTTTTATAGAGATGTGGTCCCAGCTGCTTGGTTGGGGGAGGCTAAGGTGGGAGGATTGCTTGAGCCTGGGAGGTCAAGGCTGCAGTGAGCTGTAATTGAGCTACTGCACTGCAGCCTCAGCAATAACCTGCGGAAAGGGGAGATCTGGTTACGTGAATGAAGGCAAATGTATCATGTGTCTACTTCCTCTCCCAGCTCTGAACACACAGTCCCCAACCCACGGAAGGCTTGAATTACAAAGATCCTTCATAAGACACTTGGGATTTGGAACACATTTTCTCATAGGAATAGTGGCACTTGCAGTTCTGAGTTTCCAGGACAGCTCACAACACACTGTTAGTACCAAGAATTAGCCCAGAAGCTCAGCACAAAATGACAGGATTCCAATCTGAGCTTTGCCCTTACTGGTCACATGACCTTGGACAAGTGGTCCAACCTCCCTGAATCTCAGGTAAGAATGTCTGCCCTCCTGCTTCATCTGTGGCTGATGAAGATTGAAAAGGGGTGTAGATAGAAAAGGGGGCCGTGGGTTCTGAGAGTATTAGATGATATTGCTCTCTATACTGAAGGAAAATGTAGTAAAGATTCCTTGGAATCGCTTATGTTCCAACTAGGAGCCCCAAACCCAGGTCAACAAAGCACAGTTTTCACTCTATTTTAACAACTTAACTGGGACATGGACCTGCCAGCAGTGATATTTTAAAAAATCGTGGTAAAATACCCATTTCATAAAATTTACCATTTTAACCACTTTAAAGTATACAATTCAGTGGCATTAAGTACATTCACATGTTATAAGACCATCACCACTATCTATTTCCAGAACGTTTTCATCATCCCAAAGGGAAACATCAAGCACATTAAGGAGTCCCACCCGATCCCTCTCTCCCCCCCAGTCCCTGGTAACTCCTGCTCTGCTTTCTGTCTGTATAGATTTACCTATTCTGGATGCTTCATGTAGATGAAATCATACAATATTTGCCCCATTGTGTCTGGCTTCTTTCACTTAGTAAAATGTTTCCAAGCTCCATCCATGTTGTACCATGTGTCAGTACATCATTCCTTTATTCCTTTTTCATGTCTGAATAATAGTTCATCGTAGGGGTATACCATAATTTGTCCATCCATTTACCTGTTGATGGACACTTGAGTTGTTTCCACCCTTTGGCTATGGTAAATAATGCTGCTCTTCTTTTGGGTGTGGACCTAGGAGTGGAATTGCTGGATCGTATGGTACCTGTGTTTAACTTGTTGAGGAACTGCCATTTTACATTCCCACCAGCAACATATGAGGTTCCAGTTTCTCTGCAACCTCCCCAACCCTTGTTATTTTCCACTTGTTAGTTATGGCCACTCTAGTGGGTTTGAACCAGCATCAATTTTGGCTGTTCATGGCATCTTGAGATCTGATGCAGCCAGTCCAAGATTTCATTACACTGCTCTGAAACACTGAGATTGGCTTTTTTGTGGGCTTTTTTTTCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTACCTGGCAAACTTGATTCAGCCAGGCTGTATGAAGGAATGTCACCTGTCCAAAGTACAAGCGTTGTGATTACCTGGCACACCCCACTGTCACCGGGTAAGGGACCACACCAGCAACTGTAATTGGAAAAACACAAGGCAATAACTGCTGCATTTGGGAGCCTTTCAACAAGGAGGCCTGTGTGCCTTCTGTTAGAAGGAACTGAGGCTTATGCCTCAGTTCCTCAGTTCCTCATGTTCATGTGTTTGGAGGGTGGGGAGAAGAATCTGACAGTGTTGGTGTCATCTGCTGTCTCAG
Seq C2 exon
CTGGCCTCGTCCTGGGCTCCGAACATGAGACCCGTCTGGTGGCAAAGCTATTTAAAGACTACAGCAGCGTGGTGCGGCCAGTGGAAGACCACCGCCAGGTCGTGGAGGTCACCGTGGGCCTGCAGCTGATACAGCTCATCAATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138435-CHRNA1:NM_000079:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(69.6=79.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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)