HsaINT0035167 @ hg19
Intron Retention
Gene
ENSG00000138435 | CHRNA1
Description
cholinergic receptor, nicotinic, alpha 1 (muscle) [Source:HGNC Symbol;Acc:1955]
Coordinates
chr2:175614674-175618468:-
Coord C1 exon
chr2:175618231-175618468
Coord A exon
chr2:175614898-175618230
Coord C2 exon
chr2:175614674-175614897
Length
3333 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
TTTTTTTTTGGTCTTTTCAGGGG
3' ss Score
10.99
Exon sequences
Seq C1 exon
GAAAGCGACCAGCCAGACCTGAGCAACTTCATGGAGAGCGGGGAGTGGGTGATCAAGGAGTCCCGGGGCTGGAAGCACTCCGTGACCTATTCCTGCTGCCCCGACACCCCCTACCTGGACATCACCTACCACTTCGTCATGCAGCGCCTGCCCCTCTACTTCATCGTCAACGTCATCATCCCCTGCCTGCTCTTCTCCTTCTTAACTGGCCTGGTATTCTACCTGCCCACAGACTCAG
Seq A exon
GTGGGTGTGGTTGCCATGACTGCTGCTGCTGACGCTGATGGGTCTCGTGCTGCTATTTTGGGGAAGCCAGAAATAATCATGTGCTAACAAACAGGCAGATCGACCCGAACCATCATCATTAGGAGGGTGCATTTGCTGAGTGGGCGTGCGCAGTGGTGAGAGTCACTGTGAGTGGAGCTCACAGCTGGGGCAGACACCCCGAGCGGCAGGGAGTTGAACATGACCCTAGAGATGCACAGTGTAGCTTAGGCTGGTTAAAGTACATTAACCACCAATACCTATTTGCTGAATACCAACTGTGTGCCCAGAAGTGTACTGGGTAAGGCATGTGATCCCAGACACTTCTCATGCCACTTCCACGATGAAGTCACTTTCTATGTACTGACTAATCCTGGTCTTGCCCCTTTACCCACTGCTCACCACTTGAAAATAGATTTTGCATATCTTTTTTTCCAGATGGTGGCATCTTCACACACAAGACCCTACTTCCCAAGTGGCTGTTCTTTCTCACATATCAGCCTAGACAACTTACTTACCTCCTACTGAGTAATCCTATCTGTGACATAATTTTATCAAACAATAACAATCCACCAGAAAGGAGGAAAGGGTACCCATCTGCCTGCCAGCAAGTCACTATTCATAAACAACTTATGGCAGACAAGTTTGAAAAAAAGAAAGATGCTACAGACAGACCTCAAGCTTATGACAGGTAGCAATTTTTATCAAAATGACTTTAAAAAAAAAAAAACCACAAAATCTTAAATCCAACTTGCCAACTAGGAAAAAAGATTATTCATTTACTCATTCAGTGAATATTTGTTGAACAAATATGATGTGGTAGATAGACCGCAGAGAATAAGACAGAAAGTGCCTCACCCCTCAGAGTGCATGTTCCAGTGACTGCATTTGGGGTTTCATTTTTGTTTTTGTTTTGAGACCGGGTCTCACTCTGTTGCCCAGGCTGCAGTACAGTGGCATGATCACGGCTCACTGCAGCCTCAACCTCCTGAGCTCAAGTGACCCTTTCACCTCAGCCTCCTGAGTAGCTGGGACTACAGGCATGTGCCACCACACTCGGCTAATTTTTGTATTTTTTGTAGAAACGGGGTTGCACCATGTTGCCGAGGCCAGTCTCGAACTCCTGGGCTCAAAGATCTGCCTACCTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGTGCCTGCCCTGCACTTGTTTTTAAACAAATAATCACAAACACAATTCTTTCAACTTTCTAATCAAATGAAACTTTTTTACATTAAAAAAATAAATAAATAGAGATGGAGTCTTGCTATGTTGCCCAGGCTAGTCTCAGACTCCTGGCCTCAAGTGATCCCCCTGCCTTGGCCTCCCGGGGTGTTAGGATTACAGGCATGATCCACCGCACCAGGCCCTCAAATGAAACTTTTTAAAATAAAAACACTGTCGGGGCATTATGGGAACTAACAAGAGTCTCTATAAACGTTAAATGATTTGTGCTTGAAAAGTGCTTAGGGGCCAGATGCAGTGGCTCACACCTGTAATCCCAGCACTTTCGGAGGCCAAGGCGGATGGATCACTTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCCATCTCTATTAAAAATACAAAAAATTAGCCAGGTGTGGTGGCACGTGCCTGTAATCCCAATTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCTGGAGGCGGAGGTTGCAGTGAGCTGAGATGGCACCACTGAACTCCAGCCTGGGCAACAGAGTGAGACTCCCTCACAAAAAAAAAAAGAAGAAAAAAAGAAAGAAAAGAAAGAAAGAAAAAAGAAAAGCACTTAGCACAAAAATTATGCTTGATAAATGTTGGCTATTATTATTATCATTATTATTAATCAACAAATTTTATATAAGTGGACAAATATTTTGTATTTGTAATTGTATTCTTTTTCACTTTGAAAGGTTTTCCTACCCACCAGGTAGAATTGACAATTTCTTGTTTGTTTCCACTCTTTATCGTATACATACATACATATTCTATATATATTCTAGCATCCGGAAGCAGCCAGTAGGGGACAGCTTCATCATTGAAAGCAGGGTAACACAAGGGTTTCCAGCAGCACCAACAGCAAGGCCAGCCCAGGGAAAGTCCCTCCCAGAGCTTCTCTGCTGCACCTAAGGTGGTCAAGCCTCACAAAACTACCTCAGTGCCATTCGGCCCCTGACCTTCCTGCTGCCAAGTTTGCCCAGCCAAAACTCTCCTGAGATCAAAGGGCCTGCAGAAAAGAGGTGGGGGCTGGGGAAATCCCTGCTCCCTTAGTATGCAAAAAAAACAAAACAAGAAATAAGTGAGAAGACAAACTTCCTCTTATATGAAAATGAGACAGCGAGTGGTGTGAAACCACTGTATCAGAAGATCACTCAGGACGTCAAGGAGAACTCCTTAGCCTTCCGGATTTTGTCCTTTTCTTGGGTTTTGGTCTTACAGCTTGCTCCCTCAATAACAGAAAGATATGTGTACTTCTGGGCTGCCCATTCATCTGCTGGGTAAGAAATAGGCCAGGGGTGGTTCCGTTTTATGAGGTTTAATGCATCCTGCTGCAGAAGGGAAATGCCACACCGAGTCCAGCTTGTCCACCCAGAACTCCTTTCAGTTCCCTGGGTTCCACCAAGAATCAGAAATCTGGAGCATGAGATGAAATATTGTTCCGTTTTCTGCTTGGCAGCCTCTAATGGAAATGCTTGCCACTGGCTGCTGTCAGAAAAGTTAAGGTATGGTGGTTACATAGGAAATTCTGCAGAAAAAAATGCTTTGAGATTTCCCAGAATAATGCTTTGAGAACATGTCAGTCACATTCCTCTTACCCTTGGGTTTCAGTGGTGAATTAGTTTGCTTGGGCTGCCACACAAAACACCATAGGCTGTGAGGCTTAGATAACAGAAATGTAATTTCTCACAGTTCTGGAGACTGGAATTCCAAGATCAAGGTGCCAGTAGAGTTGGTTTCTTGTGAGGCCTCTCTCGGTTTGTAATGGCCATCTTCTTCCTGTGTCCCATGGCCTTCCGTCTATGCATCTGTGTCCTAATTCCTCTCCTTATAAGGACACTAGTCATACTTGATTACTCACTACCCCATATCACCTCGTTTTCATTTAATTACCTCCTTAAAGTCCCTGTCTTCAAATACAGTCACATTCTTAGGTCCCAGGACTCAGGACTTCCACATATAAATGGTGGGGTGGGAGGAACACTGCAGCCCAACCCAGATGGGTAGTTGTGGGATTTTTTTTTTTTTTTTTGGTCTTTTCAG
Seq C2 exon
GGGAGAAGATGACTCTGAGCATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAGCTGATCCCCTCCACGTCCAGTGCTGTGCCCTTGATTGGAAAATACATGCTGTTCACCATGGTGTTCGTCATTGCCTCCATCATCATCACTGTCATCGTCATCAACACACACCACCGCTCACCCAGCACCCATGTCATGCCCAACTGGGTGCGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138435-CHRNA1:NM_000079:6
Average complexity
IR-C
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(31.2=62.5),PF0293211=Neur_chan_memb=PU(15.3=27.5)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(73.3=100),PF0293211=Neur_chan_memb=PU(0.1=0.0)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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)