HsaINT0035213 @ hg19
Intron Retention
Gene
ENSG00000174343 | CHRNA9
Description
cholinergic receptor, nicotinic, alpha 9 (neuronal) [Source:HGNC Symbol;Acc:14079]
Coordinates
chr4:40350899-40356973:+
Coord C1 exon
chr4:40350899-40351431
Coord A exon
chr4:40351432-40355995
Coord C2 exon
chr4:40355996-40356973
Length
4564 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
3' ss Seq
GGTTGTTATTTTAATTCCAGGTA
3' ss Score
6.99
Exon sequences
Seq C1 exon
GGCTGATGATGAATCTTCAGAGCCTGTGAACACCAATGTGGTCCTGCGGTATGATGGGCTGATCACCTGGGATGCACCGGCCATCACCAAAAGCTCCTGTGTGGTGGATGTCACCTACTTCCCTTTTGACAACCAGCAGTGCAACCTGACTTTTGGTTCCTGGACCTACAATGGCAATCAGGTGGACATATTCAACGCCTTGGACAGCGGAGATCTCTCTGACTTCATTGAAGATGTGGAATGGGAGGTCCATGGCATGCCCGCTGTGAAGAATGTGATCTCCTATGGCTGCTGCTCTGAGCCTTACCCGGATGTCACATTCACCCTCCTTCTGAAGAGGAGGTCCTCGTTCTATATCGTCAACCTCCTCATCCCATGCGTCCTCATATCTTTTCTGGCTCCTCTGAGTTTTTATCTCCCAGCAGCCTCCGGAGAAAAGGTCTCCCTGGGAGTGACCATCCTGTTGGCCATGACTGTATTTCAGCTAATGGTGGCAGAAATCATGCCGGCCTCAGAAAATGTGCCCCTGATAG
Seq A exon
GTGAGTCCAAGTGTCTTCCACTTCAAGCCCAGCTTTGTAGTGCCTGGGGTCATGCCTTTAAGGTTGTGTGTGTGCCTTTAAACTTGAAAAAATGGAGCCAATTTCGACTCAATACAGACTGTCTCAAATTTTTCTGGTGGTTGCAGTTAGCATCTTTCAATATAGATGAGCCTTTTGCAATCAAAACTGGTCTTATGGTCTCTGGGTTTACACGAAAGAGCAATGAAAGACATTATACTTTAGAGCAGTAGTTCTCAAAGTGGTGGTCCCCAGATGCACAGCATCGGCATCCCCTGGGAACTTATAGAAACACAAAACCTCAGGGCCCACCGGAAGCCTACTGAATCAGACATTCTGGAGATAAGGCCCTGGCATCCTGTTTTAACAAGGCTTATGGGTGATTCTGATGCATTTTCTGTTGAAGTCTGAAATCCACTGACCCAGAGGTTAAGACCTGATTTTGAAGTCAAAGAAACTTGCATTTGAACGCTGACTTCACTGCTCACTCCTTGATCAAACAGGCAAGTTACTTGTTCTCTTAGTCTCTGCTTCATCATCTGGAAAATTTGTGTGATTGCTTCCTTCTGTGTCATTGCTTAGTGCACACCCTGGCATATGGTAAGTACTGAGTAAACAGTGACTACTGTTATCATTTCACGTGACAAGGGCTTTCTTCTTGGGAAGAGTGGCAAACATGGCAGAAAGATGTGCTTTTTAAGCCTGACATCTACCCTTAACAGAAAAATCTCATCTTCACTGGGTATAATAGCAGTGGGAGAGTGTATTAAAATGCAAGTTCCTACACCCAGAGAGTTTGATTTAGCAACTTGGCCGAGATTTGGGAATCTGAGGTGATTCCAAAGCAGACTACATTTTCAAAAATCTGCAATAATGAAATATCCCTCCAAGGGTTGGAGTGCAGACTGAGGGTACCACCCCTGCCTCCCCTATCCTTGCCTAGCTTGTTCTGAGGGCTTTCCTATCCCCTTTAACATCTACTTTCTGCCTCCAAGGATACCCTTGAGATCCAACACCTCCATCTCGAGGAGTTGCTGTTGTAACAGATGCTTACCAGAATCAAGCTAGATCTAAGTTTGAGTTCCTTAAAGTAAGCAACAAGGAGAAATTTTAGAACACCAACGAACTTAGAGTCCAATATCAGGAGATGTTGCCTTGCCCTTTTACTCTTTACTGAGTCCAGTTACCCAATATTGAGATGATACTACAGTGGCTTCTCCATTTGGAGATATCTTCCTTTTTATGTCTCTCTTTGCAAAATACACACACACACACACACACACACACACACACACCTCTCTTTTTCAGAATTAAACACAGAAGGCTTTTCCACCTCTAATAAAAAGGAGATGTATTGGCATTTTATTACCTCTCCTGAGGCAGAAATGATTGGCAGTGATGACATCCAATCATAGCCCTGTTTGAGGAAAGATCATGGGGCGGTCCCACTCTCTTCTTGGGTAGTGACATTATACAGCAAGCTGGCACAATTTCTAAAGGCAGATGTCTCACAGGAATTGCTTGTTCTGTTTTTATGATAATATGAAATTTATCTTTTAAAAATTAAATTAAATTTGTATTTTTAAATTTTATTTTAATTTATTTTTATTATTTAAAAATGAAGGCCGGGCTTGGTAGCTCACGCCTGTAATCCTAGCACTTTGGGAGGCTGAGGCAGGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAGACCCCATCTCTATAAAAAGAATTAGCTGGGCATGGTGGTGCGTGCCTGTAATCCCAGCTACTTGGGAGGCTGAGACAGGAGAATCACTTGAACCCAGGAAGTGAAGGTTGCAGTGAGCCAAGATTGCACCACTGCACTCCAACCTGGGGGACAGTGTGAGACTTCGTCTCAAAAAAAAAAAATTGAAAAAAAATAAGAAAGATAGGGTCTCACTATGTTGGCTAGGCTGGTCTTGAACTCCTGGGCTCAAGTGATCCTCCCACCTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGCAACTGGCTGAAATTTATCTTTTTAGGAAAAGTGCCCACAGATCTCTTGAGAACATTTATTTAACAATTAAAATTTGTTATTCATAGCACCCATGGAGTGTGCTCACAATATTATAGAAATATGTTTAAGTTTTCTGCATCAAATGTAGCCCTTGATATCGGTTTCTGGCCCATGGCCTTTACCATTTTAAGAAAGGTCTCATATATTAACTCAGACAAATAAAAAAGATGATAAACATTATCAAATACTTTGTCTTCATCTATTAAGATAATCATGTGAGTTTTCTTTTACTCGTCAATGTCGTGAATTACATCAATAAGTTTTCTGATGTTGAACTCTTTTGTATAACTGGACCAAACTCCTTTCTTATGATACATTATCCTTTTAAGACACTGTTGGATTCAGTTAGCTAATATTTTGTAGAGCTTTCTCAAATATGTCGATTAGTGAAATGGCTTTAATATTTCTTTTCTTGTCACTTTTGGAATCAAGGTCAAATTGACTTCACAAAATGAACTGGACAGTTTTCCCTCTTTTTCTATTTCTGGAACAAGTTGCATAAGATGGGAACTATTTGTTTCTTGAAAGTTTGGTAAAACTCACCTATAAATTATTTTTGGGCCTGGAACATTTGGTAGGGGGATGGTATTTGATTGATTCCCATTTCTATTAAAGTGTTCTTTATTCTTGCACTAATTTTGACATCTAACATTTTTCCAGCAGTTTCATCTAGATTATCAAATATGTTATTATACAGCTATTTTTATTTTTTAAGACATAGTCTAGCTCTGTTGCCCAGACTGGAGTGCAGTGGTGTAATCTCAGCTCACTGCAACCTCCGACTCCTGGATTCAAGTGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACGTGCCAATACACCCAGCTAATGTTTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCCAACTCCTGACCTCAAGTGATCCACCCACCTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGTGCCCGACTATACAGTTATTTATAATATTGTACTATTTTATAAGTCTTTTCCATCTTCTCTCTCTCTCTTTCCCTTTCTCTATTTCTCTCTCTATCCTGTAAGTGGTCTTATCAAAAGTTTATCAATTTTATTACTCTTTTCAAAAGTTTGCTTTTGGTTTTATTCATCTTCTTGGCTTTTTGTTCTATATTTCATAAATTTGTAGCCTTATCTTAATTGTTTCCTTCCTTAATTTCACTTTTTCATCAACATGTGCTTTATATAATCACATTTTGAAGACTAATAGTGATACAGTCTCCTTTCTTACCTAATAGAATTGGCTTTCATATTAATGAGGTCTGAAGACAATTCTGAGAACTGGTCAAGTTCATTAATTGTTTGTTCGTTGAGTGTGGAAAAATTTTTCACCTCATGATCTCAGCAAACATTTCCAAACTTTTTAATTTCGAGCCAGGAACAGTGCTGAGAACTTCACATGTATCATCTCAATTACGCCTCCTCATATTCCTGCGAGTTAGATATTATTATTACACCCACCACTTTACAGAGTAGGAAACTGAGGCTTAGCAGGATTATATGCCTTGCTGAAGGCCGAAAGTCCAGGATTATATGCCTTGCTGAAGGCTGAAAGTCTAGGGAGTGATAAAGCTGGGATTTGAATCCAGGAAGTCAGATTCAAAAGTCTATACTATAGCCCGGCGCGGTGGCTCACGCCTGTAATTCTAGCATTTTGAGAGGCCGGGGTAGGCAGATCTCTCAAGTTCAGGAGTTCGAGACCAGCCTGGCCAAGATGGCGAAACCCCCTCTCTACTAAAAATACAAAAATTAGCCGGGCGTAGTGGTGGGCGCCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGCCAGAGGTTGCAGTGAGCTGAGATTGCACCACTGCACTCCAGTGTGGGTGACAGAGCGAGACTCTGTCTCAAAAAAAAAAAAAAAGTCTATACTATTAACCACTAGGGTATAACACCTCCTTAGAAAGGGTGTTTGTTTCTTTTTAAGCCAAACACAGTCATGTGCCTCATAACAATGTTTTGGTAAATGACAGACCGTGTATACAACAATGGTCCCATAAGATTATAATGTCAATTTTTACTTTATCTTTTCTATGTTTAGATACACAAATATTGACCGTTTGATAATCATGTGTACAATTGCCTGCGGTATTCAATACAGTAACATGCTGCACAGGTTTGTAGCCTAGAAGCAACAGGCTACACCATTCAACCTAGGTGTATAGAAGGCTAGACCATTTAGGTTTGTGTACATACACTCTTATGATGTTCACACAACAGCAAAATCACCTAATGACTAATACCTTTCTCAGAATGTATCCCTGTTGTTAAGTGACTCGTGGCTGTATGAGGACCATTTTAAAGCAAATTCAGTTACGGTTGTTATTTTAATTCCAG
Seq C2 exon
GTAAATACTACATAGCCACGATGGCCCTGATCACAGCCTCCACTGCGTTGACCATCATGGTGATGAATATCCACTTCTGTGGGGCCGAGGCCCGGCCGGTGCCACACTGGGCCAGGGTGGTCATCCTGAAATACATGTCCAGGGTCTTGTTTGTCTATGATGTGGGTGAAAGCTGCCTCAGCCCGCACCACAGTAGAGAGCGGGACCACCTCACGAAAGTTTATAGCAAACTCCCAGAGTCTAACCTGAAAGCAGCCAGGAACAAAGACCTTTCCAGAAAGAAGGACATGAACAAACGCTTAAAGAACGACCTGGGCTGCCAGGGTAAGAACCCTCAGGAGGCCGAGAGTTACTGTGCACAGTACAAAGTGCTGACGAGGAATATTGAGTACATCGCCAAGTGCCTCAAAGACCACAAGGCCACCAATTCCAAGGGGAGTGAATGGAAGAAGGTGGCGAAAGTCATAGACCGATTCTTCATGTGGATTTTTTTCATTATGGTGTTTGTGATGACTATTTTGATCATAGCAAGAGCGGATTAGTCACAGATATTGGCTTTGCTATCTGGGTAGAAATTAATACAATTCCCTGTGATCTATTCCAATGTTCTTCCAAGATTTTTGTTCATCTATAATTTAGGGGTTATGTTGTCTGTGCTTTTTATTTTTAGCTTCAAATGAATGTCGAAGCTATCTGCTCTGTTAAATTAAGCAGAAGAACCAAAATTTCAAGGGTAGGAAGATGGAAGAAATAGGGAAAGAGCCCTTTTATAGCCCACCGTAGTGGTGGGTGACTGGCCTCTAGTTTATATAATTATTTACCTCTTTGGCAGTACAGATAACAAAATACACTTTACTGGTAAAATTTAAAACAAAAAAGGCAAAACAAAACAAACTCATTTTCCCCTTAGTTCCCATTAAAATATGCATTTGAAAAATGAAATAGTCATATATATATTAGTGTGATTTAAGTCTCAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000174343-CHRNA9:NM_017581:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.033
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=64.2),PF0293211=Neur_chan_memb=PU(24.1=31.3)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(75.4=96.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
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)