HsaEX0015320 @ hg19
Exon Skipping
Gene
ENSG00000174343 | CHRNA9
Description
cholinergic receptor, nicotinic, alpha 9 (neuronal) [Source:HGNC Symbol;Acc:14079]
Coordinates
chr4:40339227-40350156:+
Coord C1 exon
chr4:40339227-40339381
Coord A exon
chr4:40340069-40340258
Coord C2 exon
chr4:40349804-40350156
Length
190 bp
Sequences
Splice sites
3' ss Seq
TCAATATGTGAATTTTTCAGGGA
3' ss Score
7.76
5' ss Seq
CGGGTAGGT
5' ss Score
8.53
Exon sequences
Seq C1 exon
GATGAAAGAAACCAAATTCTGACTGCTTATTTGTGGATCCGCCAAATCTGGCACGATGCCTATCTCACGTGGGACCGAGATCAGTACGATGGCCTAGACTCCATCAGGATCCCCAGTGACCTCGTGTGGAGGCCAGACATCGTCTTATATAACAA
Seq A exon
GGACACAATTCAACTCTTAACAGTGACACTCACCATCCAAGATCATGTATCAATAATTAATTAAACCGGAATGGGCCATCTAGAAACTGACCTGTGGATTTGGGGCTTTGTGTGGAGTGGAGGATGAACCAGTTTACGGGATACAAAGTGACGTTTTCCCGGTCTCAGAGCAAGGGGCATTGTATAACGG
Seq C2 exon
GATCCAATCCAGAATACCACATTATATTTAGCCAAAATATACTTTTCGGGGAAAAACTTGTAAGGAAGACTTCAAAAATATGCATCCAAATGTTAACAGAAATGTACCAATTAAGGCTCTTTGGTTGTAAGCATCAGAAACTGACTTTGGCAACCTTGTGAAATAGGAATTTGTTAGAAGGATGTGGCACATCTCATTGAATTAAAGGAAAAAGTAAACAACCAGCTCTTGGAAAGGACAGAACCAAGGCTGCTCTAGTGTTCAAGGCAGGAGGGACTGTCTGTTTTTTTTCAGCCATCACTAGGGTGATGCTTTTGGTCTCTGGATCACTCTGCTTAAGATCTAAACTCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000174343-'3-5,'3-4,4-5
Average complexity
C2
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=NA
Domain overlap (PFAM):
C1:
PF039817=Ubiq_cyt_C_chap=PD(22.9=36.5),PF0293118=Neur_chan_LBD=FE(46.8=100)
A:
PF0293118=Neur_chan_LBD=PD(15.6=77.3)
C2:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGGACCGAGATCAGTACGA
R:
TCACAAGGTTGCCAAAGTCAGT
Band lengths:
248-438
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- 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)