HsaALTD0005699-1/3 @ hg19
Alternative 5'ss
Gene
ENSG00000169432 | SCN9A
Description
sodium channel, voltage-gated, type IX, alpha subunit [Source:HGNC Symbol;Acc:10597]
Coordinates
chr2:167138189-167141158:-
Coord C1 exon
chr2:167141121-167141158
Coord A exon
NA
Coord C2 exon
chr2:167138189-167138318
Length
0 bp
Sequences
Splice sites
5' ss Seq
CCAGTAGGT
5' ss Score
5.41
3' ss Seq
TTAATTGATTTTTTTTTTAGGGC
3' ss Score
9.8
Exon sequences
Seq C1 exon
ACCCCAGGAGCGACGCAGCAGTAACATCAGCCAAGCCA
Seq A exon
NA
Seq C2 exon
GGCACGACCAATCAAATACACAAGAAAAGGCGTTGTAGTTCCTATCTCCTTTCAGAGGATATGCTGAATGATCCCAACCTCAGACAGAGAGCAATGAGTAGAGCAAGCATATTAACAAACACTGTGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169432-18-21,19-21,20-21-1/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence exclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.597 A=NA C2=0.093
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(50.5=100)
A:
NA
C2:
PF119333=DUF3451=PD(15.5=81.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGAGCGACGCAGCAGTAA
R:
TCCACAGTGTTTGTTAATATGCTTGC
Band lengths:
162-287
Functional annotations
There are 1 annotated functions for this event
PMID: 22911851
This event
In conditions where the intrinsic properties of the Na(V)1.7 splice variants were similar when expressed alone, co-expression of beta1 subunits had different effects on channel availability that were determined by splicing at either site in the alpha subunit. The length of exon 11 regulated how far beta1 subunits depolarised voltage-dependence of inactivation (P_=_0.00012). The results could have a significant impact on channel availability, for example with the long version of exon 11, the co-expression of beta1 subunits could lead to nearly twice as large an increase in channel availability compared to channels containing the short version. These data suggest that splicing can change the way that Na(V) channels interact with beta subunits. Because splicing is conserved, its unexpected role in regulating the functional impact of beta subunits may apply to multiple voltage-gated sodium channels, and the full repertoire of beta subunit function may depend on splicing in alpha subunits.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
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)