HsaEX0056589 @ hg38
Exon Skipping
Gene
ENSG00000169432 | SCN9A
Description
sodium voltage-gated channel alpha subunit 9 [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:166303090-166305920:-
Coord C1 exon
chr2:166305792-166305920
Coord A exon
chr2:166304238-166304329
Coord C2 exon
chr2:166303090-166303302
Length
92 bp
Sequences
Splice sites
3' ss Seq
ATTCTGATTTAATTCTACAGGTA
3' ss Score
8.93
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
Exon sequences
Seq C1 exon
GTACACTTTTACTGGAATATATACTTTTGAATCACTTGTAAAAATCCTTGCAAGAGGCTTCTGTGTAGGAGAATTCACTTTTCTTCGTGACCCGTGGAACTGGCTGGATTTTGTCGTCATTGTTTTTGC
Seq A exon
GTATTTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTATTGAGAGCTTTGAAAACTATTTCTGTAATCCCAG
Seq C2 exon
GCCTGAAGACAATTGTAGGGGCTTTGATCCAGTCAGTGAAGAAGCTTTCTGATGTCATGATCCTGACTGTGTTCTGTCTGAGTGTGTTTGCACTAATTGGACTACAGCTGTTCATGGGAAACCTGAAGCATAAATGTTTTCGAAATTCACTTGAAAATAATGAAACATTAGAAAGCATAATGAATACCCTAGAGAGTGAAGAAGACTTTAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169432-'11-16,'11-14,12-16
Average complexity
C1
Mappability confidence:
100%=100=80%
Protein Impact
ORF disruption upon sequence exclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(17.3=100)
A:
PF0052026=Ion_trans=FE(12.5=100)
C2:
PF0052026=Ion_trans=FE(28.6=100)
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTTTTCTTCGTGACCCGTGG
R:
CAGGTTTCCCATGAACAGCTGT
Band lengths:
178-270
Functional annotations
There are 1 annotated functions for this event
PMID: 22911851
[MUTEX]. 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 identity of exon 5 determined the degree to which beta1 subunits altered voltage-dependence of activation (P_=_0.027). The results could have a significant impact on channel availability. 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
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development