MmuALTD0012458-1/3 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000075316 | Scn9a
Description
sodium channel, voltage-gated, type IX, alpha [Source:MGI Symbol;Acc:MGI:107636]
Coordinates
chr2:66537270-66540635:-
Coord C1 exon
chr2:66540297-66540635
Coord A exon
NA
Coord C2 exon
chr2:66537270-66537399
Length
0 bp
Sequences
Splice sites
5' ss Seq
GAGGTGATA
5' ss Score
3.13
3' ss Seq
TGATTGCCTTTTTTCCTTAGGGC
3' ss Score
10.2
Exon sequences
Seq C1 exon
TCACCACTCAGCATTCGTGGGTCCTTGTTTTCTGCCAGGCGCAGCAGCAGAACAAGTCTCTTCAGTTTTAAGGGGCGAGGAAGAGATCTGGGATCTGAAACGGAATTTGCTGATGATGAGCATAGCATTTTTGGAGACAACGAGAGCAGAAGGGGTTCACTATTTGTACCCCATAGACCCCGGGAGCGGCGCAGCAGTAACATCAGCCAGGCCAGTAGGTCCCCACCAGTGCTGCCGGTGAACGGGAAGATGCACAGTGCAGTGGACTGCAATGGCGTGGTGTCGCTTGTTGATGGACCCTCAGCCCTCATGCTCCCCAATGGACAGCTTCTTCCAGAG
Seq A exon
NA
Seq C2 exon
GGCACAACTAATCAGATGCGTAAAAAAAGGCTCTCTAGTTCTTACTTTTTGTCTGAGGACATGCTGAATGACCCACATCTCAGGCAAAGGGCCATGAGCAGAGCAAGCATTCTAACCAACACAGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075316-18-18,19-18,20-18-1/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.609 A=NA C2=0.098
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(50.7=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.3=81.8)
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCAATGGACAGCTTCTTCC
R:
CCTTTGCCTGAGATGTGGGTC
Band lengths:
115-148
Functional annotations
There are 2 annotated functions for this event
PMID: 22911851
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.
PMID: 22911851
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
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types