BtaALTD0019213-2/3 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30120058-30123356:+
Coord C1 exon
chr2:30120058-30120396
Coord A exon
chr2:30120397-30120429
Coord C2 exon
chr2:30123227-30123356
Length
33 bp
Sequences
Splice sites
5' ss Seq
AGCGTAAGG
5' ss Score
5.87
3' ss Seq
ATCATCTTTTTTTTTTTCAGGGT
3' ss Score
11.86
Exon sequences
Seq C1 exon
TCACCACTGAGCATCCGTGGCTCCTTGTTTTCTGCAAGGCGGAGCAGCAGAACAAGTCTTTTCAGCTTCAAAGGTCGAGGAAGAGATATTGGATCTGAGACTGAATTTGCCGACGACGAGCACAGCATCTTTGGTGACAACGAGAGCAGAAGGGGCTCCCTGTTTGTGCCCCACAGACCTCGGGAGCGGCGCAGCAGTAACATCAGCCAAGCCAGTAGGTCTCCCCCAGTGCTGCCAGTGAACGGGAAGATGCACAGCGCTGTCGACTGCAATGGCGTGGTCTCCTTGGTGGATGGACCCTCCGCCCTCATGCTACCCAATGGACAGCTCCTGCCAGAG
Seq A exon
GTGATAATAGATAAGGCAACTTCTGATGACAGC
Seq C2 exon
GGTACAACCAATCAAATACACAAGAAAAGACGTCACAGTTCTTACCTCCTTTCTGAGGATATGTTGAATGACCCCAATCTCAGACAAAGGGCAATGAGTAGGGCAAGCATATTAACAAACACTGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425-13-12,14-12,15-12-2/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.581 A=NA C2=0.136
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(52.8=100)
A:
NA
C2:
PF119333=DUF3451=PD(15.5=81.8)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTCATGCTACCCAATGGAC
R:
GCCCTTTGTCTGAGATTGGGG
Band lengths:
127-160
Functional annotations
There are 1 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.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development