GgaEX1051194 @ galGal4
Exon Skipping
Gene
ENSGALG00000006060 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chrLGE22C19W28_E50C23:104511-106993:-
Coord C1 exon
chrLGE22C19W28_E50C23:106865-106993
Coord A exon
chrLGE22C19W28_E50C23:104801-104892
Coord C2 exon
chrLGE22C19W28_E50C23:104511-104602
Length
92 bp
Sequences
Splice sites
3' ss Seq
ACTCTGGTTTAATTCTGCAGGTA
3' ss Score
8.46
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
Exon sequences
Seq C1 exon
GTATACATTCACTGGTATTTATACATTTGAATCACTTGTGAAAATTATTGCAAGAGGTTTCTGTATAGATGGCTTTACTTTCCTACGAGACCCATGGAACTGGCTAGATTTCAGTGTGATCATGATGGC
Seq A exon
GTATATAACAGAGTTTGTAAACCTAGGCAATGTTTCAGCTCTGCGCACTTTCAGGGTTCTGAGAGCTTTGAAAACTATTTCTGTAATTCCAG
Seq C2 exon
ATATGTCACAGAGTTTGTGGACCTGGGGAATGTCTCAGCATTGAGAACTTTCAGAGTTCTCCGAGCTTTGAAAACTATCTCTGTAATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060-'6-6,'6-5,7-6
Average complexity
C2
Mappability confidence:
100%=100=100%
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(17.1=100)
A:
PF0052026=Ion_trans=FE(12.4=100)
C2:
PF0052026=Ion_trans=PD(14.4=86.7)
Main Inclusion Isoform:
ENSGALT00000017935fB11735
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACTTGTGAAAATTATTGCAAGAGGT
R:
TCAAAGCTCGGAGAACTCTGA
Band lengths:
168-260
Functional annotations
There are 1 annotated functions for this event
PMID: 15664175
Mutually exclusive exons 5A and 5N alter voltage-dependent gating and/or interactions with a blocking subunit. From Vuong et al, Nat Rev Neurosci 2016.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]