GgaEX1051180 @ galGal4
Exon Skipping
Gene
ENSGALG00000006112 | SCN5A
Description
sodium channel, voltage gated, type V alpha subunit [Source:HGNC Symbol;Acc:HGNC:10593]
Coordinates
chr2:5597359-5606377:+
Coord C1 exon
chr2:5597359-5597640
Coord A exon
chr2:5605233-5605286
Coord C2 exon
chr2:5606240-5606377
Length
54 bp
Sequences
Splice sites
3' ss Seq
ATTTTGTGGTTTCTTTTCAGGCC
3' ss Score
10.13
5' ss Seq
GAGGTAGGT
5' ss Score
9.65
Exon sequences
Seq C1 exon
GTGGTGGTCAATGCCCTTGTGGGAGCCATCCCTTCCATCATGAACGTTCTGCTCGTCTGCCTCATCTTCTGGCTCATCTTTAGCATCATGGGAGTCAACCTGTTTGCTGGGAAGTTTGGGAAGTGCATTAATAAGACAGAAGGAGATATGCCTTTAGACTCTAAAATTATTAACAACATGACTGACTGCATACTCTATAATGTTTCTGGCACATTTTACTGGACAAAAGTTAAAGTTAACTTTGACAACGTTGGCGCTGGGTACCTGGCTCTCCTGCAGGTG
Seq A exon
GCCACATTTAAAGGTTGGATGGATATTATGTATGCAGCAGTGGATTCACGAGAG
Seq C2 exon
TGTGAGGAGCAGCCTGAATGGGAATGTAATTTATACATGTACCTGTACTTTGTGATTTTCATCATCTTCGGGTCTTTCTTCACACTGAACCTCTTCATTGGTGTCATCATTGACAATTTCAACCAACAGAAGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006112-'28-35,'28-34,29-35
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(40.6=100)
A:
PF0052026=Ion_trans=FE(7.4=100)
C2:
PF0052026=Ion_trans=PD(15.3=76.1)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Primers PCR
Suggestions for RT-PCR validation
F:
TAACTTTGACAACGTTGGCGC
R:
TCAGTGTGAAGAAAGACCCGA
Band lengths:
134-188
Functional annotations
There are 1 annotated functions for this event
PMID: 20398673
HsaEX0056554 encodes 18 amino acids in the D3 pore region. Isoforms lacking HsaEX0056554 were tested by exogenous expression in Xenopus oocytes and HEK293 cells. Electrophysiological recordings of these cells suggest that the isoform is non-functional. Skipping this exon is speculated to be relevant for limiting Nav1.5 sodium currents in several tissues, including brain.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]