HsaEX0056554 @ hg38
Exon Skipping
Gene
ENSG00000183873 | SCN5A
Description
sodium voltage-gated channel alpha subunit 5 [Source:HGNC Symbol;Acc:HGNC:10593]
Coordinates
chr3:38556441-38560428:-
Coord C1 exon
chr3:38560147-38560428
Coord A exon
chr3:38557231-38557284
Coord C2 exon
chr3:38556441-38556578
Length
54 bp
Sequences
Splice sites
3' ss Seq
ATCTTGTCTTTTCCTCCCAGGCA
3' ss Score
9.83
5' ss Seq
GGGGTAGGT
5' ss Score
6.59
Exon sequences
Seq C1 exon
GTGGTGGTCAATGCCCTGGTGGGCGCCATCCCGTCCATCATGAACGTCCTCCTCGTCTGCCTCATCTTCTGGCTCATCTTCAGCATCATGGGCGTGAACCTCTTTGCGGGGAAGTTTGGGAGGTGCATCAACCAGACAGAGGGAGACTTGCCTTTGAACTACACCATCGTGAACAACAAGAGCCAGTGTGAGTCCTTGAACTTGACCGGAGAATTGTACTGGACCAAGGTGAAAGTCAACTTTGACAACGTGGGGGCCGGGTACCTGGCCCTTCTGCAGGTG
Seq A exon
GCAACATTTAAAGGCTGGATGGACATTATGTATGCAGCTGTGGACTCCAGGGGG
Seq C2 exon
TATGAAGAGCAGCCTCAGTGGGAATACAACCTCTACATGTACATCTATTTTGTCATTTTCATCATCTTTGGGTCTTTCTTCACCCTGAACCTCTTTATTGGTGTCATCATTGACAACTTCAACCAACAGAAGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183873_CASSETTE1
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)
Other Inclusion Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAAGAGCCAGTGTGAGTCCT
R:
TGTATTCCCACTGAGGCTGCT
Band lengths:
135-189
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]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development