HsaEX0056562 @ hg19
Exon Skipping
Gene
ENSG00000136546 | SCN7A
Description
sodium channel, voltage-gated, type VII, alpha subunit [Source:HGNC Symbol;Acc:10594]
Coordinates
chr2:167288828-167298262:-
Coord C1 exon
chr2:167297906-167298262
Coord A exon
chr2:167292857-167292950
Coord C2 exon
chr2:167288828-167289262
Length
94 bp
Sequences
Splice sites
3' ss Seq
ACTGACTCACGGTTCCACAGGGC
3' ss Score
7.69
5' ss Seq
AAGGTGGGG
5' ss Score
5.87
Exon sequences
Seq C1 exon
TTAAGAATTTTCAAGTTGGGAAAGTATTGGCCAACATTCCAGATTTTGATGTGGTCTCTTAGTAACTCATGGGTGGCCCTGAAAGACTTGGTCCTGTTGTTGTTCACATTCATCTTCTTTTCTGCTGCATTCGGCATGAAGCTGTTTGGTAAGAATTATGAAGAATTTGTCTGCCACATAGACAAAGACTGTCAACTCCCACGCTGGCACATGCATGACTTTTTCCACTCCTTCCTGAATGTGTTCCGAATTCTCTGTGGAGAGTGGGTAGAGACCTTGTGGGACTGTATGGAGGTTGCAGGCCAATCCTGGTGTATTCCTTTTTACCTGATGGTCATTTTAATTGGAAATTTACTG
Seq A exon
GGCTTGGGAGGCCTCAGGAAACTTACAATCACGGTGGAAGAGGAAGCAGGCATGTCCTTCACATTGCAGCAGCAAGGAGAAGTGCAGAGTGAAG
Seq C2 exon
GTACTTTACCTGTTTCTGGCATTGGTGAGCTCATTTAGTTCATGCAAGGATGTAACAGCTGAAGAGAATAATGAAGCAAAAAATCTCCAGCTTGCAGTGGCAAGAATTAAAAAAGGAATAAACTATGTGCTTCTTAAAATACTATGCAAAACACAAAATGTCCCAAAGGACACAATGGACCATGTAAATGAGGTATATGTTAAAGAAGATATTTCTGACCATACCCTTTCTGAATTGAGCAACACCCAAGATTTTCTCAAAGATAAGGAAAAAAGCAGTGGCACAGAGAAAAACGCTACTGAAAATGAGAGCCAATCACTTATCCCCAGTCCTAGTGTCTCAGAAACTGTACCAATTGCTTCAGGAGAATCTGATATAGAAAATCTGGATAATAAGGAGATTCAGAGTAAGTCTGGTGATGGAGGCAGCAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136546_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.421
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
PF0052026=Ion_trans=PD(1.1=6.2)
C2:
PF0052026=Ion_trans=PD(4.2=5.5),PF065128=Na_trans_assoc=PU(60.1=84.1)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACTGTATGGAGGTTGCAGGC
R:
GCCACTGCAAGCTGGAGATTT
Band lengths:
176-270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)