HsaEX0056579 @ hg19
Exon Skipping
Gene
ENSG00000169432 | SCN9A
Description
sodium channel, voltage-gated, type IX, alpha subunit [Source:HGNC Symbol;Acc:10597]
Coordinates
chr2:167151109-167159812:-
Coord C1 exon
chr2:167159600-167159812
Coord A exon
chr2:167158671-167158810
Coord C2 exon
chr2:167151109-167151172
Length
140 bp
Sequences
Splice sites
3' ss Seq
TCTAAACAATTATCCCCTAGCAT
3' ss Score
4.69
5' ss Seq
CAGGTGTGG
5' ss Score
6.34
Exon sequences
Seq C1 exon
GCCTGAAGACAATTGTAGGGGCTTTGATCCAGTCAGTGAAGAAGCTTTCTGATGTCATGATCCTGACTGTGTTCTGTCTGAGTGTGTTTGCACTAATTGGACTACAGCTGTTCATGGGAAACCTGAAGCATAAATGTTTTCGAAATTCACTTGAAAATAATGAAACATTAGAAAGCATAATGAATACCCTAGAGAGTGAAGAAGACTTTAGAA
Seq A exon
CATGGTGTCTCTCACTGGAACGGTTGATGAATATTGGATGAAGATATGATCAAGATTGTACTTTCTGTCTGACACCTGGAATGTATCTATCTGATGGTGCCCACGTGAATACATAAATCTTAATAGATAATTTGACCCAG
Seq C2 exon
AATATTTTTATTACTTGGAAGGATCCAAAGATGCTCTCCTTTGTGGTTTCAGCACAGATTCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169432-'11-15,'11-14,13-15
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=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(28.6=100)
A:
PF0052026=Ion_trans=PD(4.5=50.0)
C2:
PF0052026=Ion_trans=FE(8.5=100)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
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:
GGGGCTTTGATCCAGTCAGTG
R:
GCTGAAACCACAAAGGAGAGC
Band lengths:
249-389
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- 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)