HsaALTA0007522-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000196876 | SCN8A
Description
sodium channel, voltage gated, type VIII, alpha subunit [Source:HGNC Symbol;Acc:10596]
Coordinates
chr12:52077958-52080241:+
Coord C1 exon
chr12:52077958-52078076
Coord A exon
chr12:52080152-52080153
Coord C2 exon
chr12:52080154-52080241
Length
2 bp
Sequences
Splice sites
5' ss Seq
TTCATATCC
5' ss Score
-14.87
3' ss Seq
GCCCCTTGACTCTTCTCTACAGT
3' ss Score
-1.37
Exon sequences
Seq C1 exon
ACCTTTGTAGTATTAAACAGAGGGAAAACTCTCTTCAGATTTAGTGCCACGCCTGCCTTGTACATTTTAAGTCCTTTTAACCTGATAAGAAGAATAGCTATTAAAATTTTGATACATTC
Seq A exon
AG
Seq C2 exon
TATTTAGCATGATCATTATGTGCACTATTTTGACCAACTGTGTATTCATGACTTTTAGTAACCCTCCTGACTGGTCGAAGAATGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196876-4-6,4-5-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.8=6.5)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCACGCCTGCCTTGTACATTT
R:
AGTGCACATAATGATCATGCTAAA
Band lengths:
99-101
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
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)