HsaALTD0005696-3/3 @ hg19
Alternative 5'ss
Gene
ENSG00000144285 | SCN1A
Description
sodium channel, voltage-gated, type I, alpha subunit [Source:HGNC Symbol;Acc:10585]
Coordinates
chr2:166898802-166900559:-
Coord C1 exon
chr2:166900263-166900559
Coord A exon
chr2:166900179-166900262
Coord C2 exon
chr2:166898802-166898934
Length
84 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGG
5' ss Score
6.17
3' ss Seq
ATTAGCATTTTTTTTTACAGGGA
3' ss Score
8.45
Exon sequences
Seq C1 exon
TCTTTGTTGAGCATCCGTGGCTCCCTATTTTCACCAAGGCGAAATAGCAGAACAAGCCTTTTCAGCTTTAGAGGGCGAGCAAAGGATGTGGGATCTGAGAACGACTTCGCAGATGATGAGCACAGCACCTTTGAGGATAACGAGAGCCGTAGAGATTCCTTGTTTGTGCCCCGACGACACGGAGAGAGACGCAACAGCAACCTGAGTCAGACCAGTAGGTCATCCCGGATGCTGGCAGTGTTTCCAGCGAATGGGAAGATGCACAGCACTGTGGATTGCAATGGTGTGGTTTCCTTG
Seq A exon
GTTGGTGGACCTTCAGTTCCTACATCGCCTGTTGGACAGCTTCTGCCAGAGGTGATAATAGATAAGCCAGCTACTGATGACAAT
Seq C2 exon
GGAACAACCACTGAAACTGAAATGAGAAAGAGAAGGTCAAGTTCTTTCCACGTTTCCATGGACTTTCTAGAAGATCCTTCCCAAAGGCAACGAGCAATGAGTATAGCCAGCATTCTAACAAATACAGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285-12-12,13-12,14-12-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.636 A=NA C2=0.222
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=PD(16.8=32.3),PF119333=DUF3451=FE(47.1=100)
A:
NA
C2:
PF119333=DUF3451=PD(15.7=82.2)
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTAGGTCATCCCGGATGCTG
R:
ATTGCTCGTTGCCTTTGGGAA
Band lengths:
182-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)