HsaALTD0005696-5/5 @ hg38
Alternative 5'ss
Gene
ENSG00000144285 | SCN1A
Description
sodium voltage-gated channel alpha subunit 1 [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:166042292-166044049:-
Coord C1 exon
chr2:166043836-166044049
Coord A exon
chr2:166043669-166043835
Coord C2 exon
chr2:166042292-166042424
Length
167 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
TCTTTGTTGAGCATCCGTGGCTCCCTATTTTCACCAAGGCGAAATAGCAGAACAAGCCTTTTCAGCTTTAGAGGGCGAGCAAAGGATGTGGGATCTGAGAACGACTTCGCAGATGATGAGCACAGCACCTTTGAGGATAACGAGAGCCGTAGAGATTCCTTGTTTGTGCCCCGACGACACGGAGAGAGACGCAACAGCAACCTGAGTCAGACCA
Seq A exon
GTAGGTCATCCCGGATGCTGGCAGTGTTTCCAGCGAATGGGAAGATGCACAGCACTGTGGATTGCAATGGTGTGGTTTCCTTGGTTGGTGGACCTTCAGTTCCTACATCGCCTGTTGGACAGCTTCTGCCAGAGGTGATAATAGATAAGCCAGCTACTGATGACAAT
Seq C2 exon
GGAACAACCACTGAAACTGAAATGAGAAAGAGAAGGTCAAGTTCTTTCCACGTTTCCATGGACTTTCTAGAAGATCCTTCCCAAAGGCAACGAGCAATGAGTATAGCCAGCATTCTAACAAATACAGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285-24-44,25-44,26-44,27-44,28-44-5/5
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.645 A=NA C2=0.231
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)
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCTTTAGAGGGCGAGCAAA
R:
ATTGCTCGTTGCCTTTGGGAA
Band lengths:
250-417
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains