HsaALTD0005697-5/6 @ hg38
Alternative 5'ss
Gene
ENSG00000153253 | SCN3A
Description
sodium voltage-gated channel alpha subunit 3 [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:165139476-165140998:-
Coord C1 exon
chr2:165140798-165140998
Coord A exon
chr2:165140651-165140797
Coord C2 exon
chr2:165139476-165139608
Length
147 bp
Sequences
Splice sites
5' ss Seq
GAGGTGATA
5' ss Score
3.13
3' ss Seq
CATCAGTATTTGGTTTGCAGGGC
3' ss Score
5.44
Exon sequences
Seq C1 exon
TCTCTCTTGAGTATCCGTGGCTCCCTGTTTTCCCCAAGACGCAATAGCAAAACAAGCATTTTCAGTTTCAGAGGTCGGGCAAAGGATGTTGGATCTGAAAATGACTTTGCTGATGATGAACACAGCACATTTGAAGACAGCGAAAGCAGGAGAGACTCACTGTTTGTGCCGCACAGACATGGAGAGCGACGCAACAGTAAC
Seq A exon
GTTAGTCAGGCCAGTATGTCATCCAGGATGGTGCCAGGGCTTCCAGCAAATGGGAAGATGCACAGCACTGTGGATTGCAATGGTGTGGTTTCCTTGGTGGGTGGACCTTCAGCTCTAACGTCACCTACTGGACAACTTCCCCCAGAG
Seq C2 exon
GGCACCACCACAGAAACGGAAGTCAGAAAGAGAAGGTTAAGCTCTTACCAGATTTCAATGGAGATGCTGGAGGATTCCTCTGGAAGGCAAAGAGCCGTGAGCATAGCCAGCATTCTGACCAACACAATGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153253-17-25,18-25,19-25,20-25,21-25,22-25-5/6
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.628 A=NA C2=0.222
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(46.2=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.4=82.2)
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCGGGCAAAGGATGTTGGAT
R:
GTGTTGGTCAGAATGCTGGCT
Band lengths:
253-400
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains