GgaALTD0004399-2/3 @ galGal4
Alternative 5'ss
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19351077-19352309:-
Coord C1 exon
chr7:19352138-19352309
Coord A exon
chr7:19352105-19352137
Coord C2 exon
chr7:19351077-19351209
Length
33 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGA
5' ss Score
5.55
3' ss Seq
TATCAGTGTTTTATTTTCAGGGC
3' ss Score
9.16
Exon sequences
Seq C1 exon
ACATGGTGAACGGCGCAACAGTAACATTAGTCAGGCCAGTAGGTCATCCAGGACAGTACCTCCACTTCCAGTGAACGGGAAGATGCACAGCACTGTGGATTGTAATGGAGTAGTTTCTTTAGTCGGTGGGCCTCCAGCTCTGACGTCGCCTACTGGACAGCTTCTGCCAGAG
Seq A exon
GTGATGATTGATAAAGCAACCACTGCTAGCAAT
Seq C2 exon
GGCACTACTACAGAAACTGACTTAAGAAAAAGAAGGTCTAGTTCTTACCAGGTTCCTATGGACTACCTAACAGATCCTAGTGCAAGGCAGCGAGCAATGAGTATAGCCAGCATGCTCACAAATACGATGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009-12-12,13-12,14-12-2/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.311
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(51.3=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.5=82.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTACTGGACAGCTTCTGCCA
R:
TACTCATTGCTCGCTGCCTTG
Band lengths:
127-160
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]