GgaALTA1028317-2/3 @ galGal4
Alternative 3'ss
Gene
ENSGALG00000006112 | SCN5A
Description
sodium channel, voltage gated, type V alpha subunit [Source:HGNC Symbol;Acc:HGNC:10593]
Coordinates
chr2:5544395-5559148:+
Coord C1 exon
chr2:5544395-5544865
Coord A exon
chr2:5559002-5559004
Coord C2 exon
chr2:5559005-5559148
Length
3 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
CCATTTAGGATTATTTCCAGCAG
3' ss Score
0.47
Exon sequences
Seq C1 exon
GTGCTCAACCTGTTCCTTGCCTTGCTGCTCAGCTCTTTCAGTGCTGACAACCTTTCGGCACCAGACGAGGATGGAGAGATGAACAACCTGCAGCTTGCCTTTGCTCGGATCAACAGGGGTCTTCAGTATGTGAAACACACCACGTGGGATTTTTGCTGCAACGTCCTCCGGCATCCCAAGACAACAGCTGAGAAGAAGGCAATGATGAAGCTTGCTGCCCAGAATACAGGTGCCCTTAACAATTGTGTCAACAGCCACCCAACTGCTGAGCTTGGCAAAGAGATGGAGAATCACAAAGAGAACCACACAGAGGATGGGACGAATAAAAATGTGGAGAAACACCTGGGAATTACAGACAACGATGACTTTATGACCAATCCTGACCTATCAATTTGTGTTCCTATTGCTGTGGGAGAGTCTGATATCGAGGAGGAAGATGAGGAGCAAAGCACGTTTACAGAAATGGAGCAG
Seq A exon
CAG
Seq C2 exon
GAAAAGCAGCTGCAGCTGAGGGGGCAGCGATGCCAAAGCCCAGGCGCCCGAAGTCAGAACTCTGAGATTTGTGAAGAGTTAAGTGAGTTGCACGTGGATAAGCAGTTGAAGGCTGAGCCACCACCTCCAGTAGGGCAAAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006112-20-24,20-23,20-22-2/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.433 A=NA C2=0.776
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.1),PF065128=Na_trans_assoc=PU(49.6=84.7)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(17.9=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
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:
AGATGAGGAGCAAAGCACGTT
R:
CAGAGTTCTGACTTCGGGCG
Band lengths:
101-104
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]