RnoALTD0026713-3/5 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000005007 | Scn3a
Description
sodium voltage-gated channel alpha subunit 3 [Source:RGD Symbol;Acc:3635]
Coordinates
chr3:51580790-51582220:-
Coord C1 exon
chr3:51582085-51582220
Coord A exon
chr3:51582072-51582084
Coord C2 exon
chr3:51580790-51580922
Length
13 bp
Sequences
Splice sites
5' ss Seq
CCAGTATGT
5' ss Score
5.8
3' ss Seq
CATCAGTATTTGGTTTGCAGGGT
3' ss Score
5.3
Exon sequences
Seq C1 exon
CTTCAGAGGTCGGGCGAAGGACGTGGGGTCTGAGAATGACTTTGCAGACGATGAGCACAGCACCTTCGAGGACAGCGAGAGCAGGAGAGACTCCCTGTTTGTGCCGCACAGACCTGGAGAGCGACGCAACAGTAAC
Seq A exon
GTTAGTCAGGCCA
Seq C2 exon
GGTACCACCACTGAAACGGAAGTCAGGAAGAGAAGGCTAAGTTCTTACCAGATTTCGATGGAAATGCTGGAGGATTCCTCTGGAAGACAAAGAGCCATGAGCATAGCCAGTATCCTGACCAACACCATGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005007-18-18,19-18,20-18,21-18,22-18-3/5
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.617 A=NA C2=0.393
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(46.8=100)
A:
NA
C2:
PF119333=DUF3451=PD(0.7=2.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
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:
GATGAGCACAGCACCTTCGAG
R:
TTCCGTTTCAGTGGTGGTACC
Band lengths:
108-121
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]