RnoALTA0035245-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000005309 | Scn8a
Description
sodium voltage-gated channel alpha subunit 8 [Source:RGD Symbol;Acc:3638]
Coordinates
chr7:142594430-142595693:+
Coord C1 exon
chr7:142594430-142594548
Coord A exon
chr7:142595604-142595605
Coord C2 exon
chr7:142595606-142595693
Length
2 bp
Sequences
Splice sites
5' ss Seq
CTCATATCC
5' ss Score
-13.36
3' ss Seq
TCCCCTTAACTCCGATCTACAGT
3' ss Score
-2.15
Exon sequences
Seq C1 exon
ACCTTTGTAGTATTAAACAGAGGGAAAACTCTCTTCAGATTTAGTGCCACACCTGCCTTGTACATTTTAAGCCCTTTTAACCTGATAAGAAGAATAGCTATTAAAATTTTGATACACTC
Seq A exon
AG
Seq C2 exon
TTTTCAGCATGATCATCATGTGCACCATCCTGACCAACTGTGTGTTCATGACCTTTAGTAACCCTCCAGAATGGTCCAAGAATGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005309-7-7,7-6-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.8=6.7)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCACACCTGCCTTGTACATT
R:
GTCAGGATGGTGCACATGATGA
Band lengths:
108-110
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]