GgaINT1024566 @ galGal4
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chrLGE22C19W28_E50C23:106865-107291:-
Coord C1 exon
chrLGE22C19W28_E50C23:107202-107291
Coord A exon
chrLGE22C19W28_E50C23:106994-107201
Coord C2 exon
chrLGE22C19W28_E50C23:106865-106993
Length
208 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGT
5' ss Score
8.57
3' ss Seq
CTCTTTGTTCCTTTTAACAGGTA
3' ss Score
12.21
Exon sequences
Seq C1 exon
AGTATTTAGCATGATCATTATGTGCACTATTTTGACCAACTGTGTATTCATGACTTTTAGTAACCCACCTGAATGGTCGAAGAATGTGGA
Seq A exon
GTAAGTAATATTTCTTCTATTTTTATACAGAATGTTGCTTTTCTTCTCTTCAGAAACCTGTTCTTGCTCATATTTCAGTTAGCTTGAATGCAAGTTGCCTTTCTATCCACTTTGTTGAGACAGAAGTGTTTCTAATTCACCTGTTAGCATGCCTAGCATTACATTCCTGCAAACTTCTCAGCGCAGCTCTCTTTGTTCCTTTTAACAG
Seq C2 exon
GTATACATTCACTGGTATTTATACATTTGAATCACTTGTGAAAATTATTGCAAGAGGTTTCTGTATAGATGGCTTTACTTTCCTACGAGACCCATGGAACTGGCTAGATTTCAGTGTGATCATGATGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000017935:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(0.8=6.5)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTAGCATGATCATTATGTGCACT
R:
GCCATCATGATCACACTGAAATCT
Band lengths:
215-423
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]