GgaINT1024562 @ galGal4
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chrLGE22C19W28_E50C23:79663-80140:-
Coord C1 exon
chrLGE22C19W28_E50C23:80087-80140
Coord A exon
chrLGE22C19W28_E50C23:79801-80086
Coord C2 exon
chrLGE22C19W28_E50C23:79663-79800
Length
286 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAG
5' ss Score
8.04
3' ss Seq
TCTTCTCATTTCCCATTCAGCAA
3' ss Score
8.04
Exon sequences
Seq C1 exon
GCAACATTCAAGGGCTGGATGGACATCATGTATGCAGCAGTAGATTCCAGAAAG
Seq A exon
GTACAGTGCATGGCCACAAGCACTCTTACCCCCCAGCAAAAATGGTAGAGCTGTGTTTATATCATGTATTTCATTTCGTTATAGCGTGGTTTTTCATTTGCTGGTGTTGCTGTGGTAAGTTAAAAGATGCTGGAGCAAATCCCCGAAAGAGCATTTGTTTGGTTGCTTTATTAAGGGCAGGGAAACTCCTGATTGCCTAAAAATACACTGAAAAAGATCTCATTTTGACTCCATGGGTAAGATGTCTTTGCAATGTCATTTCCTTCTCTTCTCATTTCCCATTCAG
Seq C2 exon
CAAGAAGAGCAACCCAAGTACGAGGACAACATCTACATGTACATATATTTTGTTATCTTCATCATCTTTGGCTCCTTTTTCACTCTGAACTTGTTCATCGGTGTCATCATTGACAACTTCAATCAACAAAAGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000017935:22
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=FE(7.4=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(15.2=76.1)
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:
GCAACATTCAAGGGCTGGATG
R:
TTTTCTTTTGTTGATTGAAGTTGTCA
Band lengths:
190-476
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]