GgaINT1024572 @ galGal4
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chrLGE22C19W28_E50C23:98080-98764:-
Coord C1 exon
chrLGE22C19W28_E50C23:98558-98764
Coord A exon
chrLGE22C19W28_E50C23:98368-98557
Coord C2 exon
chrLGE22C19W28_E50C23:98080-98367
Length
190 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
ATTTCCCCATTCTCCTTCAGGCT
3' ss Score
9.85
Exon sequences
Seq C1 exon
ACCTTACGAGCAGCTGGAAAAACCTACATGATCTTCTTTGTCCTGGTGATCTTCGTGGGCTCGTTCTATCTGGTCAACCTGATTCTGGCTGTGGTGGCCATGGCTTACGAAGAGCAGAACCAGGCTACGTTGGAGGAGGCAGAGCAGAAAGAGGCCGAATTTAAGGCCATGTTAGAACAGTTGAAAAAGCAGCAGGAGGAGGCACAG
Seq A exon
GTGAGTGTTTTGGTTGTCAGTTCTTTATTCATCTGCATTTTTTTGATTATCTATTTCCCTGTTATCACAGTGATGTATAATAAAAAAAATGCAGCAATGTCACGGTTGGCTTTCTGGCACTCTCTCTTAAAGCAGCAAATGGAGTGTTGTTCATTGTGAAGCTCTGATTTATTTCCCCATTCTCCTTCAG
Seq C2 exon
GCTGCTGCCATGGTCACTTCTGCAGGGACGGTCTCTGAGGATGCTGTGGAAGATGATGGTGGTGGGAGGATGTCTCGGAGCTCATCAGAGATCTCTAAACTGAGTTCCAAGAGTGCCAAAGAGCGCCGTAACCGGAGGAAGAAGCGGAAGGACAAAGAGCTGTCGGAAGGGGAGGAGAAGGGCGACAACGAGAAAGTGTTCAAGTCTGAATCAGAGGATGGCATGAGGAGAAAAGCCTTCAGGCTGCCAGATAACAGGATAGGAAGAAAGTTTTCCATCATGAACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000017935:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.072 A=NA C2=0.812
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(12.4=44.9)
A:
NA
C2:
PF119333=DUF3451=PU(29.8=69.8)
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:
ACGAAGAGCAGAACCAGGCTA
R:
TTCCGCTTCTTCCTCCGGTTA
Band lengths:
250-440
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]