GgaINT1024571 @ galGal4
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chrLGE22C19W28_E50C23:98558-99367:-
Coord C1 exon
chrLGE22C19W28_E50C23:99226-99367
Coord A exon
chrLGE22C19W28_E50C23:98765-99225
Coord C2 exon
chrLGE22C19W28_E50C23:98558-98764
Length
461 bp
Sequences
Splice sites
5' ss Seq
TTAGTAAGT
5' ss Score
7.79
3' ss Seq
TGCCATTCTCTTTCCTCCAGACC
3' ss Score
10.95
Exon sequences
Seq C1 exon
TCAATGTCCAGAGGGTTACACATGCATGAAAGCAGGACGGAACCCAAACTACGGTTACACGAGCTTTGACACTTTCAGCTGGGCTTTCCTGGCTCTGTTTCGCCTTATGACTCAGGACTTTTGGGAAAACTTGTATCAATTA
Seq A exon
GTAAGTAAATGCTTTGTTACACAAGATGAGAATTAGGGGAGAAGACAAGGGAGAAGGTGTCAAGTTTTATTTGACTTTTTCCTTGGAACTTTGCTGAAATGTTGTTTGTTTGTTTACTTTAATTTCATTTTGCTTCGTTTTGAAGGAGTTTAGGCTATGAGTTTTGCATTGCACACTCAACTCCTTTTCATTTTGCATGTGTTGGATGATCCTTTCAGAAGAGAGATGTCACCTTCTCTGTTTATGGCTTTGAACGTGCAGGGTCTTTGTGCTTGGCAGTGGAAGCACTGTGATTTTTAATATTCAGCATCACTGATATCTTAAATATATTCAGAAAGTACTGTAATTTTCTTGGGAGCGTTCAGGTCAAGAAACTTTGGATTGGCTCACATACATGCGTCACTCTGGAAATGGCATCCCCATCTCCTTCCCTCTTCCCTCTGCCATTCTCTTTCCTCCAG
Seq C2 exon
ACCTTACGAGCAGCTGGAAAAACCTACATGATCTTCTTTGTCCTGGTGATCTTCGTGGGCTCGTTCTATCTGGTCAACCTGATTCTGGCTGTGGTGGCCATGGCTTACGAAGAGCAGAACCAGGCTACGTTGGAGGAGGCAGAGCAGAAAGAGGCCGAATTTAAGGCCATGTTAGAACAGTTGAAAAAGCAGCAGGAGGAGGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000017935:8
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=0.072
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(18.7=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(12.4=44.9)
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:
ATGTCCAGAGGGTTACACATGC
R:
GCCTCCTCCTGCTGCTTTTTC
Band lengths:
342-803
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]