GgaINT1024556 @ galGal4
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chrLGE22C19W28_E50C23:88881-89829:-
Coord C1 exon
chrLGE22C19W28_E50C23:89712-89829
Coord A exon
chrLGE22C19W28_E50C23:89036-89711
Coord C2 exon
chrLGE22C19W28_E50C23:88881-89035
Length
676 bp
Sequences
Splice sites
5' ss Seq
AGGGTACGT
5' ss Score
9.15
3' ss Seq
GTGCATTGTTCCCTTTCCAGGTT
3' ss Score
10.52
Exon sequences
Seq C1 exon
AAACTGGATGATACCAGCTCCTCCGAAGGCAGCACCATTGATATAAAGCCTGAAGTGGAAGAAGTCCCTGTGGAGGCACCAGAAGAGTATCTGGACCCGGATGCATGCTTCACTGAGG
Seq A exon
GTACGTTGAGATAGACAGAACCTCTGAGCTGTTACTGGGACCCTTATCTGCTGTAAGCTTACCTTCAGGTTGGGTCTGGCATTGGGTTTTAGCTTCTTTTGAGAGCCTTCTTGGGCCCTCCATCACAGCTGAAGTAGACGGGAAGCATTTGCAGAGTGAGGGCCTCAGAGGTGTAGCTGCCATTGCTAAGATCTAGCTGACTTACAGGTAGGGAAAGCTGATCTTTTGCACAATTAATGCATTGAGTATTCAGAAGCAGAAGAACCTGGTTTTGTTTTCTTTTTTTTCCTCCCCCCTCTGTCACTGACTTCAAGGTCTTTCAGCAGCTGATCTGTTACAGATATTCCCATGGCAAAGAGATTGTAAGTGGCTCAAGGTTATTCTATGGGCAGGTTCTCCATTCCTGTCCTGGCAAGTGCATGGATCTCTCACCAAGTATAACTAGCTTAACCTGTTCAGGCATTCTTGTTAATTCAGGTTCTCAGATACAGAAATGATGGAAGTAATCCTAAAAACCTCAAAAACACTCAGAGTTTGAACTGAAAGTCAGCATGCTTAATATTATGGGCACCCAAATCAATTCCAGGCACTGAAAATGATGCGTTCTCACAATATCTCATCCACAACCCAACAAAATTTGGGGCTCATGCCTCTTGGTGCATTGTTCCCTTTCCAG
Seq C2 exon
GTTGCATGCAGCGCTGTAAGTGTTGTCAGGTCAATATTGAGGAGGGGCTGGGGAAGTCCTGGTGGACCTTGAGGAAGACGTGTTTTCTGATTGTGGAGCACAACTGGTTTGAGACTTTCATCATCTTCATGATCCTACTGAGCAGTGGAGCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000017935:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.550 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(17.9=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(20.2=84.6)
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:
TGGATGATACCAGCTCCTCCG
R:
AGCTCCACTGCTCAGTAGGAT
Band lengths:
266-942
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]