GgaINT0047679 @ galGal4
Intron Retention
Gene
ENSGALG00000010943 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr7:19146500-19147019:+
Coord C1 exon
chr7:19146500-19146553
Coord A exon
chr7:19146554-19146881
Coord C2 exon
chr7:19146882-19147019
Length
328 bp
Sequences
Splice sites
5' ss Seq
GACGTAAGT
5' ss Score
10.93
3' ss Seq
ATTTCATATTTTTTCCTCAGGTG
3' ss Score
10.51
Exon sequences
Seq C1 exon
GCTACATTTAAAGGCTGGATGGATATTATGTATGCAGCTATTGACTCAAGAGAC
Seq A exon
GTAAGTACTGAGAATATTTTGAAGTACATTTTATCCTTGACACATGTCTATCAACAAGTGTATATTTATATTTCTTCCAAAAGTGAATAATATGCATACAGGAAGATGAAACAAAATTAAATGAACTAATATGAGATTCTGCTGTGGCAAATTATTGTAACAAATTTGAATGCAAACTGCAAGATGCTGTTAGTAATAGATGGAATGGACAAAAATACACTGATATAAGTGACAAGGAAATAAAAGATATTTTGTCCAAGATTGCTGCTTGTTCAATTGAAATTTTCATATGAAATCTTAAGAATGATATTTCATATTTTTTCCTCAG
Seq C2 exon
GTGTTACAGCAACCCAAGTATGAAGACAACCTGTACATGTATTTGTATTTTGTCATCTTTATCATTTTTGGGTCTTTTTTCACCCTGAATCTGTTCATTGGTGTCATCATTGATAACTTCAATCAGCAGAAAAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010943:ENSGALT00000017814:23
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:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTACATTTAAAGGCTGGATGGA
R:
TCTTTTTCTGCTGATTGAAGTTATCA
Band lengths:
190-518
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]