GgaINT0047668 @ galGal4
Intron Retention
Gene
ENSGALG00000010943 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr7:19115185-19116878:+
Coord C1 exon
chr7:19115185-19115532
Coord A exon
chr7:19115533-19116745
Coord C2 exon
chr7:19116746-19116878
Length
1213 bp
Sequences
Splice sites
5' ss Seq
GAGGTGATA
5' ss Score
3.13
3' ss Seq
TATTACTGTTCCCTGTGTAGGGC
3' ss Score
10.16
Exon sequences
Seq C1 exon
TCTTTGCTGAGCATTCGTGGCTCCCTGTTTTCCCCAAGGCGCAACAGCAGAACCAGTCTTTTCAGCTTCAGAGGTAGAGCAAAGGATATAGGATCTGAAAATGACTTTGCTGATGATGAGCACAGCACTTTTGAAGACAATGATAGCAGAAGAGATTCTCTCTTTGTGCCGCGCAGACACGGTGAACGGCGCAACAGTAACATTAGTCAGGCCAGTAGGTCATCCAGGATGCTGGCAGTGTTTCCAGTGAATGGGAAGATGCACAGCACTGTGGATTGCAATGGGGTGGTTTCCCTGGTTGGTGGACCATCTGTTCCTACATCGCCTGTTGGACAGCTTCTGCCAGAG
Seq A exon
GTGATAATAGATAAACCAGCTACTGATGACAATGTAAGAAAGTTTTAAACAGCTTAGGCATCATGGCCTTTTCTTACTGCACCAGCCAGTGTTACCTACAGAATGGAATCCTTGGCAATGCTTCCTGGTTGGTCAAGCTGTGAATGCTCCTGCATCTTGTAAAATCTTTAATAATTTAAACAGATAAGATAGGTTTGCAACATAAGCATTTACTTACTAATATTCTCATAACTAACAAATGCAATTTGCAGTTTCCACATAGTAAAATATTAACTTACTTATACATCCACAAAAGCACCATACTGTATTACCAGGCCATGCATTCATTTTGCTGCTATAAATGTCTGTCTGGTTATGGTCCACAAAATCAAAGTTACGATACAGTTGAAAACAGTATACAAAGATGTTATCATATGTCTGCAATCAAACTGCTATTACCACTGTATCAAAATTAGCATTATTGGTTAATTTTGATAATATACAATTCTATATCAGACCCACTAAAAATGTAAGGAAGTAGTCAGTTCTTTATTACCATTTGTTTCTCATTTCTGTATGCTTCCATCCTTTGCTGGTGGAGTTCTATAGTATAAACACATAGTTAATTGGAAGATTGCATTTCTGCACATACTACCAAAAATACCAGTTATAAATGTCTGTGTGAACATATTTGCAGCACATATTGCTGTCACTGTGTATGTATATGCAGGTAAGAGAGAAGAACACTGAAATAAATTACTTAGTTCAAAATTGTCTACTCACATTAATTAGAAACATACTAGCATGGGAAAGCATGAGGAAGTCATACTTTTCTTACTTGCTACTGTTTGTCTAGTGTAAAAAAAACTATTATGTCATAGGAAATTGAATATTCTGTCAGCAAGAGCAAGGAGAAAACAGTTTACAAAAAAAGTACAGTTTTTTGAATTCAGTCCTTTTTTATTTCTTTAAATAATTCTTTTTCTAAGCTTGAAGGAAAGAAATGCAATAGTTAAGTGAATAAACTCTCACTAAATCTTGAACAGTTAGATAACTATTGCCTATTATCATTTAAAAATTATCTTAAAGATATTAAAAAGTAAGAAAAGTCTGACATGATAAAACTTGAAGTGCACGAAGCACGTATATATGCATATTAATAACAGGGATCTATGTAGTATTTGTCCATTTTATTATTCATATGTAGTCTCACCTATTACTGTTCCCTGTGTAG
Seq C2 exon
GGCACCACTACAGAGACAGAAATGAGGAAGAGAGTATCAGGCTCTTTCCATGTTTCTATGGACTATCTGGAAGATCCAGCTTTAAGAGAGAGAGCAATGAGCATTGCTAGCATCCTTACGAACACTGTGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010943:ENSGALT00000017814:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.552 A=NA C2=0.222
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(51.1=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.4=82.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTCGTGGCTCCCTGTTTTCC
R:
TTCTGTCTCTGTAGTGGTGCC
Band lengths:
357-1570
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]