GgaINT0048549 @ galGal4
Intron Retention
Gene
ENSGALG00000011040 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr7:19415980-19416706:+
Coord C1 exon
chr7:19415980-19416108
Coord A exon
chr7:19416109-19416614
Coord C2 exon
chr7:19416615-19416706
Length
506 bp
Sequences
Splice sites
5' ss Seq
GGCGTAAGT
5' ss Score
9.39
3' ss Seq
ACTGTGATTTAATCCTACAGGTA
3' ss Score
9.97
Exon sequences
Seq C1 exon
GTACACTTTCACTGGAATTTATACCTTTGAATCACTGATAAAAATTCTTGCAAGGGGCTTCTGCTTAGAAGGTTTTACTTTTCTGCGAGACCCATGGAACTGGCTTGACTTCAGTGTCATTCTAATGGC
Seq A exon
GTAAGTGGTTCAAGAACTTCTTAAGCTTTTAGGGCATGAAATTAGTGGCAAACACTATTATTATCATGAATATATTCATTTAAAAATATTTAATTTCTGCAACCTGTGAAGTTTAGATGCTGTGTCACACATTGTAGTATGCATAAATCAAAGCTAAATATGGCAGTAACAAGCACAGAGTGTCAGCCACCAGTGTAATTACTGCTGAGGGACACTAATTTCATGTCCTATATTTTTCTGCTCACCAGAATAGAAGCCATCCCTTTGAGTTATGTCACTGTCCTATTATAAGCTAATTAGTTTAATTAGCTGTTCAAATGTAAATCAGTGAGTTACACGTCAATGACGTTTAAACATAACTCATGAAAATATGTATAGCAAGGTGTACTGGAGAGACAGGTAAATTTTCGAGTACGATTGTTAATGTTGACACAGAGGTTTTGAAGACCCTCATAATTAGTGTAAAATCTGCCTCAATTCTGAATAACTGTGATTTAATCCTACAG
Seq C2 exon
GTATGTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTATTGAGAGCTTTGAAAACTATTTCTGTAATCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011040:ENSGALT00000017981:4
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:
PF0052026=Ion_trans=FE(16.0=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(11.6=100)
Main Inclusion 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:
ACACTTTCACTGGAATTTATACCTTT
R:
GGGATTACAGAAATAGTTTTCAAAGC
Band lengths:
217-723
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]