GgaINT0048556 @ galGal4
Intron Retention
Gene
ENSGALG00000011040 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr7:19425337-19427423:+
Coord C1 exon
chr7:19425337-19425684
Coord A exon
chr7:19425685-19427290
Coord C2 exon
chr7:19427291-19427423
Length
1606 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATT
5' ss Score
8.88
3' ss Seq
CCTCAGTATTTCATTTACAGGGC
3' ss Score
7.23
Exon sequences
Seq C1 exon
TCTTTGCTAAGCATCCGTGGTTCCCTGTTCTCACCAAGGCGCAACAGCAAAACAAGCATTTTCAGTTTCAGAGGTCGCACAAGGGATATAGGATCTGAAAATGACTTTGCTGATGATGAGCACAGCACTCTTGAGGACAACGAAAGCAGAAGGGATTCTCTCTTTGTTCCAAATCGACATGGAGAAAGGCGTAACAGCAACATCAGTCAGGCCAGTATGTCATCCAGAGTGGTGCCAGCCCTTCCGGCCAATGGGAAGATGCATAGCGCTGTAGATTGCAACGGAGTAGTCTCCTTAGTTGGAGGACCTTCAACTCTAACTTCACCTACTGGACAGCTTCTACCAGAG
Seq A exon
GTAATTATAAGCAAACAAGCAATTCCTGCAGTTTTGTTCAGGCACATAATTTTTTTCTTACTGTTCACTTCTGCATGCCTTACCATTTCTTACAGCTGTGAGAAATAACTTGCAATAGTTTCTAAACTACAGGAGATAAGGGAAAAAACATCCTCAAGCTTGTATGTCTGAGCCTTACGATAGTATTATATTCTCCTTGCCTCCAGCAAGAGATTTGCACAGAGAAAACAGTATGTATAGATATATAAACTAAATCTACCATTTTGTACACAGTTTTGCCTCAAAAACGAAGGTAGGCGTTTGACATAAAACTAAGGATATGGGAATAGGAAACCACCTGCAAAATGTGAAGGAAAGCAGTTACTATTCCCATGATTGTTTGCTGTTACCATGCATTTCAGTTGATTTCCATAAGCTAAAATGTTTCTTCAAACTTTGAAAAAAGCAAGTTTTTTAATACAAAATATTTTAATATGGTATTTTGGTGGCTATAATACTCTGACAAAATATTTTCATTATAAATAAATATTGAGATTTCATTACTACTATCATACATTTTATTTTCTCTCCTATCTTGATACAGAGCTTCATACAAAAAATCAAATAAAATTATGTTAGATATTACGCATATATAGTTCTATTCCAGAAAAATACTCACTTGAAAAAAAAGAACTATCCATTTAAGTCAAGACCCTTTGCAAAGGAAATAGAGCTAATGAATACTCAAAAATGTTTTTTCATCTTCACACTAATATAACCTTGAAATCCTCTGAAAGTTCTGAAAGGTTTATTCTTCTTTTTCTGGAGAGGGACAAAATAATGAAAAAAGAATGAGAGGTTTACATGAATGACAGTGAGAAGCAAGAACCAAGATTTAGGAACATTTTAGTACCACTCTTGTGGTCAGATTCCTGGGCTGTGCTCCAAAAGAAGAGAAGAGCATCTGTAAGGACAGCCGCATACTACTGAATAGTGGCATGTCTGTGACATTTAAATCAGAGTTGGGTATTGCTGTTTTGAAAAGATAACTAGAAGCCATAGAAAACAGAGAGGAAAATGTAAAGGGACTTGCATACTCATTATAGGAATATATAATGACTTCTGTATGAGTATTGTGGTGGACAAGAATTAGGTAGATGAAACATTAATATGATGTGATTTCTTTCTCATATAAAATTTTCCAACCACGCTTGTCAGGCTAAGAATGCAGTATATAGTATTGCTGAGATAATTAATTCCTAGAATTATAATCATTTAACATGACTAGTTGCTGAAAATTAAGGTGACAGGTTTCAACTTAGATAATTTTTTTTTCTTGAAATAATAATAATCACTATCGAAAATACACCTTAGCAAAAGTTTTGCTCACTCTGCCACTTAAATGAGAGCCATCTTTGCTCCCACCTTGCTTGTTCCTACTGTTGCCTATTTATTGCATTTTCTCTGAGTTGCTCAAAAACAAAAAGGCTCCTACAGGAAGAGAATTCTTCAGTGTGTTAGAAAGATCTACAAGTCTGATTTTGATTGTCACTATGCACTTATGCAGTAAGTGTTATTAATTGGCTGCTGAAGAGAATGGTTTAATTCCTCAGTATTTCATTTACAG
Seq C2 exon
GGCACCACTACTGAAACAGAAATAAGAAAAAGAAGACTGAGTTCTTATCAGATTTCCATGGAAATGCTGGAAGATTCTGCTGCAAGACAAAGAGCAATGAGTATAGCCAGTATACTTACAAACACAATGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011040:ENSGALT00000017981:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.638 A=NA C2=0.133
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(50.9=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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTGATGATGAGCACAGCAC
R:
CTCATTGCTCTTTGTCTTGCAGC
Band lengths:
342-1948
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]