GgaINT0047350 @ galGal4
Intron Retention
Gene
ENSGALG00000011040 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr7:19462800-19464236:+
Coord C1 exon
chr7:19462800-19462904
Coord A exon
chr7:19462905-19463965
Coord C2 exon
chr7:19463966-19464236
Length
1061 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGA
5' ss Score
8.24
3' ss Seq
TTCTGTTTTTGTTTTCGCAGAAC
3' ss Score
10.19
Exon sequences
Seq C1 exon
TTTGGAGGTCAGGATATATTTATGACAGAAGAACAGAAGAAATATTACAATGCAATGAAAAAACTGGGATCCAAAAAACCACAGAAACCTATACCAAGGCCAGTG
Seq A exon
GTAAGAACTATTTGACTTCAATAGCACTAATATTAAATATTCATCTGGGAATATGATTTTGCCCAACAAGGAAAGTTAGATATCTGGAAGGAAAATATTTCTTTTGGTTTTCTTATAAGGTGTAATTTCTCTTTTTTTAATTAAGTGAATAGATCTTTCATATTTATTTTAAAAGCACAGACTCTGATATATGAAATGTTGGATTTAATGAGGTTAATGTGCTAAGTTTCATAATTCCCTCCCTGAGCCCCAGATAAATACTGTTAATTGGCTCATTTACTGGTCCTTGTTTACATTGGATAAGCTTAGTGTCTTACAGAGAATTTGTAGGAAGAGGGGATGTACTGACTATTGCTGTAGACAGAAGGGGGCACCGATCACTTAATGTGAAAGAGAAAGGTAATCCCACAGAATAAAAGAATGCCCTGGGGCGTACAGGATAAACTAGAATATGTTCACCCCTAAGATAAGAAAGCACTTTGTTATTTCCTGAAATTCTACAGAACTTGGAAATGAAAACACTTGTTGCACCTTGTTCACTGGGTGGTGAACTCTCTAAGAAGCATATAGGCATAAATAATTAGCAAAGTAGAAAAGGAAAACCAGGATATTGCAGTCAGAATGTTTGAGACACGCAACTTCAGCTGTCCAGCAACCTCACCAAGCACAACTAATTTAACAAAGAGAGAGATCTCTAGGGGTTGGTATTCTAAAGCCAGCTAAGGATAAGAATGAGAAAACGAGTTTCTATTTGGTAGGTACTTATCTGGTATCAAGTTATGCCACCTTTTTTATACTACTATTATCAATTTTAAATGTTATTGGTATTATCATTTCAGTGCTTCTCTTTCTATTCCTCCAGTCAACAGTGGTACATTTCTTCATCCACTATAAAAGGCCTAGACAAAATCCAAAAAGGGGTAGGTGTAAATTAACAGATATATGACGAATGGGTCTTGCTCTGCACTCCCAAGATCTTGCAGGAACTTGGTTTCCCATGTGACATTTCTGAAAGCAAATATTTTCAGAGTATAAGGAGTATTCTGTTTTTGTTTTCGCAG
Seq C2 exon
AACAAATTCCAAGGCATGGTCTTTGATTTTGTCACCAAACAAGTATTTGACATCAGCATCATGATACTTATCTGCCTTAATATGGTCACAATGATGGTAGAAACAGATGACCAGAGTAAGGAAATGGAAACAATTTTATCCCGGATTAACCTTGTGTTCATTATCCTTTTCACTGGAGAATTTGTCCTCAAACTGATTTCTCTTCGCCATTACTACTTCACTATAGGCTGGAATATTTTTGATTTCGTGGTTGTGATTCTCTCCATAGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011040:ENSGALT00000017981:24
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.4=47.3)
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:
TGGAGGTCAGGATATATTTATGACAG
R:
ACCACGAAATCAAAAATATTCCAGCC
Band lengths:
354-1415
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]