GgaINT1024537 @ galGal4
Intron Retention
Gene
ENSGALG00000011040 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr7:19416615-19418088:+
Coord C1 exon
chr7:19416615-19416706
Coord A exon
chr7:19416707-19417815
Coord C2 exon
chr7:19417816-19418088
Length
1109 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TGGAACTTTTCTCTTTGCAGGCC
3' ss Score
10.62
Exon sequences
Seq C1 exon
GTATGTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTATTGAGAGCTTTGAAAACTATTTCTGTAATCCCAG
Seq A exon
GTAAGAAGTAACTGTGTAAGGTGTTAGGCCCCTTGTAACTCCAATTGTTATTTGTGTGCTGTCATTGTGTTTGTGTGTGAACTCCCCTATTACAGATATGTGACAGAGTTTGTGGACCTGGGCAATGTCTCAGCGCTGAGAACATTCAGAGTTCTCCGAGCTTTGAAAACAATATCAGTCATTCCAGGTGAGAGCTAGGTTAAACACTGAGGCTGACTGTTGTTCCATTGAAGTTGAATTCACTTCTTTTGAGCATAAGCCTTGATATTCGCTGCTCATGTTACAAAAAGAAAAAAAAAATAAAAGGAAAAAGAAAAAAAGGCATGGATCATAAGCCAGGGTTATGATTCTTTACCTTTTTAGCATTAGCTTCTTTTATTTTGCAAAATCAGCCTTTGCGTTTAACAGATTCTTGCATGAAACAAGAAATGTGAGGCCTATGGATTATTTTGCTTTATTTTTCCATGTTTATTATGACAGATTGTCTCTTTAACATTAAAAATGCTTTAGTGCTTTGGCTTTTTTGATTTTGATTATTTTCCTTTATTTTACCACTTAAAATTTAACTTGGCCTTGAAGACAACCAACTAACAACAAAGCTACAGAACAGGAGATAAGTATTGCACAGGAAAATTTATCAACTAAAACTATTTTTCTTTTCTCAAAATCACTTGCAATTCTATCCCAGTTTGTGCTGTTGTGGAGTCACTGGAAATTGATTTATTGGCAGAACATAAAATAGTAACTATAATATAAATTGTTATTATTATTAAATATTAAATATTGTAGTAAATACTATTATTGAATATCAAATATAATATTAAGTGGAGAGAAAAATTAAAGAGATCAAATCTATAACAGAAAAGCATGGTTGATAAATTTCCTGCTTGAGAATTATATGATATTTTTGTGTATTTGAATGTATGTACATTGCTTATTCATAAAAATAAAATTATTTTTCTTTCATTCATCTTCACAAGCTCTGAGGCTGTTCATGAAGCTTTATTTTTTGACAGATAACAGTAATTTAAGTGTCTGCATGACATCTGAGTTATATGGGAAGGGCAAAGATCCTCTTTGATAAACCTATGGAACTTTTCTCTTTGCAG
Seq C2 exon
GCCTAAAGACTATTGTAGGAGCCCTAATTCAGTCTGTGAAGAAGCTCTCGGATGTTATGATCCTGACTGTGTTTTGTCTGAGTGTATTTGCACTAATAGGGCTGCAGCTGTTCATGGGCAACTTGAGGAATAAATGCCTGCAGTGGCCTCCAGACAATTCTACTTTTGAAATAAATGTTATTTCCTACTTTAATAGCACAATGGATGAAAATGGTACATTTATTAATACAACTGTGAGCACATTTAACTGGAAGGATTACATCGAGGATGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011040:ENSGALT00000017981:5
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(11.6=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(34.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCTAGGCAATGTTTCAGCTCT
R:
CATCCTCGATGTAATCCTTCCAGT
Band lengths:
342-1451
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]