GgaINT0048546 @ galGal4
Intron Retention
Gene
ENSGALG00000011040 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr7:19411316-19413499:+
Coord C1 exon
chr7:19411316-19411582
Coord A exon
chr7:19411583-19413378
Coord C2 exon
chr7:19413379-19413499
Length
1796 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
GTATAATTTTTGTTTTGCAGACT
3' ss Score
8.85
Exon sequences
Seq C1 exon
ATGGCACAGGCACTGCTGGTACCGCCAGGACCTGAAAGCTTCCGCTATTTTACTAGAGATTCTCTCGCAGCTATTGAAAAGCGTTCTGCAGAAGAAAAAGCTAAAAAGCCCAAGCAAGAACATACTGATGATGATGATGAAAATGGTCCAAAACCAAACAGTGACTTGGAGGCAGGAAAGACACTGCCATTTATTTATGGTGACATACCTCCAGGAATGGTTTCTGAACCTTTGGAAGACCTGGACCCATATTATATCAATAAAAAA
Seq A exon
GTGAGTGAATATTCTTTTGCACAAAATAGAATATCATTTTCTGCACTTGAGATAATTTTTTTATCAGAAAAATATGATGGTTAGAGTCACCCAGCCGCTAAATACATTGAAATATCTTTTCATCTAAGAGAACTGATTTATGCTCTTCTACACTGTGACTTCTTCAGCATCTATTGAATTACTTGCTATTTACCTTAGTTTAAGGGAGCTATAACTTCCTTGAACTTTCTTGAAGTTGAGCACATGGCTGAATTTTCCTGATTTCACTGTAGCAGTAAGGCTGGATATGGGAAACAAAATAGTCCAAGCATGATTTTTCAGTGAAGATGGTTGTATATAACCAGATAGCATCAGATCACCTAGTTCAGTGAAATAAAAGACTATAGCCGTATTTCTTACTTCTGCTATAGCTTCTTACATTCTTACATAGATATATATATAAATGGCACAGGGTCTTTTTAAATCTTGGATCTTACAAAACAGACTAGTTGTAAAACAACTCTGGAATAAAGTTTCATAAATAAGTTCAGGTATAAAGTTCTTTGAACAGGTCTACAAATGAAGTGTCAGAAAACTGAGCACTGAAGTGTAATTCCTGATATCCAATCAGAAAAAGTAGTCATAGCTTGAGAAACTCAGACTACTGATGGACTTGTTAGGCTACTGAAAATAATCAGTGAACTGCAGAATCTTTTATCACAGGTGACATCTGCATTTACATTAAATACTAGCCTAATGTGCTCAACAGAAAACAAATGGACATCTTAAATGATGAACAGGAATTAATCATCCCTCCTTCAATTTGTAGCAGAAATTACTCTTAATCACTGCCTTGTCCATGCAGAGAAAATCATACAGGACTTGGAGGCTGCCTTCAGGGTGACCTTGGGACAGGCAGAATTGTTCTACTATTTCTAACTGGGTGAAAGACTGACAAGCAGAGAGAAATGCCAGTAGGTGTAAGGGCACTGTCATCCTCAAAGCCATGCACAGCATCACTGTGTGAGCAGGTGCTGGCAATGGTCCATTGCCTGTAGGCTTTCCCAGCAGAATGAGGTCTTCTTTCTCTCCCAGAGGGAGCAGGCCAGGTAGGCAGCAAAGGCCATGGGCAGGGCAGCACTTTTCTGATCAGAGGCAGGAGAATAGAAATCAACATGGAAAGCAGTGATACTATATAGCTCTGCTGAGACCATAAAAAAGACTCTATTATGGCAACACAAAGCAGAGCCATTAGCACTGACAAAGAGCAAAAGGAATGAACAATGGTCACCTCCTGAAGAAATTTCAGACAGTACTAAAGATGCAAGTATATCGCAAGCACAAATAAACTTGGAATAAAAATTAAGACACTTTGGCAATGACTGCCAACGGGAACAAAATGAAAGTGAACGCTCACCATATGTTTATCAGGTTATATTTAAAAAGATAATAACTACCTAGATTTGGTGCCCACAGATGTGGAAAACAAGAGCATATTATTATATTATTGAAAATATTTTTTATTGATGAAATGCCGTATTTTGCTATGACTGATAAACTGAAATTTTTGCTGATAATTCCCACCAATGTTAATAGTATTTGAATTCAGTCTGTGTGCTAGGAAAGTCAGTGAACTGGAGAATCATTAATAGAAGGTTTAATCCATTGTATTTATAGAAATCAGTTGTTTTCCTACCACAGGTAGACAGTAGAATGAAACTTGAAACTACCAGATGGAGAATGGAATACTTAATAAGGAGATGAAGACACTTGTACAGTCAATGCTGCATTTTAATTGTATAATTTTTGTTTTGCAG
Seq C2 exon
ACTTTCATAGTATTGAATAAGGGAAAGGCAATTTTCCGATTCAGTGCCACATCTGCCTTGTATATTTTAACTCCTTTTAATCCCATCAGAAAAATTGCTATCAAGATTTTGGTACATTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011040:ENSGALT00000017981:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.348 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GCCAGGACCTGAAAGCTTCC
R:
TCTTGATAGCAATTTTTCTGATGGGA
Band lengths:
350-2146
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]