GgaINT0046959 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19323536-19325137:-
Coord C1 exon
chr7:19324856-19325137
Coord A exon
chr7:19323590-19324855
Coord C2 exon
chr7:19323536-19323589
Length
1266 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
CAGCAGTATTCTGTTTATAGGCT
3' ss Score
3.51
Exon sequences
Seq C1 exon
GTGGTTGTAAATGCCCTCTTAGGAGCAATTCCATCCATTATGAATGTGCTTCTTGTTTGCCTTATATTCTGGTTGATCTTCAGTATCATGGGAGTAAATCTATTTGCTGGAAAATTTTACTACTGTGTTAACACTACAACTGATGAGAGATTTGATATCAGCCAAATCAACAATTATAGCCAATGCGAAGAGCTCATTAAAAACAATGAAACTGCCAGATGGAAGAATGTGAAAGTTAACTTTGATAATGTAGGCCTTGGTTACCTTTCTCTACTTCAAGTG
Seq A exon
GTAAGTCATCACTCCTGAATTTCTATTTCTCTTTTCATATCTCTGTGGTTTACTTCTAACAGAAAAAGTTATTTCAATTTGTTCCTTTCAAATAGAAATATTTTTCCTCACTTCTTTTGGCATTATGCTTATAAAAATCCTTAAGTAATCTGTGGAATCTGTGTTTTAAAAATATATACATATGTATGTGTGCATATACATGTCTCTGTGTGGAAAACTGTAAGCAGAAATGGATTTTTAACATATATAGAATGTATTTTTAACCTTTCTTCAAGTATACATCAGCCTTACATCTCAGTTCATCTGATTATAGATTGGCTTTGCTTTTTTTTCTGTTTGATTATGTATATAGTATGCTTCAACTTGTTGGAAGTTGAGCTTGGTTTCAAAAGAGCTGAACTTGTAGGAGCATATGTGAAAGTTTGGTGCTTTCAGAATTCTCACAACTGAGATATAAATAGTTAACTGTTAACGATATATTCCTGTTTGTAAAGCTTCTCTAAAATTGAACTTACATATACTTAAAATTCTTAATATACTTTACAGGATTCTAACTTAAAACTACTATATGAAAACATGCTTCCCAGGATATTTTGCCAGCAATTCTAAGAATCCTGTGAATTCATACATTCCAAATTAAATATGTTTCTCTTATCTTTCTGATTATTAGGGCTTTAATATGTTCTTTAGATTTGGGATCACCTGTGCTTATACATAGGAACAATAGTTATTCCTGATCCAGAGTGCTATTTATTTCCGTGAGCTATAAAGTCAAATAAATCTGAACTCTTGCTCAAAAACTGTGGTATCACCTCAACAGTTGATAAAAGTCATCCATTAGAGCCAAGAGCTGGGGATAACTCTTAAGTGTGAATAAGTCTGTGAAACTGCATAAATAATATGAAGTATAGAGGCCGTAGTGACTATCGTAAGAAAAACAAGCAATTAAATTTACCCAAGTTGTGTTGAATCTGTATCAAGTTTACCTACTTTGCTCATACACCGAAAATAACTTGTATCGGGTGTTACTCATTACACATAAAAGTTCCTAATTTAATGGAGGTTGTGTCCTTTATAGTCAGATATTACAATTTGCTTGTGATTCTCATATATGAATAAACGTACAATGTTTTATTGCCTATTAATATTACACTGAGCTGGTGTTTTGGATAAGTTCTAAACACACTTAGTCTTCAGCTCTTAAATATTTCTGACAAGCCATTTCCCAGGAAAAGCATGAGGTAAACAGCAGTATTCTGTTTATAG
Seq C2 exon
GCTACATTTAAAGGATGGATGGATATCATGTATGCAGCTGTGGATTCTCGTAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:19
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(40.6=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.4=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:
GTGGTTGTAAATGCCCTCTTAGGA
R:
TTACGAGAATCCACAGCTGCA
Band lengths:
335-1601
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]