GgaINT0046953 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19344978-19347468:-
Coord C1 exon
chr7:19347112-19347468
Coord A exon
chr7:19345458-19347111
Coord C2 exon
chr7:19344978-19345457
Length
1654 bp
Sequences
Splice sites
5' ss Seq
GTGGTACGT
5' ss Score
8.61
3' ss Seq
ATATCCTTACTGTCTTTCAGGTA
3' ss Score
11.2
Exon sequences
Seq C1 exon
CTTCGAGTTTTCAAATTGGCAAAATCTTGGCCAACTTTAAATATGCTGATTAAGATTATTGGCAACTCAGTGGGGGCTTTGGGCAATTTGACCCTGGTGCTGGCCATCATTGTGTTCATTTTTGCTGTGGTTGGGATGCAGCTGTTTGGAAAAAGCTACAAGGAATGTGTCTGCAAGATCTCCAGCGACTGTGAACTTCCACGCTGGCACATGCATGACTTTTTCCACTCTTTCTTGATTGTATTCCGAGTGCTGTGTGGAGAATGGATAGAAACAATGTGGGACTGCATGGAGGTTGCAGGCCAAACTATGTGCCTTACTGTCTTCATGATGGTCATGGTGATTGGAAACCTAGTG
Seq A exon
GTACGTAATCAGTGGGAGTTTTTATAACTAGTAAGAATGTATTTCCTGCTTTTCATAGTTCAGAAATCAGAGATGAAGACTCTTTCAGAAATCATGTAATTCATTTGCCCTTCCTCTAAACCAGGTGCAAGTATACCTTGATAAGCTATGAAAAGTGGTTTGTTTTTTTTTTTTTTACTTCTTTCAAATCTTTAGTGGGTTTGTAATCTCTTCATTAAGATCATAGCTGAATTATTTTAATAAGGTATTTCCATTAAAATGCCTTTAAAAAAATCCAACTTAATCCACCATTGCAGCCAGTTAAACTGCCTAGTCTCAAATAGTTATGGGAAATAATTGGTCATGATAACATTTATATTACTGGAATGGCTTACTTTTTCCAATTTCAGTCTTGTTTCCCAATCAAAATAACATGGCTCTTCAATTTTTTCTCATAACTGATGACTTCTAAACTACTTATGCCTTTCACTGCTGGCCTTTTAATTACTCCCAAACTGCATTCTAGATAGAGATACAAGTATCGAATAATATGGGATAGTTATACTCCATGTCCTACACATAGCATTCCTCATTATATATCCCCAAATAACATAAGACATTTCAGTACCAGCATTGCTTTCCTGATGCACTCTATATGCCTATTTCTGCAGCACTTCTGCCTTGCTAGTTTTTAACCCTTCTGTATATACTTACATTTCATTTTTCCTACCCAACATTTCCACACTAGTATTTCATCATTAAATGTCATACTGGTTTTGAATAATTTCACCAGCTTGCCATGGTTATTCCTAATTGCAGTATTTTCTTTTTGAGCAGTAGCATCACTTCTCTCTTTGATACCATGCAAAGAATTTATAAATATGCCTCAAATTTTATAAATACGCTTTTTCACAGAGATACCAAAATACTGAGTTTAACCAAACTAACTTGAGACTCCTGTGGCATACCTTCTAAATATACAGCAAAATTGAACAGAAGTAATTGATAAATATTTTTAACTATCATTTTTAGTGAAGCTTTCACTTATGCTAACATAATTACATGTAGCCCAAATTCATCTACTGTATTTGTATTGTGTAATGACAGTATGAAAAAGCTTCCTAAAACCATTTCTGAAAACATCTAAGGATTCTTTACCTTGTAGCTAGTTTTCTGGCACAAAACAAAAAATGGTATGATACAGGTATTCGAGGCAAATATATGTTTTGTTGTATCCTGAATTAGACATACTGCAATTATGGTCTTCTGAACTGTAGAAGTCTGGAATCTGCCTGCATTCCCCTTGTCTGTAAACACTGCTGAAGAAATGACTTGCATCTCTTGCATACTACATCATGTTACATCCTTTTTCTTTATGGCGTTCTCCATTATAGGGAGCAGACCTGGAAGACTTCCAGTGTGGAGTAGAAAGGAGAAAGACAAGAGTTAAATTTTCACCTATATTGGTCAAGATATGTAATTTTAAAATATTTTTAACAAGTTATAAAAAAATACCAGAGATAAGAGTATGGACTTGAAATAATAGCAACAATATGGATTGGATAAAGTGCTTGTTATGATATAAATTTTATATCACATCGAACAACATTTAGTGAAATTATTTTGTGACTTACAAGTAAGAGATCCAAAATATTATATCCTTACTGTCTTTCAG
Seq C2 exon
GTACTCAACCTGTTTCTGGCCTTGCTCCTGAGCTCCTTTAGTTCAGACAACCTTGCAGCTACAGATGATGATAATGAAATGAACAACCTCCAGATTGCTGTGGCAAGGATTCAGAAAGGCATAGATTTTGTGAAGAGAAAAGTGCGTGAATTCATCCAAAAAGCCTTTGTTAGAAAGCAGAAAGTTTTAGATGAAATCAAACCTCTTGAAGACCTAAACAACAAAAAAGACAGCTGTATTTCCAATCACACGATAGTAGAAATAGGTAAAAACCTTGCCTATCTTAAAGAAGGGAATGGAACTACCAGTGGCATAGGCAGCAGCGTGGAAAAATATGTTGTTGATGAAAGTGATTACATGTCCTTCATAAACAACCCAAGTCTCACTGTGACAGTGCCAATTGCCGTTGGGGAATCTGATTTTGAAAATTTAAATACAGAGGAGTTTAGCAGCGAGTCAGACCTGGAAGAAAGCAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:13
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=0.100
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(61.3=85.0)
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:
TGGGATGCAGCTGTTTGGAAA
R:
TGCCTTTCTGAATCCTTGCCA
Band lengths:
347-2001
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]