DreINT0131534 @ danRer10
Intron Retention
Gene
ENSDARG00000005775 | scn8aa
Description
sodium channel, voltage gated, type VIII, alpha subunit a [Source:ZFIN;Acc:ZDB-GENE-000828-1]
Coordinates
chr23:27363655-27366871:-
Coord C1 exon
chr23:27366599-27366871
Coord A exon
chr23:27363791-27366598
Coord C2 exon
chr23:27363655-27363790
Length
2808 bp
Sequences
Splice sites
5' ss Seq
GAGGTGATA
5' ss Score
3.13
3' ss Seq
AATTGTTTTCCTCCTGACAGCCG
3' ss Score
8.8
Exon sequences
Seq C1 exon
TCTTTGCTCAGCATCCCAGGCTCTCCATTCCCTTCGAGGCGCAACAGTAAGAGCAGCATCTTCAGCCGCTGTAAAGACGGAGGCTCTGAGAACGAGTTTGCAGATGATGAGCACAGCACGGTTGAGGAGTACGACGAGCGGCGCGACTCCTTCCTAAGCCCTCAGCGTCGCAGCAGCTACACAGGCTTCTACGGCAAGCGCAACAGCACAGTGGATTGCAATGGAGTGGTGTCTCTCATTGGGCCGGGGCCTGGCGGACGCCTTCTGCCTGAG
Seq A exon
GTGATAATAGATAAGGCAGCCACTGATGACAGCGTAAGGAAGTCTAAGAGTAGATCAGTCTAGGCATGGGCATTATCTATCTCTGAATCGTGGCTCTCTTTCTCTCTCTGTTTGGCTCTTTCTCTTTCTGATGCATTCGTGTAATGGTTATTTTGACTTTGCTCTAAAAGTAGCTGCCTTTCAGTTGAGGACTGCTCTCAAAGCCTGTGTGATATGCTGCCTTCCTATGCTAGTTTAAAATTAGCTTACTACCGTATAGATAGATCTCACTAAATAAACTGCTAAGATTTAGCTGTTTCCTACACTACTGTTGCAAAGTTTGGAGTTTTGTAAGATGTTTTACATATATATTTTTTGAAGACTGCATTCATTTGATCAAAAGCACAGCAAAGATTTAGTAAAATTGTATTGCATTATAAACTGTACACTTAAACTACTTAAAAATGTAATTTGTTCCTGTTTTTCGTTAGTCATTTCTTCTGTTTTTAGTGCTAAATTGTTGGAAAATCTAATCAATTTCATGCATGTTCAATAAAAAAGGTCAGGAGCAGTTTTTCTTCAATGTTAAAAATCTTAGTAGTTTATTGGATACAAAGTGAATAGTTCTATTCACAGAACTCTGGTATCCCCAATGCAACGCAAGAGTTATATTCAGAGGTGCGCAATAAATTTCATTTCCTGATTCGCGCTTTTATACCTAGCTGATATAAACAGGTGGAGTTTAGTAGAGTTTGTCACTTGTCAAGCCTTCTCAAGTCCTCCATTGGCCGCACCCATACATACTTCCTCTTTCTCTCGAAATTCTCTGCACAGCATTAAAAGCATAAGACTTTCAAACACATTTCTGCTGTCAGGAAGTTTAACTGCCGAGTTAAGTTTAGACCATCAGGCCTTTGCATTTCTATCAGCTTCATCTACTTCTCAAACAATGCTTTATTAGCATGCAGGGCATATCACACTCAACAGAAGAAATTCAGTTAATGAATCACCTTTAAGCAATACAAATACAATTGTTTAATTAAAAGAAAAAGAGACAAAAACTATTTTAAAAATTTATTTTTTTCACAATACGTTATACTGTAGAAATCATTCCTTTGTGCTGATTTGTTGCTGAAAATACAGTTAGCATCAGTGTTGAAAGCAGATTTACTAGTTGATATTTCTGTGGGTCAATAGAAAGTAAAAAGAATCTAATTGAAATCTTTTGTGGCATTATAAACTGTCCATTTTGATCAACGGAATGCATCCTTGCTGAACAAAAAGTATGAATTATGTTTCAAAAGATCTTCATGGCACCAAGATTTTTAACAGTAGTCTATGTCTTAGTAGCCGCAATTTAGTATTCATTGCATCATCTCATTACACATTCATCCCACCAGCAAAGTCTATCCTTATTTTTTTCCCCTCATTTCATTTACTTGATAATAAAGTGCTCTTTTTCAAGTAAATTTTAACTCAGTGTATGTATCTGTATTTCAGTTTATATTCATGTAAAGGTGAATTAACCATGAAATGAGGCCACCACATCCACCCTCCAGGCTTTAGTTCTTTTTTCATATTTTTTCTTCATCTTTCCACCATATATTTACTGTATATACATTTCCTATATAATTCCTTCATCGTAGTGTATGCATGTATTATTTAGACAGTCAGCACCGTTGCTCAATATTGTAATTTTAGTTGAAGTTTTGTAGTTAGCATGGTAGTCTGCTAGCTTTTATGGATTGTATAGAGGTAAGGTACAGCTTCAGATCTTAAGCATGAGGTTAATGGATCATGATATTTACTCTTTTTCTCTCTTGACTTCTTTGATTGAATGCATGCTGATGCATGCTGACTGGATCTCCTAAAAGCTGGAGATGCAGGGGCTTCAGATGAGAGGAGGAAGGGAGCGGAGGACCATCACTGGTTTACATAGCCTTTTCAGCATTGTAGATATGTAAAGCGTAGATTATACTGTAAAACAAATGCTTTACTATTTAAATGTCCGTATGAGGGCAAATCTTTTTGATTCTCTATCCTTGAGCATTTTAATAATGTTCAGCATGTTATTCATGTTCTTGTTGGTTAGCAATGGGCGATATGAACTTCTATAACACCATTCGTCAGTGACAATAATTCAGATGTACTGTTAGCACTGAGAGACATTAAAGATATGTACAGTATCTTTAGAGAAAGACATTAAGGCACACATGTAATGTAATATCTGTTTCATTCATACTGGACGCAAAGAGGAAGTAAAGACATCAAATATTTCTGTAGCTAAAGAAAAAGAAGACGAATAAAAGCAAAGAATGTATAAACTGATCAAATCTGCATACAATAAACCATATCTTTGGGTATTTTTTTTTTTTAAGAATAATATATATTTATAATCCAATGATAATAGACGACTACTGTTCACGTATATAATATTAGCAAATCTTGTTTGCTTGATTTTTAAACACTGGACTGATGTTAGCAAATTCCTCTGTTTTCTAATTCTTATCGTGGGTACAATTTGTATTGGTATATTTCAAAAATAAGATATCGCCAATCTCTAATATTGGTAATATGTATGACACAAATGGTAATGACAATTTAGCATTTATCTCCACCCTACCTTCTCTCTTACTGACAGCCCAGCATGTTTCTGCTTCAATGCATTCAAGTGGTTCCTATTGAACAAACCTATAAATTGTATCAACTGTTGTGCTTCTTCTAACCAACCTTCTAACCAACTAGCTTTGTATTGCAGATTTTTTCTTCCAGCTGCACTGTATTATGTTATGATGGGTCTGTTTAACCTAATTGTTTTCCTCCTGACAG
Seq C2 exon
CCGACCACTGATCTTGAAATTAAGAAGAAACTCTCAGGCTCTCTCATGGTTTCCGTAGAGCAGCTTAACACATCATTCGGGCGCAAGGAGCGAGCAAACAGCGTGATGAGTGCGTTAACCAACACATTGGTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005775:ENSDART00000022042:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.571 A=NA C2=0.022
Domain overlap (PFAM):
C1:
PF0310514=SPX=PD(30.8=67.0),PF119333=DUF3451=FE(46.4=100)
A:
NA
C2:
PF119333=DUF3451=PD(19.1=80.4)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]