DreINT0131582 @ danRer10
Intron Retention
Gene
ENSDARG00000018032 | scn8ab
Description
sodium channel, voltage gated, type VIII, alpha subunit b [Source:ZFIN;Acc:ZDB-GENE-060906-2]
Coordinates
chr6:39441322-39442503:-
Coord C1 exon
chr6:39442362-39442503
Coord A exon
chr6:39441529-39442361
Coord C2 exon
chr6:39441322-39441528
Length
833 bp
Sequences
Splice sites
5' ss Seq
CTGGTGCGC
5' ss Score
6.68
3' ss Seq
CATGTCCTTCTTTCTCTTAGACT
3' ss Score
9.55
Exon sequences
Seq C1 exon
ACGGTGTCCGGAGGGCTATACTTGCATGAAGGCTGGACGCAACCCAAACTATGGCTACACAAGCTTTGACTCCTTCGGTTGGGCTTTTCTTGCTCTCTTCCGACTGATGACACAAGATTTCTGGGAGAATCTGTACCAGCTG
Seq A exon
GTGCGCATTCATTCCTCTAACGCTTGCTTTTTTATATATACTCTATGTGTTATACTCTATATATACTCTATGTGTTATACTCTATATATGTCTATGTGGTACTGGATGATTTTCTTCTTTTTGTGTCACTTTTCGTGACTGAGTGTGGAGTCGTGGGAGTTGTCGTCTTCATTACATCCTACAGGACTCCTGCAGAAATCATGTTCATGGATGAGCTAAAGTATTTAAAACCTATTAGCATGATAGTTTGAAACAGAATTAAAACGCTGAAGCAATTGCTGATAAGAGGAATTATGATGCAGCAGAGCTTTTATTATGTCAAAATCGACTGCTTCTGGTTCTTCCAGTCTTGATCATATTAAGATAATTTATCATATTAAATACACTTTACATGTTTATAATGCTAATAAAACACACAATATAGTAAATCCTATAAAACTTGGGAAAACAAACAAATCGGAAATCAAGTGTTTCAGACGACATTAGCAAGACAACACAGGACTTATTCCATCTCACTAGTTAACACTAGTAACATTTTTCTAAAATTTGGGAGAATGTAAGCAGACAAGTCAGCAAACTGTTTTTTTTTTTTTTGCTTCAACCCAAAATGGGACTAAAGGTATTTTGAGAAAAACAATTAATAATAGACCCCTTTAAACCAAGTTGGTTCTGTGAGTTTTTATTAATAATCTGAAAAAATCAGCCCTCTGAATTGGATTACATAGTCCAGCACTTTGATACACGCCTGATATTGCATGGATTAAGTAAATTGGATGGTATTTGTGCTACAGTGTTTCAAACAATTACAAAAGCCATGTCCTTCTTTCTCTTAG
Seq C2 exon
ACTCTACGAGCTGCGGGAAAAACATACATGATCTTTTTCGTTCTGGTGATCTTTGTGGGATCGTTCTACCTGGTGAATCTGATCCTGGCTGTGGTGGCCATGGCCTATGAAGAACAGAACCAGGCCACCATTGAGGAGGCTGAACAGAAGGAAGCGGAGTTTAAAGCCATGCTGGAGCAGCTGAAGAAACAACAGGAGGAGGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018032:ENSDART00000151299:9
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=0.058
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(18.7=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(12.4=44.9),PF0043013=ATP-synt_B=PU(51.7=89.9),PF0310514=SPX=PU(19.6=55.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAGGGCTATACTTGCATGA
R:
CTGTGCCTCCTCCTGTTGTTT
Band lengths:
341-1174
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]