DreINT0131581 @ danRer10
Intron Retention
Gene
ENSDARG00000018032 | scn8ab
Description
sodium channel, voltage gated, type VIII, alpha subunit b [Source:ZFIN;Acc:ZDB-GENE-060906-2]
Coordinates
chr6:39442362-39442918:-
Coord C1 exon
chr6:39442855-39442918
Coord A exon
chr6:39442504-39442854
Coord C2 exon
chr6:39442362-39442503
Length
351 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAAG
5' ss Score
5.2
3' ss Seq
ATTTGTGTGTGTTTTTGTAGACG
3' ss Score
8.8
Exon sequences
Seq C1 exon
CAAACTTCTACTTCCTGCCAGGCATGTTGGATGCACTGCTATGTGGAAACAGCTCAGATTCAGG
Seq A exon
GTAAAGAGTGAAAACATACACCTATAATTATTCAACATTCCCACTACTAAATCTAAATACTAAATGTATTTCATTATTTCAAGTCTGGAAATTACATTTACACATGAAGCTCTATGGGGTGACCATTCAATGTCAAGATATGATGCATTAAAGAAATTGTTAAAGTAAACTCGTTGCCTATAATCATTAAGTAAATAAACTCTTTGCACAATGATAAAAGGTAAGTCAAAGAGTTTCAATGAGAATCAACTTGTTGCTTTTAAGGCAAAGGGCTTACTCAGTTATTTAAAGTAATTAATCATTTTTTACAGTGTGCAGTGTTGGTGGATTTATTTGTGTGTGTTTTTGTAG
Seq C2 exon
ACGGTGTCCGGAGGGCTATACTTGCATGAAGGCTGGACGCAACCCAAACTATGGCTACACAAGCTTTGACTCCTTCGGTTGGGCTTTTCTTGCTCTCTTCCGACTGATGACACAAGATTTCTGGGAGAATCTGTACCAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018032:ENSDART00000151299:8
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(8.4=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(18.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTTCTACTTCCTGCCAGGCA
R:
TGGTACAGATTCTCCCAGAAATCT
Band lengths:
199-550
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]