DreINT0131551 @ danRer10
Intron Retention
Gene
ENSDARG00000005775 | scn8aa
Description
sodium channel, voltage gated, type VIII, alpha subunit a [Source:ZFIN;Acc:ZDB-GENE-000828-1]
Coordinates
chr23:27388261-27388569:-
Coord C1 exon
chr23:27388480-27388569
Coord A exon
chr23:27388390-27388479
Coord C2 exon
chr23:27388261-27388389
Length
90 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
ACCTCCTGCTTTTTCCTCAGGTA
3' ss Score
11.87
Exon sequences
Seq C1 exon
AGTATTCAGCATGTTCATTATGTGTACGATTTTGACCAACTGTGTGTTCATGACTTTTAGTAATCCTCCCGAGTGGTCCAAACAAGTAGA
Seq A exon
GTAAGTATTGATCCAAACCACATAATGCCTCATTCACAATATATACCACAGTTGTTTTATATATATTTTAACCTCCTGCTTTTTCCTCAG
Seq C2 exon
GTATACTTTCACTGGAATTTATACGTTTGAATCAGCAGTAAAAATCATTGCCCGTGGATTCTGTATAGATGGCTTCACATTCCTTAGAGATCCATGGAACTGGCTGGATTTCATGGTCATCTCAATGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005775:ENSDART00000022042:4
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=PU(0.8=6.5)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.1=100)
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:
ACGATTTTGACCAACTGTGTGT
R:
TCCAGCCAGTTCCATGGATCT
Band lengths:
173-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]