DreINT0131546 @ danRer10
Intron Retention
Gene
ENSDARG00000005775 | scn8aa
Description
sodium channel, voltage gated, type VIII, alpha subunit a [Source:ZFIN;Acc:ZDB-GENE-000828-1]
Coordinates
chr23:27327571-27327848:-
Coord C1 exon
chr23:27327795-27327848
Coord A exon
chr23:27327709-27327794
Coord C2 exon
chr23:27327571-27327708
Length
86 bp
Sequences
Splice sites
5' ss Seq
AGGGTAATT
5' ss Score
6.62
3' ss Seq
AAATTTCATTCTCTTCTCAGGTG
3' ss Score
8.98
Exon sequences
Seq C1 exon
GCAACCTTTAAAGGATGGATGGACATCATGTATGCAGCAGTTGACTCACGAAGG
Seq A exon
GTAATTTGTTTGTAGAGTTTTAAATGCCAATTAGTCGTGAGTAAGTGAGTTCCAAGCACCCATTTCAAATTTCATTCTCTTCTCAG
Seq C2 exon
GTGGAAGACCAGCCGAAGTATGAAGACAATATCTACATGTATATCTATTTTGTCATCTTCATTATATTTGGCTCTTTCTTCACCCTCAATCTCTTCATTGGTGTGATTATTGATAACTTCAACCAGCAGAAGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005775:ENSDART00000022042:23
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(7.4=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(15.2=76.1)
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:
TGGACATCATGTATGCAGCAGT
R:
TCTTCTGCTGGTTGAAGTTATCA
Band lengths:
168-254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]