DreINT0131545 @ danRer10
Intron Retention
Gene
ENSDARG00000005775 | scn8aa
Description
sodium channel, voltage gated, type VIII, alpha subunit a [Source:ZFIN;Acc:ZDB-GENE-000828-1]
Coordinates
chr23:27327795-27328236:-
Coord C1 exon
chr23:27327952-27328236
Coord A exon
chr23:27327849-27327951
Coord C2 exon
chr23:27327795-27327848
Length
103 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGA
5' ss Score
8.24
3' ss Seq
ATACTGATTCTCCCTATTAGGCA
3' ss Score
6.87
Exon sequences
Seq C1 exon
GTGGTAGTCAACGCCTTGGTGGGTGCCATCCCCTCCATTATGAATGTGTTGCTGGTTTGCCTCATCTTTTGGCTGATTTTCAGTATCATGGGTGTCAATATGTTTGCGGGAAAGTACTACTACTGCTACAACGAGACTGAAAAGGCATACTTTGAGCTAGATGTGGTCAACAACAAATCTGAGTGCTTTGCGTTAATTGAGCAAAACTACACTGAGGTGCGTTGGAAGAACGTCAAAATCAACTTTGACAACGTGGGTGCTGGTTACCTGGCTCTTCTGCAAGTG
Seq A exon
GTAAGACTGTCTCACAATTTTAGTTCCTATAAAGTTGGTATACTGGCTACAGAAAAAGCTTTGTGTTGAACAGCTAAATTAACATACTGATTCTCCCTATTAG
Seq C2 exon
GCAACCTTTAAAGGATGGATGGACATCATGTATGCAGCAGTTGACTCACGAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005775:ENSDART00000022042:22
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(40.9=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.4=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:
GGGTGTCAATATGTTTGCGGG
R:
CTTCGTGAGTCAACTGCTGCA
Band lengths:
249-352
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]