DreINT0131548 @ danRer10
Intron Retention
Gene
ENSDARG00000005775 | scn8aa
Description
sodium channel, voltage gated, type VIII, alpha subunit a [Source:ZFIN;Acc:ZDB-GENE-000828-1]
Coordinates
chr23:27327014-27327477:-
Coord C1 exon
chr23:27327373-27327477
Coord A exon
chr23:27327285-27327372
Coord C2 exon
chr23:27327014-27327284
Length
88 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGT
5' ss Score
6.99
3' ss Seq
GATCTTTTTCTCTTGTTTAGAAC
3' ss Score
9.4
Exon sequences
Seq C1 exon
TTTGGAGGTCAGGATATCTTCATGACTGAGGAACAGAAAAAGTACTACAATGCAATGAAAAAGCTTGGCTCAAAGAAACCTCAGAAGCCCATACCCAGACCCCAG
Seq A exon
GTGTGTACAGCACAGTTGAAAAGTGATTCTTTTCTCATTAAATTGACTTGAGTGGAGTTATAATATGTGATCTTTTTCTCTTGTTTAG
Seq C2 exon
AACAAGCTCCAGGGTATGGTGTTTGACTTTGTGACACAGCAGGTCTTTGATATTTCCATCATGATCCTCATCTGTTTGAACATGGTCACCATGATGGTTGAGACAGATGATCAATCACAGGAGACGGAAAACATTCTGTACTGGATCAACTTCATCTTTATTGTGGCCTTCACTTCAGAGTTTGTCCTGAAGCTCTTTGCGCTGCGTCATTATTACTTCACCAATGGCTGGAACATCTTTGACTGTGTTGTGGTCATTCTCTCTATCGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005775:ENSDART00000022042:25
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.5=47.3)
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:
AACCTCAGAAGCCCATACCCA
R:
ACAGAATGTTTTCCGTCTCCTGT
Band lengths:
168-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]