DreINT0131516 @ danRer10
Intron Retention
Gene
ENSDARG00000034588 | scn4ab
Description
sodium channel, voltage-gated, type IV, alpha, b [Source:ZFIN;Acc:ZDB-GENE-051201-1]
Coordinates
chr3:22179306-22179631:+
Coord C1 exon
chr3:22179306-22179447
Coord A exon
chr3:22179448-22179530
Coord C2 exon
chr3:22179531-22179631
Length
83 bp
Sequences
Splice sites
5' ss Seq
TAAGTGTCA
5' ss Score
-12.56
3' ss Seq
GTTTCTGTGTCTATACTTAGGAG
3' ss Score
7.69
Exon sequences
Seq C1 exon
ATTGAATCGCAGCCAGTATATGAGGCAAACCTCTACATGTACATTTACTTTGTCATCTTCATCATTTTCGGCTCATTCTTCACCCTCAATCTGTTCATCGGCGTAATCATTGACAATTTCAACCAACAAAAGGCAAAGATAA
Seq A exon
GTGTCAGCATTTGGCCTTCTGGATCTAGAGAAACACTCAAATGTTTTCTATTTTAGAATAATTGTTTCTGTGTCTATACTTAG
Seq C2 exon
GAGGAACCGATATCTTCATGACAGAAGAGCAGAAGAAATACTACAATGCCATGAAGAAACTTGGATCTAAAAAACCCCAAAAACCAATTCCAAGGCCCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000034588:ENSDART00000044157:21
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=PD(15.3=72.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCGGCTCATTCTTCACCCTCA
R:
CGTGGGCCTTGGAATTGGTTT
Band lengths:
176-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]