DreINT0131517 @ danRer10
Intron Retention
Gene
ENSDARG00000034588 | scn4ab
Description
sodium channel, voltage-gated, type IV, alpha, b [Source:ZFIN;Acc:ZDB-GENE-051201-1]
Coordinates
chr3:22179531-22180026:+
Coord C1 exon
chr3:22179531-22179631
Coord A exon
chr3:22179632-22179755
Coord C2 exon
chr3:22179756-22180026
Length
124 bp
Sequences
Splice sites
5' ss Seq
ACGGTAATA
5' ss Score
6.25
3' ss Seq
GATATTTCTGATGTTTGAAGAAC
3' ss Score
3.54
Exon sequences
Seq C1 exon
GAGGAACCGATATCTTCATGACAGAAGAGCAGAAGAAATACTACAATGCCATGAAGAAACTTGGATCTAAAAAACCCCAAAAACCAATTCCAAGGCCCACG
Seq A exon
GTAATATACTGTCTTTTTTTATTTTCAGATTATTCTTAAAATGAATAGACTTAAAGTTTATATGCTACTTATTTCACTTACTAACTGCTCTTTCTCCTCCATGGGATATTTCTGATGTTTGAAG
Seq C2 exon
AACTGCTGCCAAGGTTTGGTCTTCGACTTTGTCACACAGCAGTTCTTCGATATTTTCATTATGGTGATGATCTGCCTGAACATGGTGACCATGATGGTGGAGACTGACGACCAAAGTGCTGAGATAGAGGAAATATTGTTCTATATCAATTTCGCCTTCATCATACTCTTCACCGGGGAGTGTGTTCTCAAGATCACTGCACTGCGCTACCACTACTTCTCCATTGGGTGGAACATTTTTGATTTTGTGGTGGTCATTCTTTCAATATTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000034588:ENSDART00000044157:22
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.5=47.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAACCAATTCCAAGGCCCACG
R:
TGGAGAAGTAGTGGTAGCGCA
Band lengths:
244-368
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]