DreINT0131503 @ danRer10
Intron Retention
Gene
ENSDARG00000034588 | scn4ab
Description
sodium channel, voltage-gated, type IV, alpha, b [Source:ZFIN;Acc:ZDB-GENE-051201-1]
Coordinates
chr3:22142575-22143091:+
Coord C1 exon
chr3:22142575-22142844
Coord A exon
chr3:22142845-22142960
Coord C2 exon
chr3:22142961-22143091
Length
116 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAAA
5' ss Score
1.18
3' ss Seq
CCTTTTTTTCTGTTTCGCAGACG
3' ss Score
11.55
Exon sequences
Seq C1 exon
ATGGCGCGTCTGCTCCCTCCCACAGGCACCGATGTGTTTCGGCCCCTCACTCTGGAGTCGCTCGCTGAGATTGATCGGCGGATGGCAGAGGAAGCCGCCGAGCAGGAGCGCATGAAGGAGCAGAATGTCAAGGTGGCCGAGGAGGATCTGCCCAAACCCACCAGTGATCTGGAAGCTGGGAAAGTCCTGCCGTTTATCTATGGAGACCCTCCACCAAATCTCCTCAATGTTCCTATTGAAGAGTTGGATCCGTACTACAAAGCACAAAAA
Seq A exon
GTAAAAAGCAGCACACACTTACACATGCAGTCTGTAAATATGTTCAAATATGGGTTATCAGAATAATGGTTACCCGCTCATGTGGTATTTTTTGTACCTTTTTTTCTGTTTCGCAG
Seq C2 exon
ACGTTCATCGTTATAGACAAAAAGAACACGATATACAGATTCAACACTGAACCAGCCTGTTACTGTCTGAGTCCCTTCAACCCTGTTCGACGAGCTGCCATAAGAATACTCATACACTCATATCCTATTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000034588:ENSDART00000044157:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.289 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
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:
GAGCGCATGAAGGAGCAGAAT
R:
GTCGAACAGGGTTGAAGGGAC
Band lengths:
256-372
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]