DreINT0115079 @ danRer10
Intron Retention
Gene
ENSDARG00000051861 | pkp3a
Description
plakophilin 3a [Source:ZFIN;Acc:ZDB-GENE-060512-114]
Coordinates
chr25:22065779-22066152:-
Coord C1 exon
chr25:22066035-22066152
Coord A exon
chr25:22065944-22066034
Coord C2 exon
chr25:22065779-22065943
Length
91 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATT
5' ss Score
8.83
3' ss Seq
CTGTGTGTTTTCTATATCAGGGT
3' ss Score
10.43
Exon sequences
Seq C1 exon
GAACATGAGCTCTGTAAATGAGAAGACCAGACAACTGATGAGAGAAACCAAAGGCCTCATAGACGCTCTGGTCGGCTACATTAAGAAATGTGTGGTGGACAGTAAAGTGGAAGAGAAG
Seq A exon
GTAATTGTGCAACACACACTGTACTTCTGTCTCTGTTGTTAAAAGCTGTGTGTTTTTATTTGAGAATTTATCTGTGTGTTTTCTATATCAG
Seq C2 exon
GGTGTGGAGAACTGTGTGTGTGTGTTAAGGAATCTGTCCTATCAGGTGTACAACGAGATCCCCCCCTCTATAGCCTCACGTCTAGATGGTCCGCGTCGTGCTCAGAGCTCTTCAAAAGCAGAACCCATCGGCTGCTTCACTCCTAACAGCAAGAAAGCCAAAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000051861:ENSDART00000123211:7
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=0.273
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TGTGTGGTGGACAGTAAAGTGG
R:
CTGTTAGGAGTGAAGCAGCCG
Band lengths:
179-270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]