RnoINT0108901 @ rn6
Intron Retention
Gene
ENSRNOG00000017816 | Pde6a
Description
phosphodiesterase 6A [Source:RGD Symbol;Acc:1306835]
Coordinates
chr18:56609191-56609563:+
Coord C1 exon
chr18:56609191-56609254
Coord A exon
chr18:56609255-56609488
Coord C2 exon
chr18:56609489-56609563
Length
234 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
ATCGGGTCCATTGGTCGCAGGTG
3' ss Score
4.95
Exon sequences
Seq C1 exon
GGCCATGATGATGACCGCCTGTGACCTCTCAGCCATCACCAAGCCCTGGGAGGTGCAGAGCAAG
Seq A exon
GTATGGACACTTCTTGGCCTGGCAGAGGGAGCTCGGTATTGCTGACCACAGTTACTGAGGCTGGACCCTCTTAGCCCAACCCTACCTTCTCTCCAGTGATGAGGGGGAGTACCAGGGAGGGGGTGGGCTTGCCTCTTTTGCTGAGCTTGAAAGCACAAGTGGAGTGGGAGTAGGGATAGGAGGGGTGGGCAGTGCACATGTATGCATGTATGTGATCGGGTCCATTGGTCGCAG
Seq C2 exon
GTGGCTCTGCTGGTGGCTGCTGAATTCTGGGAGCAAGGTGACCTGGAGCGCACAGTGCTGCAACAGAATCCCATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017816:ENSRNOT00000024171:18
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=0.200
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(8.4=100)
A:
NA
C2:
PF0023314=PDEase_I=FE(9.6=100)
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:
CCATGATGATGACCGCCTGTG
R:
TGGGATTCTGTTGCAGCACTG
Band lengths:
135-369
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]