DreINT0111808 @ danRer10
Intron Retention
Gene
ENSDARG00000000380 | pde6a
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:ZFIN;Acc:ZDB-GENE-030616-42]
Coordinates
chr14:24732104-24732579:-
Coord C1 exon
chr14:24732427-24732579
Coord A exon
chr14:24732194-24732426
Coord C2 exon
chr14:24732104-24732193
Length
233 bp
Sequences
Splice sites
5' ss Seq
GAGGTACCG
5' ss Score
8.5
3' ss Seq
TCCAATGTTCTGTCTTGTAGACA
3' ss Score
9.53
Exon sequences
Seq C1 exon
GACAGCCATTTCAGTGACTTTGTGGACAACTTGACAGAGTACGAGACCAAGAATGTGCTTGCGACCCCTATCATGAATGGCAAGGACATGGTGGCTGTCATGATGGCAGTCAACAAGATCGGGGCTCCTCATTTCACTGCTCAGGATGAAGAG
Seq A exon
GTACCGTTCACTCATACCATACTCAACACTAACTTCGAGCCTTGGTGTGATGATGTCAATTTGAAACGTAAACACTGCAGAAAAAATTAATTATATGCATTGTGCGACCTACGCATTTCTAATCTCCAAAAGTTTCACTGAATATTAAAACTGTTTAAGCATTCTGATTAAACTGACTTTAACAGAACAGATTAAACACTCTGCTGAACTGAATCCAATGTTCTGTCTTGTAG
Seq C2 exon
ACACTGAAGAAATATCTCAACTTTGCTAATCTTGTGCTCCGAGTGTTTCACCTGAGCTACCTGCACAACTGTGAAACCAGAAGAGGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000000380:ENSDART00000000392:2
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:
PF0159021=GAF=FE(33.3=100)
A:
NA
C2:
PF0159021=GAF=PD(8.0=40.0)
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:
AGCCATTTCAGTGACTTTGTGGA
R:
TGTCCTCTTCTGGTTTCACAGT
Band lengths:
239-472
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]