RnoINT0108913 @ rn6
Intron Retention
Gene
ENSRNOG00000017816 | Pde6a
Description
phosphodiesterase 6A [Source:RGD Symbol;Acc:1306835]
Coordinates
chr18:56580935-56581632:+
Coord C1 exon
chr18:56580935-56581084
Coord A exon
chr18:56581085-56581488
Coord C2 exon
chr18:56581489-56581632
Length
404 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGG
5' ss Score
8.98
3' ss Seq
AACTCGTTCTTTCTCTACAGTCT
3' ss Score
8.85
Exon sequences
Seq C1 exon
AAAGAGCCTCTGGATGAATCTGGATGGATGATTAAAAACGTACTCTCCATGCCGATTGTCAACAAGAAGGAAGAGATCGTGGGCGTGGCCACATTTTACAATCGCAAAGATGGGAAGCCCTTCGACGACATGGACGAGACCCTTATGGAG
Seq A exon
GTATGGGATGCTGGGTGGCCCTTGGTTGATGGGGTTCAGCTTCGGGGTTGCCCTCCAGAGTTGTGCAGCTGTGAGGGGGTGGGGTGGGAGGTCATAATCCTGAGGATCCTTGAGAGCCGCTTTCTCCACACTCCTTCCTTACTTCCACCCTTCACTATGGGGAGCAGTTTTGGGGTCACCTGTTGAGTTCCTCCGCACATCCTGCTTGCTCCACACATTTCTATTCATGACATTATTACTTGCCAGTCTTCCCTTAAAATGCATTCACACCCATCATTTTATCACAGCCTGGCTGCCCCACACAGCTTTTGCAAAACCCACTTTATAGCTGAGAAAACTGAGGTCTCAACAGTCAGCATCCGACTCCAGGCTGCCACCGCCTCTAACTCGTTCTTTCTCTACAG
Seq C2 exon
TCTTTGACTCAGTTTCTGGGCTGGTCAGTCTTAAACCCTGACACCTACGAGTCCATGAACAAACTTGAGAACAGGAAGGATATCTTCCAGGACATCGTAAAATATCACGTCAAGTGTGATAATGAGGAAATTCAGAAGATCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017816:ENSRNOT00000024171:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0159021=GAF=FE(27.5=100)
A:
NA
C2:
PF0159021=GAF=PD(5.1=18.8)
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:
AGAGCCTCTGGATGAATCTGGA
R:
TCTTCTGAATTTCCTCATTATCACAC
Band lengths:
287-691
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]