RnoINT0108903 @ rn6
Intron Retention
Gene
ENSRNOG00000017816 | Pde6a
Description
phosphodiesterase 6A [Source:RGD Symbol;Acc:1306835]
Coordinates
chr18:56558432-56559830:+
Coord C1 exon
chr18:56558432-56558584
Coord A exon
chr18:56558585-56559740
Coord C2 exon
chr18:56559741-56559830
Length
1156 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
CATGCCGTTTGAATTTGCAGATT
3' ss Score
9.37
Exon sequences
Seq C1 exon
GATGAGCATTTCTGCGACTTCGTGGACAGCCTCACAGAATATCAGACCAAGAGCATCCTGGCATCCCCCATCATGAATGGGAAGGACGTGGTAGCCATAATTATGGCTGTGAATAAAATAGATGAACCCCACTTCACCAAGAGAGATGAAGAG
Seq A exon
GTAAGGCTGCTTGAGATACTGCTGAGGAGGCCGCGCTAACCCATTCTTCCAGCTCATGGAATTCTCCAACCTTGCTGTTAGGCTTGGCTTTAGTTTTCCCAAATCTAAGGCTGGGGGACAGCCAAGCACGGTGGTCCATGCCTCCAATTTCAGTATTTGACAGGCTGTGGCAGGAGTACTGGCATAAGTCTGGTGCACACCCGTAATTATAATTGTATAGCCTGGGCTCCAGTTCCAGAGTAGCACACACTACAGATCAGACCCTGTCTCACAACTAAAAGAGAGAGAAAGAGGGGTGTGGGGGTTCACCTGCTAGTCTCTGAGAGAGACAGGGGAAGATGACAGTGCAGACACTGGATTTGGGGGTTAGGAATGGAGAGGTGATTGGTCTGGGACTCTCAAAATCTTGTTTTCTTTGGACAAATCACTCTTTGTCTTAGGGTTCTATTGTTATGAAGAGACACCGTGAGGACAGCAACTCTAACAAATGAAAACATTTACTTGGGGCCGACTCATACACAGAGATGTAGTCCATTGTCCTCATGCTGAGACACATGGCAGCATCCAGGCAGGCATGGTGCTGGAGAGTTAGCTATGAGTTCTATATCTGGATCGGCAGGCAGCAAGAAGAGAAAGAAAGAGAGAGCCTGGATTGAGCTTCTGAGATCTCAAACCCATCCCCAGGGACACACTTCCTTCAGGAAGGCCACACCTACTCCAACAAGGGCACAGGTCCTAATCATTTCAAATAAAGCCACTCCCCAGGAGCCCTTGGCGGCCATTTTCATTCAAACCACCTGATTTATCTTCCCTGAATGTATTGGGTTTTTTATTTGTAAACTGGTGTGATTTCACAGGATCTACCTCACAGTGACTTGTAATGACCAGGTGCCATATACCGGTGACTTATCACAGGGGCATCAAGTTCCATACATACTAAATATTTGTATTAATACACCCCCATTAACTAACCAACACGCACTTTGAGTTTCCATTCACAGTGAGACAAGTGAAGGGTCTGCACTCCACGGCTCAGCTGTGCAAATTACTTCTGTGCTGGCTTTAATGGGGGATCAGACATTTGCTGGTGGCAGAAGAATCGAGAAGAAGGATTTCTCCTTCTCATCGGCTTCCCTCATGCCGTTTGAATTTGCAG
Seq C2 exon
ATTCTTCTCAAATACCTCAACTTTGTGAATCTGATCATGAAGGTATTCCACCTGAGTTACCTGCACAACTGTGAGACCCGGCGTGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017816:ENSRNOT00000024171:2
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:
GCATTTCTGCGACTTCGTGGA
R:
GCCGGGTCTCACAGTTGTG
Band lengths:
230-1386
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]