RnoINT0108955 @ rn6
Intron Retention
Gene
ENSRNOG00000016593 | Pde6c
Description
phosphodiesterase 6C [Source:RGD Symbol;Acc:1309844]
Coordinates
chr1:256849250-256850422:+
Coord C1 exon
chr1:256849250-256849399
Coord A exon
chr1:256849400-256850278
Coord C2 exon
chr1:256850279-256850422
Length
879 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
TCACCGTTCTTCCACTTCAGACT
3' ss Score
9.31
Exon sequences
Seq C1 exon
AAAGGACCAGTGGACGAAACTGGCTGGGTCATTAAAAATGTCTTGTCCCTGCCTATTGTCAACAAGAAAGAAGACATCGTGGGTGTGGCTACGTTTTACAACCGGAAGGATGGGAAACCCTTTGATGAGCATGACGAACACATCACTGAG
Seq A exon
GTAAGCGTGGGAAAGAACAGCAGATGTATCTGAGGATATCACGAAATGATGCCAGCCGTGGAGCTACTCCTGAGTCTGCAGGGATATTGTGAAGAGCACGTAAGACACGAGTCTCATAATTGTAATCAGGATATCGTTACTGTGCCATTTCTGTTTCCAGGTTGCTATATACTGCAACATTTTCTGTTTGATTTCACCCAAAATCTTTCCAATCCTATAAAAACATTGAAGAGTACTTTTTATTCCTCCCTTTCTTTTTATAATCTCTCTCCTTCTCAGTCTCAAACTTCTGTCTAATTTTTAGCTCCTACTTTATTTTATTCTCTTCGGCATTCCTTTCCTGCAGGAGAACATCCTTGAGGCTTGGCACTTTGAAAAGCAAAGCTTGTTAATTTTACTGTCTGGGCAATAAATTCAGTTTTTTCCCCCTTAGGTTGATACAAAGAACTGGGTTGGCATTGTGAGAGAAGGAGGGCTCCTGAGTCCCACCCCTTAGCTGAGGAGCCATCGTTAATTGGTGGCTGCTGGAGAAGGGTCAGTTTTCTTTAGGAAAGAGCCCCTGAGAAGCTACTTATGCTCCAGTAGCTGGTTCCACACCCACGCACATACAGGCAGCCCTGAGTGGCTCTGAACACACAGGTCATGAAGTCAGGAAGTAGGATGGTAGGGGAGGAACTAGAAAGAAGAGAACAGAGGTGAATTTGATTAAAGAGATTATATGCACGCATTCATTTCTCAAGCAATAATAATTTTTTAAAGGCAAGAACTGGGTTGGTGGTGGTGGAAGGAAGATCAGTATAGCAAAGTATGCGGGGTTTTGTCCACAAAGCAATTTTTATTTAATGTTAGAGGATCTGAGTCACCGTTCTTCCACTTCAG
Seq C2 exon
ACTTTAACCCAGTTTCTTGGATGGTCTCTTTTAAACACCGATACCTATGAGCGAGTGAACAAGCTGGAAAGCCGAAAGGACATTGCTCAGGAAATGATTATGAACCTCACCAAAGCCACCCCTAGTGAAATCAGCTCTATTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016593:ENSRNOT00000022317:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.040 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:
AAAGGACCAGTGGACGAAACTG
R:
CAAAATAGAGCTGATTTCACTAGGGG
Band lengths:
294-1173
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]