RnoINT0108947 @ rn6
Intron Retention
Gene
ENSRNOG00000016593 | Pde6c
Description
phosphodiesterase 6C [Source:RGD Symbol;Acc:1309844]
Coordinates
chr1:256874188-256874982:+
Coord C1 exon
chr1:256874188-256874271
Coord A exon
chr1:256874272-256874825
Coord C2 exon
chr1:256874826-256874982
Length
554 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
CCACCTCAACTTCTCTGCAGGAG
3' ss Score
8.24
Exon sequences
Seq C1 exon
CCTATGATGGACAGAAACAAAAAGGGTGAACTCCCAAAACTTCAAGTGGGATTCATTGATTTTGTTTGTACTTTTGTATATAAG
Seq A exon
GTATGTAAACAAATTATTTGAATGGACTGTATAATCGTTTCATTGAGAAGTTTGCTTTCCGACTATAATTAAAGTGAGCTAGGTGTGGTGGTGCACACCTGCGATCCCAGCACTCGGGAGGCAGGAGTCAAGATTTCAGAGTCACCTTGGACTACATGCTAAGTTTCAAGCCAGCCTGGGCTACATAGCAAGACCTTATCTAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAATAAATAAATAAAACTAACCAAAGTAAAAAAAAGTTAGCAATGAAGAAAAGCCATTAGGTTATTCCTCCCCTAGTAGTCTGAGTACTCACGTTTTTTTATTCAGAGTGGAGTAAAATGTACAAGAACTTACATATGAGCCATTGACAGACCTCAAAGAGCACCCATCTTTCCCAAGCTTCAGACACAGCCAGGCTCACCCCAGCAGCTCCAAACTCTGCTCCCCTCACAGCTTCTCTTTTACACAAGAACGCTACTGAAAGTCAAACATCTGATTAGCCAGTCTCCCACCTCAACTTCTCTGCAG
Seq C2 exon
GAGTTCTCTCGCTTTCACGGGGAGATCACCCCCATGCTGACCGGCCTTCAGAATAACAGAGTGGAATGGAAATCACTGGCGGAGGAGTATGAGGCGAAGGTGAAGGTGACTGAAGAGGAGGTGGGAAAGCAGGAAGAAGTTACCTCAGATGGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016593:ENSRNOT00000022317:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.214 A=NA C2=0.264
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(10.8=100)
A:
NA
C2:
PF0023314=PDEase_I=PD(7.6=35.8)
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:
ATGATGGACAGAAACAAAAAGGGTG
R:
AACTTCTTCCTGCTTTCCCACC
Band lengths:
222-776
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]