RnoINT0108936 @ rn6
Intron Retention
Gene
ENSRNOG00000016593 | Pde6c
Description
phosphodiesterase 6C [Source:RGD Symbol;Acc:1309844]
Coordinates
chr1:256850279-256851633:+
Coord C1 exon
chr1:256850279-256850422
Coord A exon
chr1:256850423-256851564
Coord C2 exon
chr1:256851565-256851633
Length
1142 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
AAATTGTGTTTCCATTTTAGAAA
3' ss Score
8.98
Exon sequences
Seq C1 exon
ACTTTAACCCAGTTTCTTGGATGGTCTCTTTTAAACACCGATACCTATGAGCGAGTGAACAAGCTGGAAAGCCGAAAGGACATTGCTCAGGAAATGATTATGAACCTCACCAAAGCCACCCCTAGTGAAATCAGCTCTATTTTG
Seq A exon
GTAAGTGGGGAATCCAGGCCTGTGAACAGCAGGTGGCATTGGACTTCAGTTTCTGCAAACCACCGGTGAGCAGAGGCTTGCTTCTGGGGTCAAGAGATGAAGATAGAGGAGAGGTCGGGGAGGAAGGAGCCCTGTCAGCTGGTAAGCTTTTCTTCCTGGAATTCCAGACCACAGTGTTACATTAGCACTTGGTGAAAAACAGCTCCTGAGTTTGTAGGAGCAGAAACAATGTATCTGGATTCATGTATATCAGTGAGGAAAAGAATATTGTGAAGAAGGGCAACATGTCAACCATTATCCTAGCAGGCTGTGTAACAACCAGTGTTTCATCTCAGTGGCCTTCGTTAATAAGCATCTACCTTCTCCTTACTAGCTGTGGGTTGAGCGGGCTCTAAGTGACCTTGGTGACCCAGCTGTGAGTCTCGTTTGCCCTATGGCCTCTTATCTTTTGTGGACCAGCAGCAACCTGGTGATGTTAAAGTCTTTGCTCACATGACAGTCTCTAAAATTCTCACTGGCTAAAGCCAAGTCAGGCGATCGAGTCCAATATCATTTTCTGATGAGGAAGCCGGTGGATTTTTGCTGAAAATGTTCTAATTACCACAAAAGTAAGGGGAAAACACCCCACAATCACTTTTTTTTTGCTCTTTTTCTTAATTTTTTAGAGTGTGTATTTAGATGTAGTCTGGTGTCGGTGTCTGGTTTCGGTTTGCTGGGGCCATTAAAAGTTAAAAAGATTTTTGACTAAAGTATTTGAGATGATAAAGATGAGGTCATGGGCGGGAATCCTTGCAACTGCTATTGGCAATCAAAAACAAAACAAAAATCCAACCAATCAACCAACCAACCAAACAAACAAACAGAAAACCCCTTTTCCTTTTTTTGCCTACCTATAGCCCATAGCTTGGTTTTCAGACGGCTACTGCTACATTTTGGAGAGTGAGAGAACTCAATTGTTTTAGGACATTTCTTCGAAACAATTCTTCCTAATCACTTGCTATCAGTCTTTCCTCATGCAGAAAGTCTTCATTTGTAACAGATGGGTGGCCTATTTTAGATAGAGCTCAACTGGTTTTAGCATTAGAGCCACCAGACAGAAATCTCTGTAGTAATTCCATACTTAAATTGTGTTTCCATTTTAG
Seq C2 exon
AAATTTAAAGAGAAGTTAAACATAGATGTAATTGAAGAATGTGAGGAGAGACAGCTCCTGGCCATATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016593:ENSRNOT00000022317:10
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=PD(5.1=18.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACCCAGTTTCTTGGATGGTCT
R:
ATATGGCCAGGAGCTGTCTCT
Band lengths:
206-1348
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]