RnoINT0108953 @ rn6
Intron Retention
Gene
ENSRNOG00000016593 | Pde6c
Description
phosphodiesterase 6C [Source:RGD Symbol;Acc:1309844]
Coordinates
chr1:256843313-256845306:+
Coord C1 exon
chr1:256843313-256843379
Coord A exon
chr1:256843380-256845258
Coord C2 exon
chr1:256845259-256845306
Length
1879 bp
Sequences
Splice sites
5' ss Seq
TTTGTAAGT
5' ss Score
7.4
3' ss Seq
CTCTGTCTCTTACTTCACAGATC
3' ss Score
11.53
Exon sequences
Seq C1 exon
GTCACCTCCAGCAGATCACTGGACACTCGTTAGTGGATTGCCAACATACATTGCTGAAAATGGATTT
Seq A exon
GTAAGTCATTAGACAAACTTAAAGGCTACAGTGCATTATGGTGTGCAAAACACTTACTAGTTACAAAATAAATATAGCCACTGAATCAAAAACGAACGAGACAAGGGTAGATGGCTTTCTTGGCATAGGAGAAAGGCTAGGGGAAAAAAATAAAATAGGAATTGATTGGTTTGTATCTTTAAACCACATTTGGGGGATCCACAGTTCAAGAAATAACATTAAATATTCAAGTTAGATCATGAAATTAAGGATGGCACCAAAGAGTCCTCGGGTTCTTAACTTATGACTGCTCATGGGAACAGCATGCAAAGCTACGCAGGGAAATCCAGACTCAAAGAAAGAAGCAAAAGACCCCCAAAGGAAATACGCACAAATAAAGAAACCAAAGCTTCAGAAGGGTTCCATGTTTTCTTTGTAAGGCTAGAGGACAAAGAGTAGACATGTTTCATCCACTCCTAGAAGGCACTTAACATCAGCTCACAGAGCTTGGAGGGTTGGGTAAGATACACTTCAACCTCAACACAAACTGTCGGGTTTTTCCCCCCAGAATTTCATGAGTGGGTAAATGCTGGTAGAAGTATTTACACCAGAAGTAGTCTTCATGGTAGGGGTATTTGCACTAAGGTTTTCCATGGTAGGGGTATTTGCACTAGGGTTTCTCCCGCCCTTACTCAGGAGAGCCCATCCCATCAGCCCATCCTGTCAACCCCTCTTTGGAGTTTCCAAATCATGATTCAAGTTTCACCCAGTGGATCTGAACAGAGCACTAAACCTTTTTGGACTTCAATGCCCTCATCTTTTAAAGGAGACAATGACTCAACCATTACCACCAGACTTGAAATGCTATCTATCATTTTAAGTGGAACTCTGGTAGAACGGAGAGTAGAGTCTTGCATTAAGGCCCACCTGTGTATACGACCCAGGCACAGACAATTCAGAGCAACTCAAGATGGGTATGAGAAACAGTCTCCGAATTCTGTCAGTAAGCGCAGTATTTCATACGGAATTCTTACTTTAGAGCGGGTGAAACATTGTCTGGCCTTTTCCCCTTGCCCCTCAAGCCACCTTACTTTTTTTCCCCCTCCATCTTTATTAACTTGAGTATTTCTTATTTACATTTCAATTGTTATTCCCTTTCTCGGTTTCTGGGCCAACATCCCCCTAACCCCTCATCCTCCCCTTCTATATCTATATGGGTGTTCCCCTCCCCATCCTCCCCCCATTACCACCCTCCCCCCAACAGTCACATTCACTAGGGGGTTCAGCCTTGGCTTCCCCTTCCACTGGTGCTCTTACTAGGCTATTCATTGCTACCTATGAGATTGGAGCCCAGGGTCAGTCCATGCATAGTCTTTGGGTAGTGGCTTAGTCCCCGGAAGCTCTGGTTGGTTGGCGTTGTTGTACATATGGGGTCTCCAGCCCCTTCAAGCTCTTTCAGTCCTTTCTCTGATTCCTTCAATGGGGGTCCCGATCTCAGTTAAGTGGTTTGCTCAAGCCACCTTACTTTATAAAAGAATAAAGCAAGATCAGCCCCCACGTTCAAACGTTCCTCAGCAGGGCAGTCTTTCTCTTTTGCTTGGGCTGAGGAGGTTGTTTGGTAGTTGAAGGGCATCACTCGGATGATGACATCACTTGGAAGTGGGAGAGTGGGGAGGAGCAAAGATAGCAGGAAATGCCACTCAATGGCATAGCAGAAGAGGAGGTGACTTCAGTTAGCAAATATGGCCTAATGTATGGAGCATGCCTTACTGTGTTTACCAAGCAGCCAAGAGCTTCGTGGGAAACTCACCCCCAACATGCCTTCTCTCACCCTCCTCCGTGGGCTTTCGTGGTCCTAACCTCACCATGTTTCAGAATGACTCTGTCTCTTACTTCACAG
Seq C2 exon
ATCTGTAACATGATGAACGCCCCTGCAGATGAGTACTTCACATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016593:ENSRNOT00000022317:7
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(12.4=100)
A:
NA
C2:
PF0159021=GAF=FE(8.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]