RnoINT0110771 @ rn6
Intron Retention
Gene
ENSRNOG00000016794 | Phyhd1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:RGD Symbol;Acc:1310377]
Coordinates
chr3:8841290-8841494:+
Coord C1 exon
chr3:8841290-8841345
Coord A exon
chr3:8841346-8841431
Coord C2 exon
chr3:8841432-8841494
Length
86 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGTGTGGTTTCATCTTCTAGGCT
3' ss Score
9.93
Exon sequences
Seq C1 exon
CTCTGCATGCCCATGACCCTGTCTTCAGGAGCATCACACACTCTCCCAAGGTGCAG
Seq A exon
GTGAGTGGGAGCTGGAGGTAAGGGCGGGAAGGTGGGAGGAGCAGATACGAACCATCAGGCTGCTGCTGTGTGGTTTCATCTTCTAG
Seq C2 exon
GCTTTGGTCAGAAGTCTGGGCCTCCAGATACCAGTGGTGGTACAGAGCATGTATATCTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016794:ENSRNOT00000022552:5
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:
PF057218=PhyH=FE(6.9=100),PF063756=BLVR=PU(15.9=52.6)
A:
NA
C2:
PF057218=PhyH=FE(7.6=100),PF063756=BLVR=FE(31.7=100)
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:
CATGCCCATGACCCTGTCTTC
R:
AAAGATATACATGCTCTGTACCACCA
Band lengths:
111-197
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]