MmuINT0119256 @ mm9
Intron Retention
Gene
ENSMUSG00000079484 | Phyhd1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:MGI Symbol;Acc:MGI:3612860]
Coordinates
chr2:30132523-30132730:+
Coord C1 exon
chr2:30132523-30132578
Coord A exon
chr2:30132579-30132667
Coord C2 exon
chr2:30132668-30132730
Length
89 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
ATGTGGCTTTCATCTTCTAGGCT
3' ss Score
9.96
Exon sequences
Seq C1 exon
CTCTGCATGCCCATGACCCTGTCTTCAGGAGCATCACACATTCTCCCAAGGTGCAG
Seq A exon
GTGAGTGGGTGCTGGAGGTGAGGGTGGGGAGGTGTGAGGGGCACATACGAATGGGATCAGGCTGGTGGCATGTGGCTTTCATCTTCTAG
Seq C2 exon
GCTTTGGTTAGAAGTCTGGGCCTCCAGATGCCAGTGGTGGTGCAGAGCATGTATATCTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079484-Phyhd1:NM_172267:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.002 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF057218=PhyH=PU(40.0=94.7)
A:
NA
C2:
PF057218=PhyH=FE(14.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTGCATGCCCATGACCC
R:
CTTAAAGATATACATGCTCTGCACCA
Band lengths:
119-208
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: