HsaINT0124461 @ hg19
Intron Retention
Gene
ENSG00000175287 | PHYHD1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:HGNC Symbol;Acc:23396]
Coordinates
chr9:131696061-131696337:+
Coord C1 exon
chr9:131696061-131696136
Coord A exon
chr9:131696137-131696289
Coord C2 exon
chr9:131696290-131696337
Length
153 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTGG
5' ss Score
5.28
3' ss Seq
ATCTGTTCTTTGTGCCACAGGAA
3' ss Score
9.52
Exon sequences
Seq C1 exon
GGCAGCACAGACTATTTCTTGAGCAGTGGTGACAAGATTCGATTCTTCTTTGAGAAAGGCGTTTTTGATGAGAAAG
Seq A exon
GTTTGGAGCTGGGGCCCTAGAGCTGGGGAGGAGCCATGGTGAGGGTAGGCTGGACCTGGGAATCTGCCCCCTGGGCTGGAAGCATGCTGAAGCCAGCTGCCCATGGAAGGCTGGACACCAGTTCTCTGCCTTTATCTGTTCTTTGTGCCACAG
Seq C2 exon
GAAATTTCCTGGTCCCTCCGGAGAAATCCATCAACAAAATTGGCCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000175287-PHYHD1:NM_174933:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.007 A=NA C2=0.014
Domain overlap (PFAM):
C1:
PF057218=PhyH=FE(17.6=100)
A:
NA
C2:
PF057218=PhyH=FE(11.3=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:
GCAGCACAGACTATTTCTTGAGC
R:
CGTGGCCAATTTTGTTGATGGA
Band lengths:
123-276
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)