HsaINT0124456 @ hg19
Intron Retention
Gene
ENSG00000175287 | PHYHD1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:HGNC Symbol;Acc:23396]
Coordinates
chr9:131702878-131703850:+
Coord C1 exon
chr9:131702878-131702994
Coord A exon
chr9:131702995-131703723
Coord C2 exon
chr9:131703724-131703850
Length
729 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGC
5' ss Score
8.99
3' ss Seq
CCTGCTTGTGTCTCTGCCAGGGG
3' ss Score
9.51
Exon sequences
Seq C1 exon
GTGGTGTGTCAAGAAGGATGGTCCGGGCCCCTGTTGGCTCAGCGCCTGGTACCAGCTTCCTTGGGTCAGAGCCAGCCCGGGATAACAGCCTCTTTGTGCCCACCCCAGTGCAGAGAG
Seq A exon
GTAGGCAGATGCAGAGGGCAGAGAGGCAGGGGGCTGAGTCCATCAGTCTGTGCTTGCTCGACTACCCAGCGTCCAAGAGGTTGCCCTCGGGGTCATCTGAGGGCAGTGAAGTCACAGAAAGAGAAGGAGGGGCTGGATGGGCGCTGGGAAGTCAGGAAGCAGCATGTTTTCCTGCAGGCTGATCCAGATCACCCTGGAATCCACACTCTGCTACTTATGGGCTGTTTCTCTGGGCAAATGACTGACTCCCTGAGCCTTAATTTCCCCAAACGTAAAGTGGAAAGTCAGTGAGATGATAAATATGTTGATATAGAGTCTGCCTAGTGCATAGCCACTGCTCAACAAATGTTGGCTGTTGGGCGGCCCTTTTTCTTATGAAAAGGGAAAACCAATGTCTAACTCAGCATCACCGGAGAGGTCCCAGTGGACTGGCACAGGACAGAGGGCTTCTGCCTGATCCTGCAAAGACCTCGGGAGGGGAGGCCCTTCCTAAGGCTTGCCAAGGCCACAGTCCACAGCAGAGGGGACTTGATCCCAGAGGAACATGCATCTCAATAGCTTAGCTTTTGTCCCTGAGGGAGGCTGCAGATGCCTGAGCTTTCAGGGAAGGGAATGGGGATGGATGGGGGCCACAAAACCACTGGAAGGAGGAGGGCCCATGTCCCTTCCTGCTCTGGGGAGGGGGGATGTGGGGCTGGTAGGTTCCTGACCTGCTTGTGTCTCTGCCAG
Seq C2 exon
GGGCCCTGGTCCTCATCCATGGAGAAGTGGTACACAAGAGCAAGCAGAACCTCTCTGACCGCTCGCGCCAGGCCTACACTTTCCACCTCATGGAGGCCTCTGGCACCACCTGGAGCCCGGAGAACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000175287-PHYHD1:NM_174933:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.145 A=NA C2=0.293
Domain overlap (PFAM):
C1:
PF057218=PhyH=FE(17.2=100)
A:
NA
C2:
PF057218=PhyH=PD(10.6=55.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTCAAGAAGGATGGTCCGG
R:
CAGTTCTCCGGGCTCCAGG
Band lengths:
239-968
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)