HsaINT0124457 @ hg19
Intron Retention
Gene
ENSG00000175287 | PHYHD1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:HGNC Symbol;Acc:23396]
Coordinates
chr9:131703724-131704320:+
Coord C1 exon
chr9:131703724-131703850
Coord A exon
chr9:131703851-131703946
Coord C2 exon
chr9:131703947-131704320
Length
96 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
TTCTCCTCTATCCTCTGCAGGCT
3' ss Score
10.28
Exon sequences
Seq C1 exon
GGGCCCTGGTCCTCATCCATGGAGAAGTGGTACACAAGAGCAAGCAGAACCTCTCTGACCGCTCGCGCCAGGCCTACACTTTCCACCTCATGGAGGCCTCTGGCACCACCTGGAGCCCGGAGAACTG
Seq A exon
GTAGGTGACAGGGTGGGTGTGTGTGCCCGACAGTCCCCTGGAGGCTGGGAACAGTGACCCTGCACCTCAAGGTTGTTTCTCCTCTATCCTCTGCAG
Seq C2 exon
GCTCCAGCCAACAGCTGAACTGCCCTTTCCCCAACTGTACACCTAAAGGCTCTCGCAGGGCAGGAGCCCTCGCCCCTCCCGGGTGAAGCTGTGGGCTGTAAACACCAGTGCCTTGCTCAGCCTCCTGGTTGCAACAGGGAGGTCTTGTCTCCCCTCCTGGGCTTTCCTCCTGCCCTGTGGGCAGCAGCCTAGGCTGGGTCAGGGGCTTCCCTAAGATCTTCACCTCTCTGCCTCCCTACTGCCCCAACATAGCCTTGAGGAGGCTTCTCAGCCACCAAAGGGTTCTGGCCCCTTCTCACTCTCCTCTCCTCTCAGATGGAACTCTGGTTATTATGGTGTTAGTTATCGAATAAAAACGACTTCAGAATGCAGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000175287-PHYHD1:NM_174933:11
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.293 A=NA C2=0.605
Domain overlap (PFAM):
C1:
PF057218=PhyH=PD(10.6=55.8)
A:
NA
C2:
NO
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:
AGGCCTACACTTTCCACCTCA
R:
AAGGCACTGGTGTTTACAGCC
Band lengths:
172-268
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)