HsaINT0124458 @ hg19
Intron Retention
Gene
ENSG00000175287 | PHYHD1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:HGNC Symbol;Acc:23396]
Coordinates
chr9:131684209-131684635:+
Coord C1 exon
chr9:131684209-131684326
Coord A exon
chr9:131684327-131684561
Coord C2 exon
chr9:131684562-131684635
Length
235 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
AACTTTCTCCTCCCCACCAGGAG
3' ss Score
8.74
Exon sequences
Seq C1 exon
ATTGAGGCCTAGAGAGAGGCAGGCGTTCCTCAGAGTCACAGGGAATGGCGGCGCCTGGACTGGGACTCAGCCCAGCTGCTTGGCCTGACCCTCTCACAGCATAATTTCCCGGCACCTG
Seq A exon
GTAAGCAGTGGTGGGGGGTGGTTTCCAGAAGAAACACAGAGGAAGCAGATAAAATCCTTGGAGATGGGAAAGGGCAAATCCTGGATTAGTTGTGGGGGTGGGGGAGATTAGCCTGGAGGTCACAGGCTGATCTGGCTGTGTCTAGGGAAGGAGGGTTGGGTGGTGGGACCGGGTTTTCTCCGGGTAGGGAAGGGTTAAGTCCTCCCAGGCTCCTAAACTTTCTCCTCCCCACCAG
Seq C2 exon
GAGGCCGCGCTTAGAAGCCGCCCAGTGCCCTGAGCGTCTCCATGGCCTGCCTGAGCCCCTCGCAGCTCCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000175287-PHYHD1:NM_174933:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTAGAGAGAGGCAGGCGTTCC
R:
CTTCTGGAGCTGCGAGGGG
Band lengths:
184-419
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)