HsaINT0124455 @ hg19
Intron Retention
Gene
ENSG00000175287 | PHYHD1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:HGNC Symbol;Acc:23396]
Coordinates
chr9:131683174-131684326:+
Coord C1 exon
chr9:131683174-131683947
Coord A exon
chr9:131683948-131684208
Coord C2 exon
chr9:131684209-131684326
Length
261 bp
Sequences
Splice sites
5' ss Seq
AGGGTGGGT
5' ss Score
5.37
3' ss Seq
CTGCATCCCATTCTATCCAGATT
3' ss Score
6.32
Exon sequences
Seq C1 exon
AGCAAACACGACTTGACTCGAGGCCAAGGCTCTTGAGGGCTGAGCAGTGTCCCCATGCACACTCCTGAAACACTTTGTCCCTTCGCCATTCAGAAGGCATCATTTTGGGGAAGGCAGCAGCCGGTTTTTCAGAGCCAGCGAGTGGCCCTGCCAGCTGCTGAGCAGGGCAAGCTGAGAAGGGTGGTGGTGTGCAAGTGTTATTCTCTCTTTTTGTTTTTGTTTTTGTTTTTTGAGATGGAGTCTTACTCTGTCGTCCAGGCTGGAGTGAGTGCCGTGGCATGATCTCGGCTCACTGCAACCTCCGCCTCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAACTGGGACTACAGGCACCTGCCACCATGCTCGGCTAGTTTTTGGTATTTTTATTTATTATTTATTTATTTATTTTGAGACCGAGTCTCGCTCTGTCGCCCAGGCTCTAGTGCAGTGGCCCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGCGTTCACGCCATTCTCCTGCCTCAGCCTCGCGAGCAGCTGGGACTACAGGTGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATTTCCTGACCTCGTGATCCGCGCGCCTCTGCCTCCAAAGTGCTGGGATTACAGGCCCGAGCCGCCGCACCCGGCCTGCAGGTGTTGTTCTGACCCCAGCTCCACTGTGCCAGCCCGACTTGAGATGCCAAGTATCTTGGGCCTGAGG
Seq A exon
GTGGGTAACAGGAAGCATCTCTCTCTCCTCAGCCCCTTCCTCCTACTAAGATACCCCATGTCTCCTACTTTCGTCTGAGCTGCAGATGGATGCGTTAATTCCCTTCCATAATCCTCCCAGGACCGAGAGGGTTTCAGATCGGTGCTGGGAGGGGCCCAGATAGTTCTCCCCAGGACCTCTTCCACCTTTGGAATGCCCATTACCTGGAGAAGGGGGGTGCCGCACATCCCCCAGACCAACCCTGCATCCCATTCTATCCAG
Seq C2 exon
ATTGAGGCCTAGAGAGAGGCAGGCGTTCCTCAGAGTCACAGGGAATGGCGGCGCCTGGACTGGGACTCAGCCCAGCTGCTTGGCCTGACCCTCTCACAGCATAATTTCCCGGCACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000175287-PHYHD1:NM_174933:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
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:
GACGGGGTTTCACCGTGTTAG
R:
AGGTGCCGGGAAATTATGCTG
Band lengths:
300-561
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)