Phyh (phytanoyl-CoA 2-hydroxylase)

Gene: Phyh (phytanoyl-CoA 2-hydroxylase) Rattus norvegicus

Analyze

Symbol:

Phyh

Name:

phytanoyl-CoA 2-hydroxylase

RGD ID:

620317

Description:

Enables phytanoyl-CoA dioxygenase activity. Involved in 2-oxobutyrate catabolic process and fatty acid alpha-oxidation. Located in peroxisome. Biomarker of metabolic dysfunction-associated steatotic liver disease. Human ortholog(s) of this gene implicated in Refsum disease; Zellweger syndrome; orofacial cleft; and peroxisomal disease. Orthologous to human PHYH (phytanoyl-CoA 2-hydroxylase); PARTICIPATES IN phytanic acid degradation pathway; Refsum disease pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,3,4,7,8-Pentachlorodibenzofuran.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

phytanic acid oxidase; phytanoyl-CoA alpha-hydroxylase; phytanoyl-CoA dioxygenase, peroxisomal; phytanoyl-CoA hydroxylase; phytanoyl-CoA hydroxylase (Refsum disease)

RGD Orthologs

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	PHYH (phytanoyl-CoA 2-hydroxylase)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Phyh (phytanoyl-CoA hydroxylase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Phyh (phytanoyl-CoA 2-hydroxylase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PHYH (phytanoyl-CoA 2-hydroxylase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LOC478000 (phytanoyl-CoA hydroxylase-like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PHYH (phytanoyl-CoA 2-hydroxylase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PHYH (phytanoyl-CoA 2-hydroxylase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Phyh (phytanoyl-CoA 2-hydroxylase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	CCDC198 (coiled-coil domain containing 198)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	PHYH (phytanoyl-CoA 2-hydroxylase)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Phyh (phytanoyl-CoA hydroxylase)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	phyh (phytanoyl-CoA 2-hydroxylase)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	ZK550.5	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	ZK550.6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	YJR154W	Alliance	DIOPT (OrthoFinder\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	phyh	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	17	78,238,747 - 78,255,645 (-)	NCBI		GRCr8
mRatBN7.2	17	73,329,461 - 73,346,359 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	17	73,329,082 - 73,346,409 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	17	76,834,020 - 76,851,123 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	17	80,658,833 - 80,675,645 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	17	74,709,804 - 74,727,044 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	17	77,287,580 - 77,304,482 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	17	77,287,188 - 77,304,530 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	17	78,953,400 - 78,970,299 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	17	84,418,173 - 84,435,073 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	17	84,429,005 - 84,445,906 (-)	NCBI
Celera	17	72,770,062 - 72,786,946 (-)	NCBI		Celera
Cytogenetic Map	17	q12.3	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Adult Refsum Disease, 1 (ISO)

Familial Hypophosphatemic Rickets (ISO)

fundus dystrophy (ISO)

genetic disease (ISO)

hypoparathyroidism-deafness-renal disease syndrome (ISO)

Hypophosphatemic Rickets (ISO)

metabolic dysfunction-associated steatotic liver disease (IEP)

orofacial cleft (ISO)

peroxisomal disease (ISO)

Refsum disease (ISO,ISS)

retinitis pigmentosa (ISO)

vitamin D-dependent rickets type 2A (ISO)

Zellweger syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (EXP,ISO)

17beta-estradiol (EXP)

2,3,4,7,8-Pentachlorodibenzofuran (EXP)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2-acetamidofluorene (EXP)

2-methylcholine (ISO)

3,3',4,4',5-pentachlorobiphenyl (EXP)

3,3',4,4'-tetrachlorobiphenyl (ISO)

5-aza-2'-deoxycytidine (ISO)

5-fluorouracil (ISO)

5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole (EXP)

6-propyl-2-thiouracil (EXP)

acetamide (EXP)

acrylamide (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

amiodarone (EXP)

amitriptyline (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

aristolochic acid A (ISO)

Aroclor 1254 (ISO)

arsane (ISO)

arsenic atom (ISO)

benzbromarone (EXP)

bis(2-chloroethyl) sulfide (ISO)

bisphenol A (EXP,ISO)

chlorpromazine (ISO)

chlorpyrifos (ISO)

chromium(6+) (ISO)

cisplatin (ISO)

clarithromycin (ISO)

clofibrate (EXP)

clofibric acid (EXP)

clomipramine (ISO)

cobalt dichloride (EXP)

copper(II) sulfate (ISO)

crocidolite asbestos (ISO)

curcumin (EXP)

cyclosporin A (ISO)

dibutyl phthalate (EXP,ISO)

dicrotophos (ISO)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (EXP)

ethanol (ISO)

ethyl methanesulfonate (ISO)

fenamidone (ISO)

folic acid (ISO)

indometacin (EXP)

ivermectin (ISO)

L-ethionine (EXP)

methapyrilene (EXP)

methotrexate (ISO)

methyl methanesulfonate (ISO)

Muraglitazar (EXP)

N-nitrosodiethylamine (EXP)

nickel dichloride (EXP)

nitrofen (EXP)

ofloxacin (ISO)

omeprazole (EXP)

oxaliplatin (EXP)

ozone (ISO)

paracetamol (ISO)

paraquat (EXP)

perfluorohexanesulfonic acid (ISO)

perfluorooctanoic acid (ISO)

phenylmercury acetate (ISO)

pirinixic acid (EXP)

progesterone (EXP)

Propiverine (EXP)

resveratrol (ISO)

rotenone (EXP)

SB 431542 (ISO)

sertraline (ISO)

sodium arsenite (EXP)

sotalol (ISO)

sulfamethoxazole (ISO)

sulforaphane (ISO)

tauroursodeoxycholic acid (EXP)

Tesaglitazar (EXP)

testosterone (ISO)

tetrachloromethane (ISO)

thioacetamide (EXP)

thioridazine (ISO)

titanium dioxide (ISO)

topotecan (EXP)

trichostatin A (ISO)

troglitazone (EXP)

valdecoxib (EXP)

valproic acid (ISO)

zinc atom (EXP)

zinc(0) (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

2-oxobutyrate catabolic process (IDA)

2-oxoglutarate metabolic process (ISO)

fatty acid alpha-oxidation (IBA,IDA,ISO)

isoprenoid metabolic process (ISO)

methyl-branched fatty acid metabolic process (ISO)

Cellular Component

9+0 non-motile cilium (ISO)

peroxisome (IDA,ISO)

Molecular Function

carboxylic acid binding (ISO)

catalytic activity (ISO)

ferrous iron binding (ISO)

L-ascorbic acid binding (ISO)

phytanoyl-CoA dioxygenase activity (IBA,IDA,ISO)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

phytanic acid degradation pathway (ISO)

Refsum disease pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Using Whole Exome Sequencing to Identify Candidate Genes With Rare Variants In Nonsyndromic Cleft Lip and Palate.	Aylward A, etal., Genet Epidemiol. 2016 Jul;40(5):432-41. doi: 10.1002/gepi.21972. Epub 2016 May 27.
2.	Ataxia with loss of Purkinje cells in a mouse model for Refsum disease.	Ferdinandusse S, etal., Proc Natl Acad Sci U S A. 2008 Nov 18;105(46):17712-7. doi: 10.1073/pnas.0806066105. Epub 2008 Nov 11.
3.	Further studies on the substrate spectrum of phytanoyl-CoA hydroxylase: implications for Refsum disease?	Foulon V, etal., J Lipid Res 2003 Dec;44(12):2349-55. Epub 2003 Aug 16.
4.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
6.	Phytanoyl-CoA hydroxylase deficiency. Enzymological and molecular basis of classical Refsum disease.	Jansen GA, etal., Adv Exp Med Biol. 1999;466:371-6.
7.	Phytanoyl-CoA hydroxylase is present in human liver, located in peroxisomes, and deficient in Zellweger syndrome: direct, unequivocal evidence for the new, revised pathway of phytanic acid alpha-oxidation in humans.	Jansen GA, etal., Biochem Biophys Res Commun. 1996 Dec 4;229(1):205-10. doi: 10.1006/bbrc.1996.1781.
8.	Phytanoyl-CoA hydroxylase is not only deficient in classical Refsum disease but also in rhizomelic chondrodysplasia punctata.	Jansen GA, etal., J Inherit Metab Dis. 1997 Jul;20(3):444-6.
9.	Phytanoyl-CoA hydroxylase from rat liver. Protein purification and cDNA cloning with implications for the subcellular localization of phytanic acid alpha-oxidation.	Jansen GA, etal., J Lipid Res 1999 Dec;40(12):2244-54.
10.	Proteomic analysis of rat liver peroxisome: presence of peroxisome-specific isozyme of Lon protease.	Kikuchi M, etal., J Biol Chem. 2004 Jan 2;279(1):421-8. Epub 2003 Oct 15.
11.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
12.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
13.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
14.	SMPDB Annotation Import Pipeline	Pipeline to import SMPDB annotations from SMPDB into RGD
15.	GOA pipeline	RGD automated data pipeline
16.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
18.	The subcellular localization of phytanic acid oxidase in rat liver.	Skjeldal OH and Stokke O, Biochim Biophys Acta. 1987 Sep 4;921(1):38-42.
19.	Isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics for the investigation of the effect of Hugan Qingzhi on non-alcoholic fatty liver disease in rats.	Yao X, etal., J Ethnopharmacol. 2018 Feb 15;212:208-215. doi: 10.1016/j.jep.2017.09.016. Epub 2017 Oct 13.

Additional References at PubMed

PMID:9326939	PMID:9326940	PMID:10744784	PMID:11555634	PMID:12477932	PMID:12915479	PMID:15489334	PMID:16186124	PMID:18614015

Genomics

Comparative Map Data

Phyh
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	17	78,238,747 - 78,255,645 (-)	NCBI		GRCr8
mRatBN7.2	17	73,329,461 - 73,346,359 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	17	73,329,082 - 73,346,409 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	17	76,834,020 - 76,851,123 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	17	80,658,833 - 80,675,645 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	17	74,709,804 - 74,727,044 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	17	77,287,580 - 77,304,482 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	17	77,287,188 - 77,304,530 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	17	78,953,400 - 78,970,299 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	17	84,418,173 - 84,435,073 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	17	84,429,005 - 84,445,906 (-)	NCBI
Celera	17	72,770,062 - 72,786,946 (-)	NCBI		Celera
Cytogenetic Map	17	q12.3	NCBI

PHYH
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	10	13,277,799 - 13,300,064 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	10	13,277,796 - 13,302,412 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	10	13,319,799 - 13,342,064 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	10	13,359,802 - 13,382,136 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	10	13,359,805 - 13,382,107	NCBI
Celera	10	13,246,935 - 13,269,237 (-)	NCBI		Celera
Cytogenetic Map	10	p13	NCBI
HuRef	10	13,232,668 - 13,254,996 (-)	NCBI		HuRef
CHM1_1	10	13,319,709 - 13,342,691 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	10	13,290,862 - 13,313,116 (-)	NCBI		T2T-CHM13v2.0

Phyh
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	4,923,807 - 4,943,554 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	4,923,830 - 4,943,541 (+)	Ensembl		GRCm39 Ensembl
GRCm38	2	4,918,996 - 4,938,743 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	4,919,019 - 4,938,730 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	4,840,042 - 4,859,789 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	4,836,303 - 4,855,996 (+)	NCBI		MGSCv36	mm8
Celera	2	4,874,084 - 4,893,837 (+)	NCBI		Celera
Cytogenetic Map	2	A1	NCBI
cM Map	2	3.06	NCBI

Phyh
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955462	1,238,622 - 1,250,736 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955462	1,238,622 - 1,250,731 (-)	NCBI	ChiLan1.0	ChiLan1.0

PHYH
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	8	25,798,371 - 25,822,011 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	10	25,803,696 - 25,826,001 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	10	13,277,804 - 13,300,115 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	10	13,250,722 - 13,634,152 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	10	13,251,223 - 13,636,018 (-)	Ensembl	panpan1.1		panPan2

LOC478000
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	2	23,185,901 - 23,206,719 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	2	23,185,782 - 23,253,497 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	2	20,243,502 - 20,263,391 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	2	23,491,323 - 23,512,130 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	2	23,491,168 - 23,619,903 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UNSW_CanFamBas_1.0	2	21,525,646 - 21,546,459 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	2	22,153,837 - 22,174,674 (+)	NCBI		UU_Cfam_GSD_1.0

PHYH
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	10	48,404,293 - 48,423,973 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	10	48,404,298 - 48,423,978 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

PHYH
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	9	13,309,059 - 13,331,606 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	9	13,308,951 - 13,331,504 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666051	18,841,615 - 18,862,691 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Phyh
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624805	5,801,392 - 5,813,696 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Phyh
109 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	34
Count of miRNA genes:	29
Interacting mature miRNAs:	34
Transcripts:	ENSRNOT00000024362
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
8552928	Pigfal9	Plasma insulin-like growth factor 1 level QTL 9	9		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	17	28409147	73409147	Rat
9590107	Sffal7	Serum free fatty acids level QTL 7	4.81	0.001	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	17	28409147	73409147	Rat
2324621	Coatc5	Coat color QTL 5			coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	17	31368391	73951021	Rat
724549	Niddm56	Non-insulin dependent diabetes mellitus QTL 56		0.03	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	17	31990784	76990784	Rat
1354663	Bvd5	Brain ventricular dilatation QTL 5	3.51	0.001	brain ventricle morphology trait (VT:0000822)	hydrocephalus severity score (CMO:0001881)	17	31990784	81292925	Rat
1300148	Bp192	Blood pressure QTL 192	3.47		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	17	34550843	73951021	Rat
2301412	Kidm40	Kidney mass QTL 40		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	17	37479847	82479847	Rat
2317054	Aia12	Adjuvant induced arthritis QTL 12	4.24		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	17	38281509	83281509	Rat
2317060	Aia26	Adjuvant induced arthritis QTL 26	3.22		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	17	38281509	83281509	Rat
1598871	Memor5	Memory QTL 5	5.3		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	17	40540041	80387013	Rat
1358295	Aocep1	Aortic cell protein QTL 1	6.1	0.00000071	thoracic aorta cellular protein amount (VT:0010598)	aortic cell percentage	17	40990005	85990005	Rat
7411575	Bw140	Body weight QTL 140	30.2	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	17	48560935	86533673	Rat
8694181	Bw151	Body weight QTL 151	4.36	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	17	48560935	86533673	Rat
2317038	Ginf3	Gastrointestinal inflammation QTL 3	2.89	0.005	liver integrity trait (VT:0010547)	liver granuloma severity score (CMO:0002157)	17	49920154	86533673	Rat
2303580	Gluco49	Glucose level QTL 49	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	17	50040271	86533673	Rat
4889894	Eae33	Experimental allergic encephalomyelitis QTL 33	5.2	0.0001	nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	17	50909099	86022412	Rat
1354588	Bvd4	Brain ventricular dilatation QTL 4	5.31	0.001	brain ventricle morphology trait (VT:0000822)	hydrocephalus severity score (CMO:0001881)	17	53498828	82479847	Rat
2302365	Gluco40	Glucose level QTL 40	4.79		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	17	57246843	82046127	Rat
7488963	Bp369	Blood pressure QTL 369		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	17	59005649	77910000	Rat
2317045	Aia11	Adjuvant induced arthritis QTL 11	4.06		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	17	60781426	86533673	Rat
7411577	Bw141	Body weight QTL 141		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	17	62619516	86533673	Rat
1300131	Bp193	Blood pressure QTL 193	3.3		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	17	63640009	73951021	Rat
631502	Cm26	Cardiac mass QTL 26	3.71		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	17	65703580	81153923	Rat
1300129	Rf25	Renal function QTL 25	3.03		blood creatinine amount (VT:0005328)	creatinine clearance (CMO:0000765)	17	71003325	81153923	Rat
12904736	Cm121	Cardiac mass QTL 121		0.043	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	17	71774621	82479847	Rat

Markers in Region

RH129871

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	17	73,329,149 - 73,329,343 (+)	MAPPER	mRatBN7.2
Rnor_6.0	17	77,287,269 - 77,287,462	NCBI	Rnor6.0
Rnor_5.0	17	78,953,089 - 78,953,282	UniSTS	Rnor5.0
RGSC_v3.4	17	84,417,862 - 84,418,055	UniSTS	RGSC3.4
Celera	17	72,769,751 - 72,769,944	UniSTS
RH 3.4 Map	17	725.7	UniSTS
Cytogenetic Map	17	q12.3	UniSTS

AI256161

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	17	73,329,308 - 73,329,389 (+)	MAPPER	mRatBN7.2
Rnor_6.0	17	77,287,428 - 77,287,508	NCBI	Rnor6.0
Rnor_5.0	17	78,953,248 - 78,953,328	UniSTS	Rnor5.0
RGSC_v3.4	17	84,418,021 - 84,418,101	UniSTS	RGSC3.4
Celera	17	72,769,910 - 72,769,990	UniSTS
Cytogenetic Map	17	q12.3	UniSTS

BE114499

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	17	73,334,356 - 73,334,526 (+)	MAPPER	mRatBN7.2
Rnor_6.0	17	77,292,480 - 77,292,649	NCBI	Rnor6.0
Rnor_5.0	17	78,958,298 - 78,958,467	UniSTS	Rnor5.0
RGSC_v3.4	17	84,423,071 - 84,423,240	UniSTS	RGSC3.4
Celera	17	72,774,928 - 72,775,097	UniSTS
RH 3.4 Map	17	729.8	UniSTS
Cytogenetic Map	17	q12.3	UniSTS

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High		4	11	11		11
Medium	3	39	46	30	19	30	8	11	74	35	41	11	8
Low
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053674	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC105577	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF121345	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC086573	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473990	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ216549	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ216943	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ224924	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000017	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000024362 ⟹ ENSRNOP00000024362

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	17	73,329,082 - 73,346,409 (-)	Ensembl
Rnor_6.0 Ensembl	17	77,287,188 - 77,304,530 (-)	Ensembl

RefSeq Acc Id:

NM_053674 ⟹ NP_446126

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	17	78,238,747 - 78,255,645 (-)	NCBI
mRatBN7.2	17	73,329,461 - 73,346,359 (-)	NCBI
Rnor_6.0	17	77,287,580 - 77,304,482 (-)	NCBI
Rnor_5.0	17	78,953,400 - 78,970,299 (-)	NCBI
RGSC_v3.4	17	84,418,173 - 84,435,073 (-)	RGD
Celera	17	72,770,062 - 72,786,946 (-)	RGD

Sequence:

show sequence

GGCCCCCACCATGGACTATACGCGCGCTGGTGCCCGGCTGCAGGTCCTTCTGGGACACCTTGGC
CGACCCTCGGCCCTTCAGATTGTAGCCCACCCCGTATCAGGGCCGGCTTCCCCTGCCAATTTCT
GTCCTGAACAATTCCAGTATACTTTGGACAATAATGTCCTCAGCCTGGAGCAGAGAAAATTTTA
TGAAGAAAACGGGTTTCTCGTCATTAAAAATCTGGTATCGGATGATGATATTCAACGGTTTCGA
GCAGAGTTTGAAAGAATCTGCAGAAAGGAGGTGAAACCACCAGGGATGACTGTAATGAAAGACG
TGGCCATTGCGAAGCAGGGTTATGCGCCAAGTGAGAGGGTGGTTACGAAGATCCAGGATTTCCA
ACAAAATGAGGAGCTCTTCAGATACTGTGCCCTGCCCCAGATTGTGAAATACGTGGAGTGCTTC
ACTGGACCCAATATTATGGCTATGCACACAATGCTGATCAACAAGCCTCCGGATTCTGGCAAGA
AGACATCCCGGCATCCCTTGCATCAGGATCTGCACTTTTTCCCCTTCCGACCCAGCAACCTAAT
TGTTTGTGCTTGGACAGCCATGGAGCACATCGACAGGAACAATGGCTGTCTTGTTGTGCTCCCT
GGTACCCACAAAGGTCCCCTGAAGCCACATGATTACCCCAAGTGGGAGGGAGGAGTTAACAAAA
TGTACCATGGCATCCAAGACTATGACCCGGACAGCCCCCGCGTCCACTTGGTGATGGAAAAGGG
CGACACAGTTTTCTTCCATCCCCTGCTCATCCATGGATCTGGTCGGAACAGAACTCAAGGATTC
AGGAAAGCAATCTCCTGCCACTATGGCAGCTCCGACTGCAAATATATCAGCGTGAAGGGCACCA
GTCAAGAAAACATTGCGAGGGAAGTTATTGAGATTGCGGAGAAACGTTATGGAGTCCAAGGAGC
CCTGGACTTTGAGGACACTTGGAAGTTTCGATGCCGACTTGTGAAAGGAGAAAGAATAAACCTT
TGAAAGAGCCCTTCAGGTGGAGAGGTGGCTCAGCGGTTAAGAGCACTGATTGCTCTTCCGGAGT
CCTGAGTTCAAATCCCAGCAACCACATGATGGCTCACAACCATCTGTAATGGGATCTGGTGCCC
TCTTCTGGTGTGTCTGAAGATAGCTACAGTGTACTCATATAAATAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_446126	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAF15971	(Get FASTA)	NCBI Sequence Viewer
	AAH86573	(Get FASTA)	NCBI Sequence Viewer
	EDL78672	(Get FASTA)	NCBI Sequence Viewer
	EDL78673	(Get FASTA)	NCBI Sequence Viewer
	EDL78674	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000024362
	ENSRNOP00000024362.3
	ENSRNOP00055024442
	ENSRNOP00060012548
	ENSRNOP00065008911
GenBank Protein	P57093	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_446126 ⟸ NM_053674
- Peptide Label:	precursor
- UniProtKB:	Q9QY64 (UniProtKB/Swiss-Prot), P57093 (UniProtKB/Swiss-Prot), A6JLZ6 (UniProtKB/TrEMBL)
- Sequence:	show sequence MDYTRAGARLQVLLGHLGRPSALQIVAHPVSGPASPANFCPEQFQYTLDNNVLSLEQRKFYEEN GFLVIKNLVSDDDIQRFRAEFERICRKEVKPPGMTVMKDVAIAKQGYAPSERVVTKIQDFQQNE ELFRYCALPQIVKYVECFTGPNIMAMHTMLINKPPDSGKKTSRHPLHQDLHFFPFRPSNLIVCA WTAMEHIDRNNGCLVVLPGTHKGPLKPHDYPKWEGGVNKMYHGIQDYDPDSPRVHLVMEKGDTV FFHPLLIHGSGRNRTQGFRKAISCHYGSSDCKYISVKGTSQENIAREVIEIAEKRYGVQGALDF EDTWKFRCRLVKGERINL hide sequence

RefSeq Acc Id:

ENSRNOP00000024362 ⟸ ENSRNOT00000024362

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P57093-F1-model_v2	AlphaFold	P57093	1-338	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13700574

Promoter ID:

EPDNEW_R11098

Type:

multiple initiation site

Name:

Phyh_1

Description:

phytanoyl-CoA 2-hydroxylase

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	17	77,304,489 - 77,304,549	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620317	AgrOrtholog
BioCyc Gene	G2FUF-8687	BioCyc
BioCyc Pathway	PWY66-387 [3-methyl-branched fatty acid alpha-oxidation]	BioCyc
BioCyc Pathway Image	PWY66-387	BioCyc
Ensembl Genes	ENSRNOG00000018044	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOG00055017941	UniProtKB/Swiss-Prot
	ENSRNOG00060009493	UniProtKB/Swiss-Prot
	ENSRNOG00065007769	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000024362	ENTREZGENE
	ENSRNOT00000024362.7	UniProtKB/Swiss-Prot
	ENSRNOT00055030387	UniProtKB/Swiss-Prot
	ENSRNOT00060016033	UniProtKB/Swiss-Prot
	ENSRNOT00065012182	UniProtKB/Swiss-Prot
Gene3D-CATH	q2cbj1_9rhob like domain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7306754	IMAGE-MGC_LOAD
InterPro	PhyH	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Phytyl_CoA_dOase	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:114209	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:105364	IMAGE-MGC_LOAD
NCBI Gene	114209	ENTREZGENE
PANTHER	PHYTANOYL-COA ALPHA-HYDROXYLASE	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PHYTANOYL-COA DIOXYGENASE, PEROXISOMAL	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	PhyH	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Phyh	PhenoGen
RatGTEx	ENSRNOG00000018044	RatGTEx
	ENSRNOG00055017941	RatGTEx
	ENSRNOG00060009493	RatGTEx
	ENSRNOG00065007769	RatGTEx
Superfamily-SCOP	Clavaminate synthase-like	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A6JLZ6	ENTREZGENE, UniProtKB/TrEMBL
	A6JLZ7_RAT	UniProtKB/TrEMBL
	P57093	ENTREZGENE, UniProtKB/Swiss-Prot
	Q9QY64	ENTREZGENE
UniProt Secondary	Q9QY64	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-11-06	Phyh	phytanoyl-CoA 2-hydroxylase	Phyh	phytanoyl-CoA hydroxylase	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-20	Phyh	phytanoyl-CoA hydroxylase		phytanoyl-CoA hydroxylase (Refsum disease)	Name updated	1299863	APPROVED
2002-08-07	Phyh	phytanoyl-CoA hydroxylase (Refsum disease)			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - SMPDB

BioCyc Pathways

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Imported Disease Annotations - ClinVar

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Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - SMPDB

BioCyc Pathways