Psph (phosphoserine phosphatase) - Rat Genome Database

Name: Psph
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Psph (phosphoserine phosphatase) Rattus norvegicus

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Symbol:

Psph

Name:

phosphoserine phosphatase

RGD ID:

1308764

Description:

Predicted to enable L-phosphoserine phosphatase activity; magnesium ion binding activity; and protein homodimerization activity. Involved in response to mechanical stimulus; response to nutrient levels; and response to testosterone. Predicted to be located in cytosol. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in PSPH deficiency. Orthologous to human PSPH (phosphoserine phosphatase); PARTICIPATES IN dihydropyrimidine dehydrogenase deficiency pathway; dimethylglycine dehydrogenase deficiency pathway; nonketotic hyperglycinemia pathway; INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 17beta-estradiol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC304429; MGC109524; O-phosphoserine phosphohydrolase; PSP; PSPase

RGD Orthologs

Alliance Orthologs

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):	PSPH (phosphoserine phosphatase)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Psph (phosphoserine phosphatase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Psph (phosphoserine phosphatase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LOC100993185 (putative phosphoserine phosphatase-like protein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PSPH (phosphoserine phosphatase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Psph (phosphoserine phosphatase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PSPH (phosphoserine phosphatase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PSPH (phosphoserine phosphatase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Psph (phosphoserine phosphatase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	RABGEF1 (RAB guanine nucleotide exchange factor 1)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	PSPH (phosphoserine phosphatase)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Psph (phosphoserine phosphatase)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	psph (phosphoserine phosphatase)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	Y62E10A.13	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	SER2	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	aay	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	psph	Alliance	DIOPT (Ensembl Compara\|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	12	32,527,091 - 32,541,182 (+)	NCBI		GRCr8
mRatBN7.2	12	26,882,524 - 26,905,084 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	12	26,883,133 - 26,905,074 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	12	28,027,799 - 28,041,053 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	12	28,638,338 - 28,651,592 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	12	27,699,824 - 27,713,078 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	12	30,514,128 - 30,526,551 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	30,514,112 - 30,526,557 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	32,455,767 - 32,468,319 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	27,969,748 - 27,984,318 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	12	27,833,136 - 27,847,706 (-)	NCBI
Celera	12	28,596,700 - 28,610,791 (+)	NCBI		Celera
Cytogenetic Map	12	q13	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

amelogenesis imperfecta (ISO)

amino acid metabolic disorder (ISO)

autistic disorder (ISO)

epilepsy (ISO)

genetic disease (ISO)

Maternal Phenylketonuria (IEP)

pleomorphic xanthoastrocytoma (ISO)

PSPH deficiency (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

(1->4)-beta-D-glucan (ISO)

1,10-phenanthroline (ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (EXP,ISO)

17beta-estradiol (EXP)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

2,3,7,8-Tetrachlorodibenzofuran (EXP)

2,3-dimethoxynaphthalene-1,4-dione (ISO)

2,4-dibromophenyl 2,4,5-tribromophenyl ether (ISO)

3-chloropropane-1,2-diol (EXP)

4-hydroxyphenyl retinamide (ISO)

acrylamide (ISO)

actinomycin D (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (EXP,ISO)

antimony(0) (ISO)

aristolochic acid A (ISO)

arsenous acid (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

beta-lapachone (ISO)

bisphenol A (EXP,ISO)

butan-1-ol (ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

carbamazepine (ISO)

carbon nanotube (ISO)

ciguatoxin CTX1B (ISO)

cisplatin (EXP,ISO)

clobetasol (ISO)

cobalt dichloride (ISO)

copper(II) sulfate (ISO)

corosolic acid (ISO)

coumarin 460 (ISO)

crocidolite asbestos (ISO)

cyclosporin A (ISO)

diarsenic trioxide (ISO)

Dibutyl phosphate (ISO)

dibutyl phthalate (EXP)

diethylstilbestrol (ISO)

dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate (ISO)

dorsomorphin (ISO)

ethyl methanesulfonate (ISO)

folic acid (ISO)

folpet (ISO)

formaldehyde (ISO)

genistein (ISO)

gentamycin (EXP)

glafenine (EXP)

hydrogen peroxide (ISO)

indometacin (EXP,ISO)

ivermectin (ISO)

lead diacetate (EXP)

leflunomide (EXP)

menadione (ISO)

mercury atom (ISO)

mercury(0) (ISO)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

N(4)-hydroxycytidine (ISO)

N-methyl-4-phenylpyridinium (EXP,ISO)

N-nitrosodiethylamine (ISO)

neomycin (ISO)

nickel dichloride (ISO)

Nutlin-3 (ISO)

p-chloromercuribenzoic acid (ISO)

paracetamol (EXP,ISO)

paraquat (EXP)

perfluorononanoic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

phenylephrine (EXP)

phorone (EXP)

pirinixic acid (ISO)

quercetin (ISO)

rotenone (ISO)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

temozolomide (ISO)

testosterone enanthate (ISO)

tetrachloromethane (EXP,ISO)

thapsigargin (EXP)

thiram (ISO)

titanium dioxide (ISO)

Tributyltin oxide (ISO)

trichloroethene (EXP)

trimellitic anhydride (ISO)

triphenyl phosphate (EXP)

trovafloxacin (ISO)

tunicamycin (ISO)

valproic acid (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

amino acid biosynthetic process (IEA)

in utero embryonic development (ISO)

L-serine biosynthetic process (IBA,ISO,ISS)

L-serine metabolic process (ISO,ISS)

response to mechanical stimulus (IEP)

response to nutrient levels (IEP)

response to testosterone (IEP)

Cellular Component

cytoplasm (IBA)

cytosol (IEA)

Molecular Function

hydrolase activity (IEA)

identical protein binding (ISO)

L-phosphoserine phosphatase activity (IBA,ISO,ISS)

magnesium ion binding (IBA,ISO,ISS)

metal ion binding (IEA)

protein homodimerization activity (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

dihydropyrimidine dehydrogenase deficiency pathway (ISO)

dimethylglycine dehydrogenase deficiency pathway (ISO)

glycine, serine and threonine metabolic pathway (IEA)

nonketotic hyperglycinemia pathway (ISO)

sarcosinemia pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	The effects of hyperphenylalaninemia on fetal development: a new animal model of maternal phenylketonuria.	Brass CA, etal., Pediatr Res. 1982 May;16(5):388-94.
2.	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.
3.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
4.	The reactions of the phosphorylated pathway of L-serine biosynthesis: thermodynamic relationships in rat liver in vivo.	Guynn RW, etal., Arch Biochem Biophys. 1986 Feb 15;245(1):204-11.
5.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
6.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
7.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
8.	SMPDB Annotation Import Pipeline	Pipeline to import SMPDB annotations from SMPDB into RGD
9.	GOA pipeline	RGD automated data pipeline
10.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
12.	Comprehensive gene review and curation	RGD comprehensive gene curation
13.	Regulation of enzymes of serine and one-carbon metabolism by testosterone in rat prostate, liver, and kidney.	Sanborn TA, etal., Endocrinology. 1975 Oct;97(4):1000-7.
14.	DNA microarray reveals novel genes induced by mechanical forces in fetal lung type II epithelial cells.	Wang Y, etal., Pediatr Res. 2006 Aug;60(2):118-24.
15.	Formation of D-serine from L-phosphoserine in brain synaptosomes.	Wood PL, etal., J Neurochem. 1996 Oct;67(4):1485-90.

Additional References at PubMed

PMID:12477932	PMID:12777757	PMID:14673469	PMID:15291819	PMID:15489334	PMID:25416956	PMID:25502805	PMID:27996060	PMID:31515488

Genomics

Comparative Map Data

Psph
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	12	32,527,091 - 32,541,182 (+)	NCBI		GRCr8
mRatBN7.2	12	26,882,524 - 26,905,084 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	12	26,883,133 - 26,905,074 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	12	28,027,799 - 28,041,053 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	12	28,638,338 - 28,651,592 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	12	27,699,824 - 27,713,078 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	12	30,514,128 - 30,526,551 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	30,514,112 - 30,526,557 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	32,455,767 - 32,468,319 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	27,969,748 - 27,984,318 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	12	27,833,136 - 27,847,706 (-)	NCBI
Celera	12	28,596,700 - 28,610,791 (+)	NCBI		Celera
Cytogenetic Map	12	q13	NCBI

PSPH
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	7	56,011,064 - 56,051,444 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	7	56,011,051 - 56,051,604 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	7	56,078,757 - 56,119,137 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	56,046,238 - 56,086,762 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	7	55,852,953 - 55,893,477	NCBI
Celera	7	67,132,178 - 67,172,669 (-)	NCBI		Celera
Cytogenetic Map	7	p11.2	NCBI
HuRef	7	55,892,706 - 55,933,068 (-)	NCBI		HuRef
CHM1_1	7	56,081,776 - 56,122,305 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	7	56,170,861 - 56,211,278 (-)	NCBI		T2T-CHM13v2.0
CRA_TCAGchr7v2	7	56,082,991 - 56,123,515 (-)	NCBI

Psph
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	129,842,622 - 129,864,318 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	129,842,622 - 129,864,513 (-)	Ensembl		GRCm39 Ensembl
GRCm38	5	129,765,558 - 129,787,443 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	129,765,558 - 129,787,449 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	130,271,434 - 130,293,129 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	130,080,273 - 130,101,913 (-)	NCBI		MGSCv36	mm8
Celera	5	126,809,895 - 126,831,826 (-)	NCBI		Celera
Cytogenetic Map	5	G1.3	NCBI
cM Map	5	68.26	NCBI

Psph
(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_004955456	8,198,739 - 8,212,025 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955456	8,198,739 - 8,212,111 (-)	NCBI	ChiLan1.0	ChiLan1.0

LOC100993185
(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	6	60,590,596 - 60,615,897 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	7	108,915,322 - 108,940,625 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	7	56,351,434 - 56,376,714 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	7	56,772,872 - 56,799,703 (+)	NCBI	panpan1.1	PanPan1.1	panPan2

PSPH
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	6	493,152 - 546,176 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	6	493,176 - 512,089 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	6	2,192,384 - 2,245,452 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	6	296,475 - 349,789 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	6	295,715 - 349,758 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	6	240,702 - 293,550 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	6	234,329 - 287,631 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	6	405,548 - 458,858 (-)	NCBI		UU_Cfam_GSD_1.0

Psph
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024409344	126,114,035 - 126,136,253 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936543	7,900,283 - 7,922,541 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936543	7,900,319 - 7,922,529 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PSPH
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	16,877,923 - 16,907,952 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	16,877,904 - 16,903,062 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	17,136,056 - 17,161,335 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PSPH
(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	21	2,728,490 - 2,761,805 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	21	2,753,284 - 2,757,008 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666041	179,930,973 - 179,974,113 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Psph
(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_female_1.0 Ensembl	NW_004624740	8,213,574 - 8,226,224 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624740	8,212,051 - 8,233,358 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Psph
141 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	132
Count of miRNA genes:	104
Interacting mature miRNAs:	113
Transcripts:	ENSRNOT00000001228
Prediction methods:	Microtar, 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
631560	Apr1	Acute phase response QTL 1	6.1		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	19144362	46669029	Rat
8552964	Pigfal17	Plasma insulin-like growth factor 1 level QTL 17	3.5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564495	46669029	Rat
8693635	Alc28	Alcohol consumption QTL 28	2.7	0.439	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	12	23081340	44726024	Rat
61324	Eae5	Experimental allergic encephalomyelitis QTL 5	14		nervous system integrity trait (VT:0010566)	percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)	12	19610870	46669029	Rat
9590147	Scort7	Serum corticosterone level QTL 7	13.61	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	12	1	42110980	Rat
1549829	Scl48	Serum cholesterol level QTL 48	5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	12	9603277	46669029	Rat
61331	Eau2	Experimental allergic uveoretinitis QTL 2		0.0005	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	12	8525423	28064601	Rat
737822	Alc10	Alcohol consumption QTL 10	2.2		consumption behavior trait (VT:0002069)	ethanol drink intake rate (CMO:0001407)	12	19610870	40218516	Rat
2293684	Bmd26	Bone mineral density QTL 26	4.4	0.0002	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	12	15872653	32974238	Rat
70169	Eae13	Experimental allergic encephalomyelitis QTL 13		0.032	nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	12	24139202	36638073	Rat
1302792	Scl21	Serum cholesterol level QTL 21	3.8	0.0011	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	12	7196730	46669029	Rat
8693658	Alc33	Alcohol consumption QTL 33	2.1	0.68	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	12	23081340	43551788	Rat
1598855	Bp294	Blood pressure QTL 294	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	1	34851688	Rat
1331761	Bp218	Blood pressure QTL 218	2.973		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	11073825	45055165	Rat
8694179	Bw150	Body weight QTL 150	2.9	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	1	42110980	Rat
1331763	Wbc2	White blood cell count QTL 2	3.162		leukocyte quantity (VT:0000217)	total white blood cell count (CMO:0000365)	12	24234777	31894213	Rat
7411545	Bw128	Body weight QTL 128	5.2	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	1	42110980	Rat
7411547	Bw129	Body weight QTL 129		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	5564495	46669029	Rat
1300157	Rf21	Renal function QTL 21	4.4		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	12	9318216	32103380	Rat
737979	Pia22	Pristane induced arthritis QTL 22	53.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	1	44465750	Rat
1298081	Cia25	Collagen induced arthritis QTL 25	4.7		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	19610889	35682913	Rat
2300186	Bmd59	Bone mineral density QTL 59	7.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	12	10474137	46669029	Rat
7411660	Foco28	Food consumption QTL 28	10.9	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
1331755	Bp219	Blood pressure QTL 219	3.041		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	11073825	28064557	Rat
70213	Niddm27	Non-insulin dependent diabetes mellitus QTL 27	3.72		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	19835789	38193007	Rat
7411641	Foco19	Food consumption QTL 19	27.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
7411643	Foco20	Food consumption QTL 20		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	20328819	46669029	Rat
5684888	Pia42	Pristane induced arthritis QTL 42			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	19610870	42828880	Rat
1549912	Bp268	Blood pressure QTL 268			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	13182736	46669029	Rat
2302060	Pia37	Pristane induced arthritis QTL 37	6.1	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	13198157	46669029	Rat
1641928	Alcrsp5	Alcohol response QTL 5			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	12	12812385	46669029	Rat
8552912	Pigfal6	Plasma insulin-like growth factor 1 level QTL 6	5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564498	46669029	Rat
10059594	Kidm46	Kidney mass QTL 46	3.79	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	12	6107579	46669029	Rat
1581516	Cm56	Cardiac mass QTL 56	4.2	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	12	1	29333307	Rat
9590086	Insglur6	Insulin/glucose ratio QTL 6	18.97	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	12	1	42110980	Rat
8552918	Pigfal7	Plasma insulin-like growth factor 1 level QTL 7			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564495	46669029	Rat
1549902	Bp269	Blood pressure QTL 269			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	13182736	46669029	Rat
61404	Bw120	Body weight QTL 120	5.1		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	12	12351619	46669029	Rat
2293699	Bss49	Bone structure and strength QTL 49	5.61	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	12	10474137	46669029	Rat
634351	Apr5	Acute phase response QTL 5	6.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	12	1	44503507	Rat
634350	Apr4	Acute phase response QTL 4	6		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	1172005	46172005	Rat
61416	Pia4	Pristane induced arthritis QTL 4	8.4		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	12	13635523	30827399	Rat
7387292	Kidm42	Kidney mass QTL 42	3.03	0.0004	kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	12	1	36247923	Rat
61421	Cia12	Collagen induced arthritis QTL 12	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	13635523	35682913	Rat
2303569	Gluco44	Glucose level QTL 44	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	12812385	46669029	Rat
7411586	Foco5	Food consumption QTL 5	5.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
2303575	Insul14	Insulin level QTL 14	4		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	12	1	42450532	Rat
7411588	Foco6	Food consumption QTL 6		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
2302042	Pia38	Pristane induced arthritis QTL 38	3.5	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	1	44503507	Rat
7411595	Foco9	Food consumption QTL 9	4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
7411597	Foco10	Food consumption QTL 10		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
2293086	Iddm30	Insulin dependent diabetes mellitus QTL 30	3.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	8449490	28302290	Rat
631543	Bp83	Blood pressure QTL 83	5.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	15550826	38478808	Rat

Markers in Region

RH129042

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	12	26,904,855 - 26,905,052 (+)	MAPPER	mRatBN7.2
Rnor_6.0	12	30,526,329 - 30,526,525	NCBI	Rnor6.0
Rnor_5.0	12	32,468,097 - 32,468,293	UniSTS	Rnor5.0
RGSC_v3.4	12	27,969,774 - 27,969,970	UniSTS	RGSC3.4
Celera	12	28,610,569 - 28,610,765	UniSTS
Cytogenetic Map	9	q36	UniSTS
Cytogenetic Map	12	q13	UniSTS

AU049267

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	12	26,891,740 - 26,891,898 (+)	MAPPER	mRatBN7.2
Rnor_6.0	12	30,514,883 - 30,515,040	NCBI	Rnor6.0
Rnor_5.0	12	32,456,522 - 32,456,679	UniSTS	Rnor5.0
RGSC_v3.4	12	27,983,406 - 27,983,563	UniSTS	RGSC3.4
Celera	12	28,597,455 - 28,597,612	UniSTS
Cytogenetic Map	9	q36	UniSTS
Cytogenetic Map	12	q13	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
9	11	49	113	91	90	59	25	59	6	218	97	93	45	60	31

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001009679	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC088310	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473973	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213675	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000012	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000001228 ⟹ ENSRNOP00000001228

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	12	26,883,133 - 26,905,074 (+)	Ensembl
Rnor_6.0 Ensembl	12	30,514,112 - 30,526,553 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000093331

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	12	30,525,290 - 30,526,557 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000098380 ⟹ ENSRNOP00000097878

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	12	26,883,133 - 26,904,772 (+)	Ensembl

RefSeq Acc Id:

NM_001009679 ⟹ NP_001009679

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	12	32,527,091 - 32,541,182 (+)	NCBI
mRatBN7.2	12	26,890,986 - 26,905,078 (+)	NCBI
Rnor_6.0	12	30,514,128 - 30,526,551 (+)	NCBI
Rnor_5.0	12	32,455,767 - 32,468,319 (+)	NCBI
RGSC_v3.4	12	27,969,748 - 27,984,318 (-)	RGD
Celera	12	28,596,700 - 28,610,791 (+)	RGD

Sequence:

show sequence

GGCTTCTCCAGTTGGAAGCACACATGCCAAACTGCTCTGGAGACGCCGGAGGCATCGGCAGATC
CCAGACGAGCGTTGAGTGAAGGCTGTGATCTGCCTTACCGGTCACCTCACTCAGGACACAGCGC
TCGCACGTTGCAGCAGCTCCAGACCCCACTACTACCGGAAAGTTACAGGTACCGGAACCAAGAA
GACCAGCGCGGCCCAGGAACAGCGGAGGAAAACTCTTCCCAGGATGGTCTCCCACTCAGAGCTG
AGGAAGCTCTTCTGTTCGGCTGATGCAGTGTGCTTTGATGTTGATAGCACAGTCATCAGAGAAG
AGGGAATCGATGAGCTGGCCAAATTCTGTGGTGTGGAGGCTGCAGTGTCTGAAATGACACGGAG
AGCCATGGGAGGAGCGTTGCCTTTCAAAGATGCGCTCACTGAGCGCCTGGCACTGATCCAGCCC
TCCAGGGATCAGGTGCAGAGGCTGCTGGCTGAACACCCGCCACACCTGACCCCGGGGATAAGGG
AGCTGGTAAGCCGCCTCCAGGAGCGGAATGTTCAGGTGTTCCTCATCTCCGGGGGCTTTAGGAG
TATTGTGGAGCACGTTGCTGCAAAGCTCAACATCCCCACAACCAATGTCTTTGCCAATAGGCTG
AAATTCTACTTCAACGGTGAGTACGCAGGTTTTGACGAGACGCAGCCGACAGCCGAGTCAGGTG
GGAAAGGAAAGGTTATTGGATTTTTAAAGGAAAAATTTCACTTTAAGAAAATAATCATGATTGG
AGACGGAGCCACAGACATGGAAGCCTGCCCTCCCGCTGATGCCTTCATTGGCTTTGGAGGCAAC
GTGATCAGGCAGCAGGTTAAGGACAATGCCAAGTGGTACATCACTGACTTTGTTGAACTGCTAG
GAGAACTGGAAGAATGATCTGGACTTCCCGGTCACTCAGAACAACTCCACCTTCTCGACGCTAC
ACAGTTGGGCTCCTGGAAGAGTCTAGGAGACAGCTATTTTTTTCTACTGTAGTTCCAATATTAA
TATGACTACTAATTACATGGAGAGTTTTATATTCTGAATTCTTTGTGTATATTCCTCGGAATAT
TTTACCTGGAGCTTTCTGAGGTGCATAGTAAATTAAATGCCTTTACTCTTGCAAAAAAAAAAAA
AAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001009679	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH88310	(Get FASTA)	NCBI Sequence Viewer
	EDM13488	(Get FASTA)	NCBI Sequence Viewer
	EDM13489	(Get FASTA)	NCBI Sequence Viewer
	EDM13490	(Get FASTA)	NCBI Sequence Viewer
	EDM13491	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000001228.4
	ENSRNOP00000097878.1
	ENSRNOP00055000493
	ENSRNOP00060014684
	ENSRNOP00065001234
GenBank Protein	Q5M819	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001009679 ⟸ NM_001009679

- UniProtKB:

Q5M819 (UniProtKB/Swiss-Prot), A6J0P9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MVSHSELRKLFCSADAVCFDVDSTVIREEGIDELAKFCGVEAAVSEMTRRAMGGALPFKDALTE
RLALIQPSRDQVQRLLAEHPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVAAKLNIPTT
NVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIGFLKEKFHFKKIIMIGDGATDMEACPPADA
FIGFGGNVIRQQVKDNAKWYITDFVELLGELEE

hide sequence

Ensembl Acc Id:

ENSRNOP00000001228 ⟸ ENSRNOT00000001228

Ensembl Acc Id:

ENSRNOP00000097878 ⟸ ENSRNOT00000098380

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q5M819-F1-model_v2	AlphaFold	Q5M819	1-225	view protein structure

Transcriptome

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

Promoters

RGD ID:

13698587

Promoter ID:

EPDNEW_R9112

Type:

initiation region

Name:

Psph_1

Description:

phosphoserine phosphatase

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	12	30,514,147 - 30,514,207	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308764	AgrOrtholog
BioCyc Gene	G2FUF-19497	BioCyc
BioCyc Pathway	SERSYN-PWY [L-serine biosynthesis I]	BioCyc
BioCyc Pathway Image	SERSYN-PWY	BioCyc
Ensembl Genes	ENSRNOG00000000925	Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ENSRNOG00055000356	UniProtKB/Swiss-Prot
	ENSRNOG00060011144	UniProtKB/Swiss-Prot
	ENSRNOG00065001341	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000001228.8	UniProtKB/Swiss-Prot
	ENSRNOT00000098380.1	UniProtKB/TrEMBL
	ENSRNOT00055000631	UniProtKB/Swiss-Prot
	ENSRNOT00060018845	UniProtKB/Swiss-Prot
	ENSRNOT00065001775	UniProtKB/Swiss-Prot
Gene3D-CATH	3.40.50.1000	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7324292	IMAGE-MGC_LOAD
InterPro	HAD-like_SerB	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HAD-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HAD_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PSP	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:304429	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:109524	IMAGE-MGC_LOAD
NCBI Gene	304429	ENTREZGENE
PANTHER	PHOSPHOSERINE PHOSPHATASE	UniProtKB/Swiss-Prot
	PHOSPHOSERINE PHOSPHATASE	UniProtKB/Swiss-Prot
	PHOSPHOSERINE PHOSPHATASE	UniProtKB/TrEMBL
	PHOSPHOSERINE PHOSPHATASE	UniProtKB/TrEMBL
Pfam	Hydrolase	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Psph	PhenoGen
RatGTEx	ENSRNOG00000000925	RatGTEx
	ENSRNOG00055000356	RatGTEx
	ENSRNOG00060011144	RatGTEx
	ENSRNOG00065001341	RatGTEx
Superfamily-SCOP	SSF56784	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A8I6B6F7_RAT	UniProtKB/TrEMBL
	A6J0P9	ENTREZGENE, UniProtKB/TrEMBL
	A6J0Q2_RAT	UniProtKB/TrEMBL
	Q5M819	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-12-06	Psph	phosphoserine phosphatase	Psph_predicted	phosphoserine phosphatase (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Psph_predicted	phosphoserine phosphatase (predicted)			Symbol and Name status set to approved	70820	APPROVED

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 - OMIM

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)

BioCyc Pathways

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)

BioCyc Pathways