Pdxp (pyridoxal phosphatase) - Rat Genome Database

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

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Gene: Pdxp (pyridoxal phosphatase) Chinchilla lanigera

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Symbol:

Pdxp

Name:

pyridoxal phosphatase

RGD ID:

8892991

Description:

ENCODES a protein that exhibits growth factor binding (ortholog); heat shock protein binding (ortholog); magnesium ion binding (ortholog); INVOLVED IN actin rod assembly (ortholog); cellular response to ATP (ortholog); dephosphorylation (ortholog); PARTICIPATES IN hypophosphatasia pathway; vitamin B6 metabolic pathway; ASSOCIATED WITH adenylosuccinase lyase deficiency (ortholog); Emery-Dreifuss muscular dystrophy (ortholog); myoclonic dystonia 26 (ortholog); FOUND IN actin cytoskeleton (ortholog); cell-cell junction (ortholog); cleavage furrow (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

pyridoxal (pyridoxine, vitamin B6) phosphatase; pyridoxal phosphate phosphatase

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

ChiLan1.0 - Chinchilla ChiLan1.0 Assembly

Position:

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955413	24,055,900 - 24,063,902 (+)	NCBI	ChiLan1.0	ChiLan1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

adenylosuccinase lyase deficiency (ISO)

Emery-Dreifuss muscular dystrophy (ISO)

myoclonic dystonia 26 (ISO)

neurodegeneration with brain iron accumulation 2A (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

actin rod assembly (ISO)

cellular response to ATP (ISO)

dephosphorylation (ISO)

positive regulation of actin filament depolymerization (ISO)

protein dephosphorylation (ISO)

pyridoxal phosphate catabolic process (ISO)

regulation of cytokinesis (ISO)

regulation of mitotic nuclear division (ISO)

regulation of modification of postsynaptic structure (ISO)

Cellular Component

actin cytoskeleton (ISO)

cell-cell junction (ISO)

cleavage furrow (ISO)

contractile ring (ISO)

cytosol (ISO)

glutamatergic synapse (ISO)

lamellipodium (ISO)

midbody (ISO)

plasma membrane (ISO)

postsynapse (ISO)

ruffle membrane (ISO)

Molecular Function

growth factor binding (ISO)

heat shock protein binding (ISO)

magnesium ion binding (ISO)

phosphoprotein phosphatase activity (ISO)

protein binding (ISO)

protein homodimerization activity (ISO)

pyridoxal phosphatase activity (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

hypophosphatasia pathway (ISO)

vitamin B6 metabolic pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Transitive Annotation Pipeline	Automated assignment of GO, PW and RDO ISO annotations across species

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

Pdxp
(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	NW_004955413	24,055,900 - 24,063,902 (+)	NCBI	ChiLan1.0	ChiLan1.0

PDXP
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	22	37,658,723 - 37,666,932 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	22	37,658,723 - 37,666,932 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	22	38,054,730 - 38,062,939 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	22	36,384,683 - 36,392,885 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	22	36,379,237 - 36,387,439	NCBI
Celera	22	21,856,602 - 21,864,785 (+)	NCBI		Celera
Cytogenetic Map	22	q13.1	NCBI
HuRef	22	21,021,805 - 21,030,000 (+)	NCBI		HuRef
CHM1_1	22	38,013,473 - 38,021,654 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	22	38,120,012 - 38,128,169 (+)	NCBI		T2T-CHM13v2.0

Pdxp
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	15	78,796,342 - 78,803,717 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	15	78,798,119 - 78,803,717 (+)	Ensembl		GRCm39 Ensembl
GRCm38	15	78,912,160 - 78,919,517 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	15	78,913,919 - 78,919,517 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	15	78,744,349 - 78,749,947 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	15	78,741,174 - 78,746,772 (+)	NCBI		MGSCv36	mm8
MGSCv36	15	79,638,039 - 79,643,637 (+)	NCBI		MGSCv36	mm8
Celera	8	110,672,269 - 110,684,203 (-)	NCBI		Celera
Cytogenetic Map	15	E1	NCBI
cM Map	15	37.7	NCBI

Pdxp
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	112,352,971 - 112,358,419 (+)	NCBI		GRCr8
mRatBN7.2	7	110,472,515 - 110,477,963 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	110,472,515 - 110,477,963 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	7	112,222,037 - 112,227,486 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	7	114,445,557 - 114,451,006 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	7	114,414,141 - 114,419,605 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	7	120,140,460 - 120,145,908 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	120,140,460 - 120,145,908 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	120,132,151 - 120,137,599 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	116,880,751 - 116,886,199 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	7	106,806,678 - 106,812,126 (+)	NCBI		Celera
Cytogenetic Map	7	q34	NCBI

PDXP
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	10	26,945,751 - 26,952,234 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	10	26,946,838 - 26,952,217 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	10	26,900,405 - 26,906,862 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	10	27,737,639 - 27,744,136 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	10	27,738,233 - 27,744,146 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	10	27,459,875 - 27,466,333 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	10	27,768,698 - 27,775,155 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	10	27,945,988 - 27,952,450 (-)	NCBI		UU_Cfam_GSD_1.0

Pdxp
(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_024404945	10,410,176 - 10,416,350 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936492	3,421,516 - 3,426,715 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936492	3,420,590 - 3,426,764 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PDXP
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	10,162,643 - 10,169,512 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	10,162,642 - 10,169,726 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	7,735,323 - 7,737,336 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

Pdxp
(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_004624752	10,243,135 - 10,251,082 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624752	10,244,424 - 10,251,072 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

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.

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005379654	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01014346	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AGCD01014347	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBDK01027422	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

XM_005379654 ⟹ XP_005379711

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955413	24,055,900 - 24,063,902 (+)	NCBI

Sequence:

show sequence

ATGGAAGGCTTCCTGGAGGTGGTGATATCTAAGGAGCAGGCCAGCCTTTCGCCCTCATTGGCCG
CGGTCCAGTCTGTGGCCCCGCCCCCTGCCCGCTCCGGCGCGCCGATTGGCCCTGCAGGACAAGT
CCGGGCGAGCGCGCCGTGCCCGCGGAGGGAGAGCGGCGCGGGCGTGCAGCTGCGCGCCGCGGGG
CTGCGCCTGGCGGAGGACCCCGGCCTCGCCCCGCGCGTGCGCGCCGTGCTCGTGGGCTACGACG
AGCGCTTCTCCTTCGCCAAGCTGAGCGAGGCGTGCGCGCACCTGCGCGACCCCGACTGCCTGCT
CGTGGCCACCGACCGCGACCCTTGGCACCCGCTCAGCGACGGCAGCCGGACCCCCGGCACCGGG
AGCCTGGCCGCTGCGGTGGAGACAGCCTCGGGGCGCCAGGCGCTGGTGGTGGGCAAGCCCAGCC
CCTACATGTTTGAGTGCATCACAGAGCACTTCAGCCTGGACCCCGCCCGCATGCTCATGGTGGG
TGACCGCCTGGAGACCGACATCCTCTTTGGCCACCGCTGCGGCATGACCACCGTGCTCACGCTC
ACGGGCGTGTCGCGCCTGGAGGAGGCCCAGGCCTACCTGGCAGCCGGCAAGCACGACCTCGTGC
CCCATTACTATGTGGAGAGCATCGCAGACTTGATCGGGGGGCTGGAGGACTGAGCCCGCCTGGC
CTGCAGCCGTGGCCCCTGCCTCCCGACCCCCGGTCCTACAGATGGAAGTGATGGGGCGTTGAGT
CTCCTTAGGCACTGCGGGCTCCCTCGCCTCAGTTTCTGTGTCCTGCTGGAGCTGCTGAGCAGGA
AGGTGTGAGGACCTTCGCGCCCCTCCCAGCGGTGGCCAGGTGCTCTGCTGTTCCGGAAGCTGCC
CCTGCAGCTTGGAGGTTCACCCTGGCCTAACCCAGCCAGTGGCTTTGTTTCCTGCCTCGTCACC
TCCCCTCCCCGAATATGGGTCTTGATGCCACTTGAAGATTTCCCCCAGCCTGGGCACTTGATGC
CCTCCCCTCCCTGGGAACGCCTGAGCCCTGCCTGCCCCTGGGTCCTGACCTTGCGCTTCCTGTT
GGCCTATGGAGGTTGAGGTCACCGCATGCTGTTACTGTCCTGAGTGGACCAGTCAAGGCTCAGC
GGCAGTGACTCGCTGAGGCCACATCCTGAGTAGACCAAATAGAAGCTAAGGAACAACGATCCTT
GCATGTCCTGGGTCCCGGGTGGACCCTTCTGGACACCAGGTAATGCTGACCCACTGGTCTCTTA
GATCCCAAATAGAGCAATTCAGGAGTCTGAGTGACAGTGACCTCCTTTAGACAGTCTGGGTCCC
ACCAGACCAGCCAGGGTTGATATTAGTCGATAAATAAGGAGCCAGGTGTGAAGACCTCATCCTC
CCTGGAGATTGGGACCCAGAGTGCTCAGAGGCCCTGGGCCTGCCACCCTCCCTGATCACAGTAC
CTGTCCAGTGTCGGTGGCCACAGCCCGGAAGGGGGCTTTGGTGTCCCCGCGTAGCTAGTGTTTG
CTGTGCCACGTCCCATCCCGACTCCCAGCTATTTATTTATCTGTTTATTTATTATTGTGTGCCA
GTGGCATGGGGGTGGGGGCTGGGCCTCCTCACCACCTCCACCCGTTGTAACCAGTCCTCCGTAC
TTAATAAAGTGCGAGTAGGAGTGCA

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Protein Sequences


Protein RefSeqs	XP_005379711	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000024569.1

RefSeq Acc Id:

XP_005379711 ⟸ XM_005379654

- Sequence:

show sequence

MEGFLEVVISKEQASLSPSLAAVQSVAPPPARSGAPIGPAGQVRASAPCPRRESGAGVQLRAAG
LRLAEDPGLAPRVRAVLVGYDERFSFAKLSEACAHLRDPDCLLVATDRDPWHPLSDGSRTPGTG
SLAAAVETASGRQALVVGKPSPYMFECITEHFSLDPARMLMVGDRLETDILFGHRCGMTTVLTL
TGVSRLEEAQAYLAAGKHDLVPHYYVESIADLIGGLED

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Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000016877	UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000024806.1	UniProtKB/TrEMBL
Gene3D-CATH	3.40.50.1000	UniProtKB/TrEMBL
InterPro	HAD-like_sf	UniProtKB/TrEMBL
	HAD_sf	UniProtKB/TrEMBL
NCBI Gene	Pdxp	ENTREZGENE
PANTHER	4-NITROPHENYLPHOSPHATASE-RELATED	UniProtKB/TrEMBL
	CHRONOPHIN	UniProtKB/TrEMBL
Pfam	Hydrolase_like	UniProtKB/TrEMBL
Superfamily-SCOP	SSF56784	UniProtKB/TrEMBL
UniProt	A0A8C2W3C0_CHILA	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-08-03	Pdxp	pyridoxal phosphatase		pyridoxal (pyridoxine, vitamin B6) phosphatase	Symbol and/or name change	5135510	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)

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Imported Annotations - SMPDB

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Imported Disease Annotations - ClinVar

Imported Annotations - SMPDB