PGK2 Gene (Protein Coding)

Phosphoglycerate Kinase 2

GC06M049785
GIFtS:
42
This gene is intronless, arose via retrotransposition of the phosphoglycerate kinase 1 gene, and is expressed specifically in the testis. Initially assumed to be a pseudogene, the encoded protein is actually a functional phosphoglycerate kinase that catalyzes the reversible conversion of 1,3-bisphosphoglycerate to 3-phosphoglycerate, during the Embden-Meyerhof-Parnas pathway of... See more...

Aliases for PGK2 Gene

Aliases for PGK2 Gene

  • Phosphoglycerate Kinase 2 2 3 4 5
  • Phosphoglycerate Kinase, Testis Specific 3 4
  • EC 2.7.2.3 4 51
  • PGKPS 2 3
  • PGKB 3 4
  • Phosphoglycerate Kinase Autosomal Pseudogene 3
  • Epididymis Secretory Protein Li 272 3
  • Testicular Tissue Protein Li 139 3
  • DJ417L20.2 3
  • HEL-S-272 3
  • PGK-2 2
  • PGK2 5

External Ids for PGK2 Gene

Previous GeneCards Identifiers for PGK2 Gene

  • GC06M049755
  • GC06M049800
  • GC06M049861
  • GC06M049753
  • GC06M049483

Summaries for PGK2 Gene

Entrez Gene Summary for PGK2 Gene

  • This gene is intronless, arose via retrotransposition of the phosphoglycerate kinase 1 gene, and is expressed specifically in the testis. Initially assumed to be a pseudogene, the encoded protein is actually a functional phosphoglycerate kinase that catalyzes the reversible conversion of 1,3-bisphosphoglycerate to 3-phosphoglycerate, during the Embden-Meyerhof-Parnas pathway of glycolysis, in the later stages of spermatogenesis.[provided by RefSeq, May 2010]

GeneCards Summary for PGK2 Gene

PGK2 (Phosphoglycerate Kinase 2) is a Protein Coding gene. Diseases associated with PGK2 include Phosphoglycerate Kinase 1 Deficiency and Testicular Torsion. Among its related pathways are Glucose metabolism and Cori Cycle. Gene Ontology (GO) annotations related to this gene include phosphoglycerate kinase activity. An important paralog of this gene is PGK1.

UniProtKB/Swiss-Prot Summary for PGK2 Gene

  • Essential for sperm motility and male fertility (PubMed:26677959). Not required for the completion of spermatogenesis (By similarity).

Additional gene information for PGK2 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PGK2 Gene

Genomics for PGK2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PGK2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PGK2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PGK2

Top Transcription factor binding sites by QIAGEN in the PGK2 gene promoter:
  • AP-1
  • c-Fos
  • c-Jun
  • CUTL1
  • FosB
  • Fra-1
  • JunB
  • Nkx6-1
  • PPAR-alpha
  • Roaz

Genomic Locations for PGK2 Gene

Latest Assembly
chr6:49,785,660-49,787,285
(GRCh38/hg38)
Size:
1,626 bases
Orientation:
Minus strand

Previous Assembly
chr6:49,753,373-49,754,998
(GRCh37/hg19 by Entrez Gene)
Size:
1,626 bases
Orientation:
Minus strand

chr6:49,753,366-49,755,053
(GRCh37/hg19 by Ensembl)
Size:
1,688 bases
Orientation:
Minus strand

Genomic View for PGK2 Gene

Genes around PGK2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PGK2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PGK2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PGK2 Gene

Proteins for PGK2 Gene

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  • Protein details for PGK2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P07205-PGK2_HUMAN
    Recommended name:
    Phosphoglycerate kinase 2
    Protein Accession:
    P07205
    Secondary Accessions:
    • B2R6Y8
    • Q9H107

    Protein attributes for PGK2 Gene

    Size:
    417 amino acids
    Molecular mass:
    44796 Da
    Quaternary structure:
    • Monomer.

neXtProt entry for PGK2 Gene

Protein Expression for PGK2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for PGK2 Gene

P07205:
  • KYSLAPVA
  • NMLDKVNEMIIGGGM
  • ELKSLLGKDVLFLKDCVG
  • LLENLRF
  • VNDAFGT
  • AILGGAK
  • YFAKALENP
  • DEEGAKIV
  • PSIKYCL
  • SLFDEEG
  • DKFDENA
  • STGGGAS
  • GSVILLEN
  • LENLRFH
  • IGGGMAYTF
  • ITNNQRI
  • DAFGTAHR
  • RVDFNVP
  • RAHSSMVG
  • TFLKVLNNMEIG
  • DVYVNDAF
  • GTKALMDE
  • DKVSHVSTGGG
  • KKELDYF
  • GGGDTATCC
  • MSHLGRP

Post-translational modifications for PGK2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PGK2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for PGK2
  • Boster Bio Antibodies for PGK2

Domains & Families for PGK2 Gene

Gene Families for PGK2 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for PGK2 Gene

InterPro:
Blocks:
  • Phosphoglycerate kinase
ProtoNet:

Suggested Antigen Peptide Sequences for PGK2 Gene

GenScript: Design optimal peptide antigens:
  • Phosphoglycerate kinase, testis specific (PGK2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P07205

UniProtKB/Swiss-Prot:

PGK2_HUMAN :
  • Belongs to the phosphoglycerate kinase family.
Family:
  • Belongs to the phosphoglycerate kinase family.
genes like me logo Genes that share domains with PGK2: view

Function for PGK2 Gene

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Molecular function for PGK2 Gene

UniProtKB/Swiss-Prot Function:
Essential for sperm motility and male fertility (PubMed:26677959). Not required for the completion of spermatogenesis (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP; Xref=Rhea:RHEA:14801, ChEBI:CHEBI:30616, ChEBI:CHEBI:57604, ChEBI:CHEBI:58272, ChEBI:CHEBI:456216; EC=2.7.2.3;.
GENATLAS Biochemistry:
phosphoglycerate kinase 2,specifically expressed in spermatogenic cell,highly homologous to PGK1,glycolysis,energy pathway,key enzyme for ATP generation

Enzyme Numbers (IUBMB) for PGK2 Gene

Phenotypes From GWAS Catalog for PGK2 Gene

Gene Ontology (GO) - Molecular Function for PGK2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0004618 phosphoglycerate kinase activity IBA,NAS 3453121
GO:0005524 ATP binding IBA,ISS --
GO:0016301 kinase activity IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with PGK2: view
genes like me logo Genes that share phenotypes with PGK2: view

Animal Models for PGK2 Gene

MGI Knock Outs for PGK2:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PGK2

No data available for Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for PGK2 Gene

Localization for PGK2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PGK2 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PGK2 gene
Compartment Confidence
extracellular 4
nucleus 4
cytosol 4
mitochondrion 2
peroxisome 2
plasma membrane 1
cytoskeleton 1
endoplasmic reticulum 1
lysosome 1

Gene Ontology (GO) - Cellular Components for PGK2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus HDA 21630459
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IBA 21873635
GO:0035686 sperm fibrous sheath IBA 21873635
GO:0070062 extracellular exosome HDA 23533145
genes like me logo Genes that share ontologies with PGK2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PGK2 Gene

Pathways & Interactions for PGK2 Gene

genes like me logo Genes that share pathways with PGK2: view

Pathways by source for PGK2 Gene

2 BioSystems pathways for PGK2 Gene
1 GeneGo (Thomson Reuters) pathway for PGK2 Gene
  • Glycolysis and gluconeogenesis (short map)

UniProtKB/Swiss-Prot P07205-PGK2_HUMAN

  • Pathway: Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5.

Gene Ontology (GO) - Biological Process for PGK2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006094 gluconeogenesis IBA 21873635
GO:0006096 glycolytic process IBA,NAS 3453121
GO:0016310 phosphorylation NAS 3453121
GO:1903862 positive regulation of oxidative phosphorylation IBA --
genes like me logo Genes that share ontologies with PGK2: view

No data available for SIGNOR curated interactions for PGK2 Gene

Drugs & Compounds for PGK2 Gene

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(3) Drugs for PGK2 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Acyclovir Approved Pharma Enzyme, substrate 124
3-Phosphoglyceric acid Experimental Pharma 0
ATP Investigational Nutra 0

(3) Additional Compounds for PGK2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
2-Phosphoglyceric acid
  • 3-Hydroxy-2-(phosphonooxy)propanoic acid
  • 3-Hydroxy-2-(phosphonooxy)propanoate
  • 2-Phosphoglycerate
  • 2-(Dihydrogen phosphate)glycerate
  • 2-(Dihydrogen phosphate)glyceric acid
 2553-59-5
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
 58-64-0
Glyceric acid 1,3-biphosphate
  • (R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydride with phosphoric propanoic acid
  • 1,3-Bisphospho-D-glycerate
  • 3-Phospho-D-glyceroyl phosphate
  • D-Glycerate 1,3-diphosphate
  • (R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydride with phosphoric propanoate
 38168-82-0
genes like me logo Genes that share compounds with PGK2: view

Transcripts for PGK2 Gene

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mRNA/cDNA for PGK2 Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PGK2

Alternative Splicing Database (ASD) splice patterns (SP) for PGK2 Gene

No ASD Table

Relevant External Links for PGK2 Gene

GeneLoc Exon Structure for
PGK2

Expression for PGK2 Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PGK2 Gene

mRNA expression in normal human tissues for PGK2 Gene
mRNA expression by GTEx for PGK2 GenemRNA expression by BioGPS for PGK2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PGK2 Gene

This gene is overexpressed in Testis (x52.6).

Protein differential expression in normal tissues from HIPED for PGK2 Gene

This gene is overexpressed in Lung (23.3), Brain (16.3), and Testis (13.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PGK2 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PGK2

SOURCE GeneReport for Unigene cluster for PGK2 Gene:

Hs.367727

mRNA Expression by UniProt/SwissProt for PGK2 Gene:

P07205-PGK2_HUMAN
Tissue specificity: Mainly found in round spermatids. Localized on the principle piece in the sperm (at protein level). Testis-specific. Expression significantly decreased in the testis of elderly men.

Evidence on tissue expression from TISSUES for PGK2 Gene

  • Nervous system(4.4)
  • Liver(2.2)
  • Blood(2.1)
  • Heart(2)
  • Gall bladder(2)
genes like me logo Genes that share expression patterns with PGK2: view

Primer products for research

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for PGK2 Gene

Orthologs for PGK2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PGK2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia PGK2 30 31
  • 99.36 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia PGK2 30
  • 88.57 (n)
-- 31
  • 86 (a)
 ManyToMany
Cow
(Bos Taurus)
 Mammalia PGK2 30
  • 88.33 (n)
Rat
(Rattus norvegicus)
 Mammalia Pgk2 30
  • 85.37 (n)
Mouse
(Mus musculus)
 Mammalia Pgk2 30 17 31
  • 84.89 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia -- 31
  • 84 (a)
 ManyToMany
-- 31
  • 83 (a)
 ManyToMany
-- 31
  • 83 (a)
 ManyToMany
-- 31
  • 82 (a)
 ManyToMany
-- 31
  • 81 (a)
 ManyToMany
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 81 (a)
 OneToMany
Chicken
(Gallus gallus)
 Aves PGK1 31
  • 82 (a)
 OneToMany
Lizard
(Anolis carolinensis)
 Reptilia -- 31
  • 83 (a)
 OneToMany
Zebrafish
(Danio rerio)
 Actinopterygii pgk1 31
  • 81 (a)
 OneToMany
Fruit Fly
(Drosophila melanogaster)
 Insecta Pgk 31 32
  • 68 (a)
 ManyToMany
CG9961 31 32
  • 53 (a)
 ManyToMany
Worm
(Caenorhabditis elegans)
 Secernentea pgk-1 31
  • 69 (a)
 OneToMany
T03F1.3 32
  • 69 (a)
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes PGK1 31
  • 63 (a)
 OneToMany
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons PGK 30
  • 56.5 (n)
Alicante grape
(Vitis vinifera)
 eudicotyledons Vvi.6705 30
Soybean
(Glycine max)
 eudicotyledons Gma.6263 30
Rice
(Oryza sativa)
 Liliopsida Os02g0169300 30
  • 55.99 (n)
Species where no ortholog for PGK2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for PGK2 Gene

ENSEMBL:
Gene Tree for PGK2 (if available)
TreeFam:
Gene Tree for PGK2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PGK2: view image

Paralogs for PGK2 Gene

Paralogs for PGK2 Gene

(1) SIMAP similar genes for PGK2 Gene using alignment to 1 proteins:

  • PGK2_HUMAN

Pseudogenes.org Pseudogenes for PGK2 Gene

genes like me logo Genes that share paralogs with PGK2: view

Variants for PGK2 Gene

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dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PGK2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PGK2 Gene

Variant ID Type Subtype PubMed ID
esv3608949 CNV loss 21293372

Variation tolerance for PGK2 Gene

Residual Variation Intolerance Score: 87.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.05; 50.43% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PGK2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PGK2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PGK2 Gene

Disorders for PGK2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PGK2 Gene - From: COP

Disorder Aliases PubMed IDs
phosphoglycerate kinase 1 deficiency
  • pgk1 deficiency
testicular torsion
  • torsion of testicular cord
- elite association - COSMIC cancer census association via MalaCards
Search PGK2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PGK2

Genetic Association Database
(GAD)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with PGK2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PGK2 Gene

Publications for PGK2 Gene

  1. Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene. (PMID: 3453121) McCarrey JR … Thomas K (Nature 1987) 2 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall AJ … Beck S (Nature 2003) 3 4
  4. Molecular cloning and structure of an autosomal processed gene for human phosphoglycerate kinase. (PMID: 3839763) Tani K … Yoshida A (Gene 1985) 2 3
  5. Testis-specific calcium-binding protein CBP86-IV (CABYR) binds with phosphoglycerate kinase 2 in vitro and in vivo experiment. (PMID: 30972801) Shen S … Wang J (Andrologia 2019) 3

ExternalLinks

View latest publications for PGK2 gene in Mastermind

Products for PGK2 Gene

  • Addgene plasmids for PGK2

Sources for PGK2 Gene