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Aliases for ME3 Gene

Aliases for ME3 Gene

  • Malic Enzyme 3 2 3 4 5
  • Malate Dehydrogenase (Oxaloacetate-Decarboxylating) (NADP(+)) 2 3
  • Malic Enzyme 3, NADP(+)-Dependent, Mitochondrial 2 3
  • NADP-Dependent Malic Enzyme, Mitochondrial 3 4
  • EC 4 56
  • NADP-ME 3 4
  • Mitochondrial NADP(+)-Dependent Malic Enzyme 3 3
  • Malic Enzyme, NADP+-Dependent, Mitochondrial 3
  • Pyruvic-Malic Carboxylase 3
  • EC 1.1.1 56

External Ids for ME3 Gene

Previous GeneCards Identifiers for ME3 Gene

  • GC11M088478
  • GC11M087691
  • GC11M086374
  • GC11M085878
  • GC11M085829
  • GC11M086152
  • GC11M082440

Summaries for ME3 Gene

Entrez Gene Summary for ME3 Gene

  • Malic enzyme catalyzes the oxidative decarboxylation of malate to pyruvate using either NAD+ or NADP+ as a cofactor. Mammalian tissues contain 3 distinct isoforms of malic enzyme: a cytosolic NADP(+)-dependent isoform, a mitochondrial NADP(+)-dependent isoform, and a mitochondrial NAD(+)-dependent isoform. This gene encodes a mitochondrial NADP(+)-dependent isoform. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for ME3 Gene

ME3 (Malic Enzyme 3) is a Protein Coding gene. Among its related pathways are Pyruvate metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include NAD binding and malic enzyme activity. An important paralog of this gene is ME1.

Additional gene information for ME3 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ME3 Gene

Genomics for ME3 Gene

GeneHancer (GH) Regulatory Elements for ME3 Gene

Promoters and enhancers for ME3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J086669 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 613.7 +0.7 708 3.9 ZNF652 NCOA3 SP1 CTCF FOXA2 CEBPB ZFX ATF3 RNF2 MXI1 ME3 PRSS23 PIR51863 GC11M086573
GH11J086674 Enhancer 0.9 ENCODE dbSUPER 600.7 -1.6 -1608 0.2 SP1 SP5 RXRA FOXA2 JUND YY1 ZBTB33 HHEX HNF4A MAX ME3 PIR50196 GC11M086573
GH11J086587 Enhancer 1.4 Ensembl ENCODE dbSUPER 37.8 +80.1 80136 11 ELF3 ZNF687 NFIB MAFK JUND TFE3 ELF1 SP7 CREM PRDM1 CREBZF ME3 EED ENSG00000279742 LOC100420680 TMEM126B CCDC89 PRSS23 GC11P086590 PIR37636
GH11J086732 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 21 -68.3 -68319 16.3 ZNF148 MLLT1 GTF2F1 NFIB ZSCAN21 NCOA3 BACH1 MAFK TRIM24 ELF1 ME3 PRSS23 EED LOC100420680 ENSG00000255250 GC11P086748
GH11J086632 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 22.8 +36.9 36921 7.4 ZSCAN21 CTCF FOSL2 ZNF600 ZIC2 REST SMARCC1 JUN SP1 RCOR1 ME3 PRSS23 PIR51863 GC11M086573
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ME3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ME3 gene promoter:
  • E47
  • IRF-2
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • Tal-1

Genomic Locations for ME3 Gene

Genomic Locations for ME3 Gene
231,529 bases
Minus strand
231,529 bases
Minus strand

Genomic View for ME3 Gene

Genes around ME3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ME3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ME3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ME3 Gene

Proteins for ME3 Gene

  • Protein details for ME3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    NADP-dependent malic enzyme, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • B7Z6V0
    • Q8TBJ0

    Protein attributes for ME3 Gene

    604 amino acids
    Molecular mass:
    67068 Da
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for ME3 Gene


neXtProt entry for ME3 Gene

Selected DME Specific Peptides for ME3 Gene


Post-translational modifications for ME3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for ME3 Gene

Gene Families for ME3 Gene

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

Suggested Antigen Peptide Sequences for ME3 Gene

GenScript: Design optimal peptide antigens:
  • Malic enzyme (B7Z6V0_HUMAN)
  • Malic enzyme (E9PMB9_HUMAN)
  • Malic enzyme (E9PNN2_HUMAN)
  • Malic enzyme 3 (MAON_HUMAN)
  • Cadherin (O15201_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the malic enzymes family.
  • Belongs to the malic enzymes family.
genes like me logo Genes that share domains with ME3: view

Function for ME3 Gene

Molecular function for ME3 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(S)-malate + NADP(+) = CO2 + NADPH + pyruvate; Xref=Rhea:RHEA:18253, ChEBI:CHEBI:15361, ChEBI:CHEBI:15589, ChEBI:CHEBI:16526, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349; EC=;.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H(+) + oxaloacetate = CO2 + pyruvate; Xref=Rhea:RHEA:15641, ChEBI:CHEBI:15361, ChEBI:CHEBI:15378, ChEBI:CHEBI:16452, ChEBI:CHEBI:16526; EC=;.
GENATLAS Biochemistry:
malic enzyme 3, NADP(+)-dependent, mitochondrial,predominantly expressed in tissues with a low division rate,catalyzing the decarboxylation of malate to pyruvate

Enzyme Numbers (IUBMB) for ME3 Gene

Phenotypes From GWAS Catalog for ME3 Gene

Gene Ontology (GO) - Molecular Function for ME3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004470 malic enzyme activity IDA 7818469
GO:0004471 malate dehydrogenase (decarboxylating) (NAD+) activity IEA --
GO:0004473 malate dehydrogenase (decarboxylating) (NADP+) activity IEA,IDA 7818469
GO:0008948 oxaloacetate decarboxylase activity IEA --
GO:0016491 oxidoreductase activity IEA --
genes like me logo Genes that share ontologies with ME3: view
genes like me logo Genes that share phenotypes with ME3: view

Animal Models for ME3 Gene

MGI Knock Outs for ME3:
  • Me3 Me3<tm1b(KOMP)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for ME3

CRISPR Products

miRNA for ME3 Gene

miRTarBase miRNAs that target ME3

Clone Products

  • Applied Biological Materials (abm): Clones for ME3 - Now 50% OFF >
  • * ME3 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * ME3 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ME3 Gene

Localization for ME3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ME3 Gene

Mitochondrion matrix.

Subcellular locations from

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 ME3 gene
Compartment Confidence
mitochondrion 5
cytosol 3
peroxisome 1
nucleus 1

Gene Ontology (GO) - Cellular Components for ME3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion TAS,IBA 7818469
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with ME3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ME3 Gene

Pathways & Interactions for ME3 Gene

PathCards logo

SuperPathways for ME3 Gene

genes like me logo Genes that share pathways with ME3: view

Pathways by source for ME3 Gene

Gene Ontology (GO) - Biological Process for ME3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006090 pyruvate metabolic process IDA 7818469
GO:0006099 tricarboxylic acid cycle TAS --
GO:0006108 malate metabolic process IDA 7818469
GO:0009060 aerobic respiration TAS 7818469
GO:0055114 oxidation-reduction process IDA,IEA 7818469
genes like me logo Genes that share ontologies with ME3: view

No data available for SIGNOR curated interactions for ME3 Gene

Drugs & Compounds for ME3 Gene

(8) Drugs for ME3 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
NADH Approved Nutra Target 0
Carbon dioxide Approved, Investigational, Vet_approved Pharma 0
Magnesium Approved, Experimental, Investigational Pharma 0
Manganese Approved Nutra 41
Pyruvic acid Approved, Investigational Nutra 0

(6) Additional Compounds for ME3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Hydrogen Ion
  • H+
  • H(+)
  • Hydrogen cation
  • Hydron
  • Proton
Hydroxypropanedioic acid
  • 2-Hydroxymalonate
  • 2-Hydroxymalonic acid
  • 2-Hydroxypropanedioic acid
  • 2-Tartronic acid
  • Tartronic acid
L-Malic acid
  • (-)-L-Malic acid
  • (S)-(-)-Hydroxysuccinic acid
  • L-2-Hydroxybutanedioic acid
  • L-Apple acid
  • Malate
  • beta-Nicotinamide adenine dinucleotide phosphate
  • NADP+
  • Nicotinamide adenine dinucleotide phosphate
  • Oxidized nicotinamide-adenine dinucleotide phosphate
  • TPN
  • 2'-(Dihydrogen phosphate) 5'-(trihydrogen pyrophosphate) adenosine 5'-ester with 1,4-dihydro-1-b-D-ribofuranosylnicotinamide
  • 2'-(Dihydrogen phosphate) 5'-(trihydrogen pyrophosphate) adenosine 5'-ester with 1,4-dihydro-1-beta-delta-ribofuranosylnicotinamide
  • Adenosine 5'-(trihydrogen diphosphate) 2'-(dihydrogen phosphate) p'-5'-ester with 1,4-dihydro-1-beta-D-ribofuranosyl-3-pyridinecarboxamide
  • Adenosine 5'-(trihydrogen diphosphate) 2'-(dihydrogen phosphate) p'-5'-ester with 1,4-dihydro-1-beta-delta-ribofuranosyl-3-pyridinecarboxamide
  • b-NADPH
genes like me logo Genes that share compounds with ME3: view

Transcripts for ME3 Gene

Unigene Clusters for ME3 Gene

Malic enzyme 3, NADP(+)-dependent, mitochondrial:
Representative Sequences:

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for ME3 - Now 50% OFF >
  • * ME3 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * ME3 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

Alternative Splicing Database (ASD) splice patterns (SP) for ME3 Gene

No ASD Table

Relevant External Links for ME3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ME3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ME3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ME3 Gene

This gene is overexpressed in Brain (25.2), Liver (14.8), and Frontal cortex (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ME3 Gene

Protein tissue co-expression partners for ME3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ME3 Gene:


SOURCE GeneReport for Unigene cluster for ME3 Gene:


mRNA Expression by UniProt/SwissProt for ME3 Gene:

Tissue specificity: Expressed predominantly in organs with a low-division rate.

Evidence on tissue expression from TISSUES for ME3 Gene

  • Nervous system(4.7)
  • Intestine(4.1)
  • Liver(2.3)
genes like me logo Genes that share expression patterns with ME3: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ME3 Gene

Orthologs for ME3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ME3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ME3 35 34
  • 99.72 (n)
(Canis familiaris)
Mammalia ME3 35 34
  • 92.05 (n)
(Bos Taurus)
Mammalia ME3 35 34
  • 91.23 (n)
(Mus musculus)
Mammalia Me3 17 35 34
  • 89.29 (n)
(Rattus norvegicus)
Mammalia Me3 34
  • 86.82 (n)
(Monodelphis domestica)
Mammalia ME3 35
  • 85 (a)
(Ornithorhynchus anatinus)
Mammalia ME3 35
  • 79 (a)
(Gallus gallus)
Aves ME3 35 34
  • 74.3 (n)
(Anolis carolinensis)
Reptilia ME3 35
  • 77 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia me3 34
  • 71.5 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.6324 34
(Danio rerio)
Actinopterygii me3 35 34
  • 72.33 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.326 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004159 34
  • 61.42 (n)
fruit fly
(Drosophila melanogaster)
Insecta Men-b 35 34
  • 58.38 (n)
Mdh 36
  • 56 (a)
Menl-1 36
  • 45 (a)
Menl-2 36
  • 42 (a)
Men 35 36
  • 39 (a)
CG7848 35 36
  • 30 (a)
(Caenorhabditis elegans)
Secernentea men-1 35 34
  • 58.3 (n)
Y48B6A.12 36
  • 54 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MAE1 35
  • 29 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons NADP-ME1 34
  • 52.56 (n)
(Oryza sativa)
Liliopsida Os01g0743500 34
  • 54.69 (n)
(Triticum aestivum)
Liliopsida Ta.14421 34
Species where no ortholog for ME3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • 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)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for ME3 Gene

Gene Tree for ME3 (if available)
Gene Tree for ME3 (if available)
Evolutionary constrained regions (ECRs) for ME3: view image

Paralogs for ME3 Gene

Paralogs for ME3 Gene

(42) SIMAP similar genes for ME3 Gene using alignment to 10 proteins:

  • B7Z6V0_HUMAN
  • O15201_HUMAN
genes like me logo Genes that share paralogs with ME3: view

Variants for ME3 Gene

Sequence variations from dbSNP and Humsavar for ME3 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000031131 -- 86,542,815(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000048741 -- 86,669,545(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000080376 -- 86,502,820(-) C/T intron_variant
rs1000081195 -- 86,496,262(-) T/C intron_variant
rs1000082688 -- 86,525,112(-) A/G genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ME3 Gene

Variant ID Type Subtype PubMed ID
dgv2046n54 CNV loss 21841781
dgv2047n54 CNV loss 21841781
dgv2048n54 CNV loss 21841781
dgv2049n54 CNV loss 21841781
dgv2050n54 CNV loss 21841781
dgv2051n54 CNV loss 21841781
dgv2052n54 CNV loss 21841781
dgv2053n54 CNV loss 21841781
dgv2054n54 CNV loss 21841781
dgv2055n54 CNV loss 21841781
dgv230e199 CNV deletion 23128226
dgv231n67 CNV loss 20364138
dgv232n67 CNV loss 20364138
dgv683n106 CNV deletion 24896259
esv2662437 CNV deletion 23128226
esv26643 CNV loss 19812545
esv2668174 CNV deletion 23128226
esv2672841 CNV deletion 23128226
esv2678915 CNV deletion 23128226
esv2744855 CNV deletion 23290073
esv2744856 CNV deletion 23290073
esv274960 CNV gain+loss 21479260
esv29418 CNV loss 19812545
esv3303304 CNV mobile element insertion 20981092
esv3398000 CNV insertion 20981092
esv3405888 CNV insertion 20981092
esv3548094 CNV deletion 23714750
esv3548095 CNV deletion 23714750
esv3627088 CNV gain 21293372
esv3627090 CNV loss 21293372
esv3627092 CNV loss 21293372
esv3627093 CNV loss 21293372
esv3627094 CNV loss 21293372
esv3627095 CNV gain 21293372
esv3627096 CNV loss 21293372
esv3627097 CNV loss 21293372
esv3627099 CNV gain 21293372
esv4749 CNV loss 18987735
nsv1119421 CNV insertion 24896259
nsv428263 CNV loss 18775914
nsv471753 CNV loss 16327809
nsv471754 CNV loss 16327809
nsv475811 CNV novel sequence insertion 20440878
nsv510265 OTHER sequence alteration 20534489
nsv520466 CNV loss 19592680
nsv522178 CNV loss 19592680
nsv522823 CNV loss 19592680
nsv528182 CNV loss 19592680
nsv555665 CNV loss 21841781
nsv555671 CNV loss 21841781
nsv555678 CNV loss 21841781
nsv555685 CNV loss 21841781
nsv555703 CNV loss 21841781
nsv555704 CNV loss 21841781
nsv819492 CNV loss 19587683
nsv826020 CNV loss 20364138
nsv8852 CNV loss 18304495

Variation tolerance for ME3 Gene

Residual Variation Intolerance Score: 10.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.59; 89.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ME3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ME3 Gene

Disorders for ME3 Gene

Additional Disease Information for ME3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for ME3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ME3 Gene

Publications for ME3 Gene

  1. Purification, cDNA cloning and heterologous expression of the human mitochondrial NADP(+)-dependent malic enzyme. (PMID: 7818469) Loeber G … Schwendenwein R (The Biochemical journal 1994) 2 3 4 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 58
  3. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F … Nebel A (Mutation research 2010) 3 45 58
  4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 45 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for ME3 Gene

Sources for ME3 Gene

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