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Aliases for PDPR Gene

Aliases for PDPR Gene

  • Pyruvate Dehydrogenase Phosphatase Regulatory Subunit 2 3 5
  • Pyruvate Dehydrogenase Phosphatase Regulatory Subunit, Mitochondrial 3
  • KIAA1990 4
  • PDP3 3
  • PDPr 4

External Ids for PDPR Gene

Previous GeneCards Identifiers for PDPR Gene

  • GC16P069883
  • GC16P069923
  • GC16P068705
  • GC16P070148
  • GC16P056002

Summaries for PDPR Gene

Entrez Gene Summary for PDPR Gene

  • Pyruvate dehydrogenase complex (PDC) catalyzes the oxidative decarboxylation of pyruvate and links glycolysis to the tricarboxylic acid cycle and fatty acid synthesis. The dephosphorylation and reactivation of PDC is catalyzed by pyruvate dehydrogenase phosphatase (PDP). The dimeric PDP has a catalytic subunit and a regulatory subunit. This gene encodes the FAD-containing regulatory subunit of PDP. The encoded protein acts to decrease the sensitivity of the PDP catalytic subunit to magnesium ions. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2017]

GeneCards Summary for PDPR Gene

PDPR (Pyruvate Dehydrogenase Phosphatase Regulatory Subunit) is a Protein Coding gene. Diseases associated with PDPR include Anismus and Rectal Disease. Among its related pathways are Metabolism and Pyruvate metabolism and Citric Acid (TCA) cycle. Gene Ontology (GO) annotations related to this gene include oxidoreductase activity and aminomethyltransferase activity. An important paralog of this gene is SARDH.

UniProtKB/Swiss-Prot for PDPR Gene

  • Decreases the sensitivity of PDP1 to magnesium ions, and this inhibition is reversed by the polyamine spermine.

Additional gene information for PDPR Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDPR Gene

Genomics for PDPR Gene

GeneHancer (GH) Regulatory Elements for PDPR Gene

Promoters and enhancers for PDPR Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J070113 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.7 709 2.1 HDGF CLOCK ATF1 MLX ARID4B SIN3A FEZF1 DMAP1 BRCA1 GLIS2 PDPR CLEC18A AARS COG4 EXOSC6 PIR41675
GH16J070287 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 57.8 +175.8 175833 4.1 PKNOX1 SMAD1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B DDX19B AARS PDPR NONOP1 NFAT5 SF3B3 COG4 SMG1P7 LOC400541 COG8
GH16J069422 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 49.2 -689.0 -688966 3.3 HDGF PKNOX1 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 CYB5B GC16M069468 GC16M069476 DDX19B PDPR NFAT5 NONOP1 CHTF8 ZFP90 LOC400541
GH16J069130 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 47.7 -981.6 -981614 3.9 HDGF PKNOX1 CLOCK SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 CHTF8 UTP4 SNTB2 NFAT5 NONOP1 PDPR PDXDC2P-NPIPB14P NPIPB14P PDXDC2P NOB1
GH16J069402 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 52.6 -705.4 -705448 11.5 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 SLC30A9 ZNF213 TERF2 NFAT5 PDXDC2P-NPIPB14P NONOP1 PDXDC2P NPIPB14P PDPR DDX19A LOC400541 SNTB2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDPR on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDPR gene promoter:
  • HFH-3
  • FOXI1
  • FOXO4
  • Max1
  • c-Myc
  • Pax-4a
  • USF-1
  • USF-1:USF-2
  • USF1
  • USF2

Genomic Locations for PDPR Gene

Genomic Locations for PDPR Gene
chr16:70,113,626-70,162,537
(GRCh38/hg38)
Size:
48,912 bases
Orientation:
Plus strand
chr16:70,147,529-70,195,203
(GRCh37/hg19)
Size:
47,675 bases
Orientation:
Plus strand

Genomic View for PDPR Gene

Genes around PDPR on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PDPR Gene

Proteins for PDPR Gene

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

    Protein Symbol:
    Q8NCN5-PDPR_HUMAN
    Recommended name:
    Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial
    Protein Accession:
    Q8NCN5
    Secondary Accessions:
    • A7E298
    • A8K8Y7
    • B3KSE1
    • Q6AI20
    • Q6AWC9

    Protein attributes for PDPR Gene

    Size:
    879 amino acids
    Molecular mass:
    99364 Da
    Quaternary structure:
    • Heterodimer of a catalytic (PDP1) and a regulatory (PDPR) subunit.
    SequenceCaution:
    • Sequence=BAC02699.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAF85191.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PDPR Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDPR Gene

Post-translational modifications for PDPR Gene

  • Ubiquitination at isoforms=100
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PDPR Gene

Domains & Families for PDPR Gene

Gene Families for PDPR Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

Q8NCN5

UniProtKB/Swiss-Prot:

PDPR_HUMAN :
  • Belongs to the GcvT family.
Family:
  • Belongs to the GcvT family.
genes like me logo Genes that share domains with PDPR: view

Function for PDPR Gene

Molecular function for PDPR Gene

UniProtKB/Swiss-Prot Function:
Decreases the sensitivity of PDP1 to magnesium ions, and this inhibition is reversed by the polyamine spermine.

Phenotypes From GWAS Catalog for PDPR Gene

Gene Ontology (GO) - Molecular Function for PDPR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004741 [pyruvate dehydrogenase (lipoamide)] phosphatase activity EXP 9651365
GO:0016491 oxidoreductase activity IEA,IBA --
genes like me logo Genes that share ontologies with PDPR: view
genes like me logo Genes that share phenotypes with PDPR: view

Animal Model Products

  • Taconic Biosciences Mouse Models for PDPR

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDPR Gene

Localization for PDPR Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDPR Gene

Mitochondrion matrix.

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 PDPR gene
Compartment Confidence
mitochondrion 5
cytosol 4
peroxisome 2
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PDPR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005739 mitochondrion IEA,IBA --
GO:0005759 mitochondrial matrix IBA,TAS --
genes like me logo Genes that share ontologies with PDPR: view

Pathways & Interactions for PDPR Gene

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

Gene Ontology (GO) - Biological Process for PDPR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation IEA --
GO:0010510 regulation of acetyl-CoA biosynthetic process from pyruvate TAS --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with PDPR: view

No data available for SIGNOR curated interactions for PDPR Gene

Drugs & Compounds for PDPR Gene

(4) Drugs for PDPR Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Magnesium Approved Nutra 0
spermine Approved Nutra Full agonist, Agonist, Antagonist, Pore Blocker, Channel blocker 0
putrescine Experimental Pharma Antagonist, Pore Blocker 0
spermidine Experimental Pharma Antagonist, Pore Blocker 0

(2) Additional Compounds for PDPR Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
N1-acetylspermine
  • N'-acetylspermine
  • N'-monoacetylspermine
  • N(1)-Acetylspermine
  • N-(3-((4-((3-Aminopropyl)amino)butyl)amino)propyl)-acetamide
  • N-Acetylspermine
25593-72-0
Norspermidine
  • 1,7-diamino-4-Azaheptane
  • 3,3'-Iminobis(propylamine)
  • 3,3'-Iminobispropylamine
  • 3,3'-Iminodi(propylamine)
  • 3,3-Diaminodipropylamine
56-18-8
genes like me logo Genes that share compounds with PDPR: view

Transcripts for PDPR Gene

Unigene Clusters for PDPR Gene

Pyruvate dehydrogenase phosphatase regulatory subunit:
Representative Sequences:

Clone Products

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

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c
SP1:
SP2: -
SP3: - -

Relevant External Links for PDPR Gene

GeneLoc Exon Structure for
PDPR
ECgene alternative splicing isoforms for
PDPR

Expression for PDPR Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDPR Gene

This gene is overexpressed in Lymph node (8.8) and Uterus (7.7).

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



Protein tissue co-expression partners for PDPR Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDPR Gene:

PDPR

SOURCE GeneReport for Unigene cluster for PDPR Gene:

Hs.744043

Evidence on tissue expression from TISSUES for PDPR Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with PDPR: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDPR Gene

Orthologs for PDPR Gene

This gene was present in the common ancestor of animals.

Orthologs for PDPR Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDPR 34
  • 100 (a)
OneToOne
LOC454207 33
  • 99.61 (n)
dog
(Canis familiaris)
Mammalia PDPR 34 33
  • 91.25 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pdpr 33
  • 88.65 (n)
mouse
(Mus musculus)
Mammalia Pdpr 16 34 33
  • 88.61 (n)
cow
(Bos Taurus)
Mammalia PDPR 34 33
  • 88.61 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PDPR 34
  • 86 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDPR 34
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDPR 34 33
  • 77.36 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDPR 34
  • 84 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdpr 33
  • 72.11 (n)
Str.18754 33
zebrafish
(Danio rerio)
Actinopterygii pdpr 33
  • 71.2 (n)
PDPR 34
  • 70 (a)
OneToOne
zgc63662 33
fruit fly
(Drosophila melanogaster)
Insecta CG3626 34 33
  • 53.38 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004715 33
  • 52.31 (n)
worm
(Caenorhabditis elegans)
Secernentea CELE_Y106G6H.5 33
  • 47.22 (n)
Y106G6H.5 34
  • 36 (a)
OneToOne
Species where no ortholog for PDPR was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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 (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PDPR Gene

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

Paralogs for PDPR Gene

Paralogs for PDPR Gene

(2) SIMAP similar genes for PDPR Gene using alignment to 9 proteins:

  • PDPR_HUMAN
  • A8MT40_HUMAN
  • B3KSE1_HUMAN
  • B7ZAR9_HUMAN
  • H3BQG3_HUMAN
  • H3BRS5_HUMAN
  • H3BU60_HUMAN
  • H3BUH3_HUMAN
  • H3BV59_HUMAN

Pseudogenes.org Pseudogenes for PDPR Gene

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

Variants for PDPR Gene

Sequence variations from dbSNP and Humsavar for PDPR Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs202246074 likely-pathogenic, Global developmental delay, Typical Joubert syndrome MRI findings 70,142,278(+) G/A/C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs200469748 not-provided, not provided 70,120,577(+) A/G 5_prime_UTR_variant, coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs1000182830 -- 70,152,394(+) C/A/T genic_downstream_transcript_variant, intron_variant
rs1000248469 -- 70,116,553(+) A/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000298414 -- 70,158,077(+) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant, non_coding_transcript_variant

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

Variant ID Type Subtype PubMed ID
dgv1365n106 CNV duplication 24896259
dgv1626e59 CNV duplication 20981092
dgv1627e59 CNV duplication 20981092
dgv25e213 CNV gain 24956385
dgv2997n100 CNV loss 25217958
dgv2998n100 CNV gain 25217958
dgv3000n100 CNV gain+loss 25217958
dgv3002n100 CNV loss 25217958
dgv3003n100 CNV gain 25217958
dgv3004n100 CNV gain 25217958
dgv3005n100 CNV gain+loss 25217958
dgv3006n100 CNV loss 25217958
dgv3007n100 CNV loss 25217958
dgv3008n100 CNV gain 25217958
dgv3009n100 CNV gain 25217958
dgv3010n100 CNV gain 25217958
dgv3011n100 CNV gain+loss 25217958
dgv3012n100 CNV loss 25217958
dgv3013n100 CNV gain 25217958
dgv485n67 CNV loss 20364138
dgv486n67 CNV gain 20364138
dgv5178n54 CNV loss 21841781
dgv5179n54 CNV loss 21841781
dgv5180n54 CNV loss 21841781
dgv5181n54 CNV loss 21841781
dgv5182n54 CNV loss 21841781
dgv5183n54 CNV loss 21841781
dgv5184n54 CNV loss 21841781
dgv5185n54 CNV gain 21841781
dgv527e214 CNV gain 21293372
dgv848e212 CNV loss 25503493
dgv849e212 CNV gain 25503493
dgv850e212 CNV loss 25503493
dgv851e212 CNV loss 25503493
esv1007882 CNV loss 20482838
esv25519 CNV gain+loss 19812545
esv2577915 CNV gain 19546169
esv2657437 CNV deletion 23128226
esv2714669 CNV deletion 23290073
esv2758652 CNV gain+loss 17122850
esv2760404 CNV gain+loss 21179565
esv2762188 CNV gain+loss 21179565
esv29970 CNV loss 17803354
esv3333319 CNV duplication 20981092
esv33745 CNV gain+loss 17666407
esv3411986 CNV duplication 20981092
esv3426771 CNV duplication 20981092
esv3571454 CNV gain 25503493
esv3571465 CNV gain 25503493
esv3638943 CNV loss 21293372
esv3638944 CNV gain 21293372
esv3638945 CNV loss 21293372
esv3892879 CNV gain 25118596
esv3892880 CNV loss 25118596
esv997919 CNV loss 20482838
nsv1058068 CNV gain+loss 25217958
nsv1060953 CNV gain 25217958
nsv1062268 CNV gain+loss 25217958
nsv1077831 CNV duplication 25765185
nsv1127511 CNV deletion 24896259
nsv1131275 CNV deletion 24896259
nsv1149117 CNV duplication 26484159
nsv1160430 CNV duplication 26073780
nsv1853 CNV deletion 18451855
nsv428328 CNV gain+loss 18775914
nsv436059 CNV insertion 17901297
nsv442725 CNV gain 18776908
nsv469646 CNV gain 16826518
nsv471391 CNV gain 19718026
nsv471695 CNV loss 15918152
nsv482195 CNV gain 20164927
nsv514810 CNV gain+loss 21397061
nsv572912 CNV gain 21841781
nsv572913 CNV gain 21841781
nsv572916 CNV loss 21841781
nsv572918 CNV gain+loss 21841781
nsv572923 CNV loss 21841781
nsv572924 CNV loss 21841781
nsv572927 CNV loss 21841781
nsv572928 CNV loss 21841781
nsv572930 CNV loss 21841781
nsv572931 CNV loss 21841781
nsv572935 CNV loss 21841781
nsv7285 OTHER inversion 18451855
nsv820087 CNV loss 19587683
nsv820860 CNV duplication 20802225
nsv827719 CNV gain 20364138
nsv827723 CNV loss 20364138
nsv827728 CNV loss 20364138
nsv833269 CNV loss 17160897
nsv833271 CNV gain+loss 17160897
nsv9455 CNV gain+loss 18304495
nsv952048 CNV duplication 24416366
nsv960372 CNV duplication 23825009
nsv977991 CNV duplication 23825009
nsv977992 CNV duplication 23825009

Variation tolerance for PDPR Gene

Residual Variation Intolerance Score: 97.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.23; 81.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDPR Gene

Human Gene Mutation Database (HGMD)
PDPR
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDPR

SNP Genotyping and Copy Number Assay Products

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

Disorders for PDPR Gene

MalaCards: The human disease database

(3) MalaCards diseases for PDPR Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
anismus
rectal disease
  • rectal disorders
intussusception
  • intussusception of intestine
- elite association - COSMIC cancer census association via MalaCards
Search PDPR in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PDPR

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PDPR: view

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

Publications for PDPR Gene

  1. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  2. Novel association strategy with copy number variation for identifying new risk Loci of human diseases. (PMID: 20808825) Chen X … Kong X (PloS one 2010) 3 44 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. Characterization of size-fractionated cDNA libraries generated by the in vitro recombination-assisted method. (PMID: 12056414) Ohara O … Koseki H (DNA research : an international journal for rapid publication of reports on genes and genomes 2002) 3 4 58
  5. Cloning, expression, and properties of the regulatory subunit of bovine pyruvate dehydrogenase phosphatase. (PMID: 9395502) Lawson JE … Reed LJ (The Journal of biological chemistry 1997) 2 3 58

Products for PDPR Gene

Sources for PDPR Gene

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