PYROXD1 Gene (Protein Coding)

Pyridine Nucleotide-Disulphide Oxidoreductase Domain 1

GC12P021437
GIFtS:
36
This gene encodes a nuclear-cytoplasmic pyridine nucleotide-disulphide reductase (PNDR). PNDRs are flavoproteins that catalyze the pyridine nucleotide-dependent reduction of thiol residues in other proteins. The encoded protein belongs to the class I pyridine nucleotide-disulphide oxidoreductase family but lacks the C-terminal dimerization domain found in other family members a... See more...

Aliases for PYROXD1 Gene

Aliases for PYROXD1 Gene

  • Pyridine Nucleotide-Disulphide Oxidoreductase Domain 1 2 3 5
  • Pyridine Nucleotide-Disulfide Oxidoreductase Domain-Containing Protein 1 3 4
  • DKFZp762G094 2
  • EC 1.8.1.- 4
  • FLJ22028 2
  • EC 1.8.1 51
  • PYROXD1 5
  • MFM8 3

External Ids for PYROXD1 Gene

Previous GeneCards Identifiers for PYROXD1 Gene

  • GC12P021482
  • GC12P021590
  • GC12P021364

Summaries for PYROXD1 Gene

Entrez Gene Summary for PYROXD1 Gene

  • This gene encodes a nuclear-cytoplasmic pyridine nucleotide-disulphide reductase (PNDR). PNDRs are flavoproteins that catalyze the pyridine nucleotide-dependent reduction of thiol residues in other proteins. The encoded protein belongs to the class I pyridine nucleotide-disulphide oxidoreductase family but lacks the C-terminal dimerization domain found in other family members and instead has a C-terminal nitrile reductase domain. It localizes to the nucleus and to striated sarcomeric compartments. Naturally occurring mutations in this gene cause early-onset myopathy with internalized nuclei and myofibrillar disorganization. A pseudogene of this gene has been defined on chromosome 11. [provided by RefSeq, Apr 2017]

GeneCards Summary for PYROXD1 Gene

PYROXD1 (Pyridine Nucleotide-Disulphide Oxidoreductase Domain 1) is a Protein Coding gene. Diseases associated with PYROXD1 include Myopathy, Myofibrillar, 8 and Myopathy. Gene Ontology (GO) annotations related to this gene include oxidoreductase activity. An important paralog of this gene is TXNRD2.

UniProtKB/Swiss-Prot Summary for PYROXD1 Gene

  • Probable FAD-dependent oxidoreductase; involved in the cellular oxidative stress response (PubMed:27745833). Required for normal sarcomere structure and muscle fiber integrity (By similarity).

Additional gene information for PYROXD1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PYROXD1 Gene

Genomics for PYROXD1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PYROXD1 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
GH12J021436 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 655.6 +0.5 486 2.6 CREB1 GATAD2A CTCF PRDM10 ZNF629 IKZF1 NFKBIZ ZNF692 POLR2A GABPA PYROXD1 ELOCP31 GOLT1B
GH12J021452 Enhancer 0.7 Ensembl ENCODE 55.7 +18.0 17958 6.3 POLR2A IKZF2 RELB JUND EZH2 ATF3 TBX21 FOS ATF7 MTA2 PYROXD1 SPX RECQL HSALNG0089760 piR-54185-002 GOLT1B
GH12J021500 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 11.3 +64.1 64086 4.2 SP1 CREB1 ZNF629 RFX1 KDM1A ZNF692 POLR2A FOS JUND GABPA RECQL GOLT1B HSALNG0089764 HSALNG0089765 PYROXD1 SPX
GH12J021419 Promoter 0.9 Ensembl 20.9 -18.1 -18114 0.6 LEF1 IKZF1 PKNOX1 BRD9 ZNF24 SOX6 MGA ZNF184 POLR2A MTA3 SLCO1A2 lnc-SLCO1A2-1 piR-46002-112 piR-57176-115 piR-45012-104 PYROXD1 IAPP
GH12J021443 Enhancer 0.3 Ensembl 55.3 +6.6 6586 0.8 REST FOSL2 PYROXD1 SPX ELOCP31 GOLT1B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PYROXD1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PYROXD1

Top Transcription factor binding sites by QIAGEN in the PYROXD1 gene promoter:
  • Arnt
  • c-Myc
  • FOXJ2
  • FOXJ2 (long isoform)
  • Max
  • NRF-2
  • Pax-2
  • Pax-2a
  • Pax-4a
  • Zic3

Genomic Locations for PYROXD1 Gene

Genomic Locations for PYROXD1 Gene
chr12:21,437,615-21,471,252
(GRCh38/hg38)
Size:
33,638 bases
Orientation:
Plus strand
chr12:21,590,538-21,624,184
(GRCh37/hg19)
Size:
33,647 bases
Orientation:
Plus strand

Genomic View for PYROXD1 Gene

Genes around PYROXD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PYROXD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PYROXD1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PYROXD1 Gene

Proteins for PYROXD1 Gene

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  • Protein details for PYROXD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WU10-PYRD1_HUMAN
    Recommended name:
    Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1
    Protein Accession:
    Q8WU10
    Secondary Accessions:
    • A6NKI6
    • B3KWN8
    • Q9H6P1

    Protein attributes for PYROXD1 Gene

    Size:
    500 amino acids
    Molecular mass:
    55793 Da
    Cofactor:
    Name=FAD; Xref=ChEBI:CHEBI:57692;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB15214.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for PYROXD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PYROXD1 Gene

Protein Expression for PYROXD1 Gene

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

Selected DME Specific Peptides for PYROXD1 Gene

Q8WU10:
  • KIYGCDFIVSATGV
  • GNGGIALEL
  • VLGIRDTDSAQEFQK
  • VGGGIAGVTCAEQ
  • RFPNIKVIESGVKQLKS
  • LEEFDVEEQ
  • YEIEGCEV
  • CEVKKIYL
  • TKFFNYKVVLLGK
  • TDLEETFENLILNQ

Post-translational modifications for PYROXD1 Gene

  • Ubiquitination at Lys142
  • Modification sites at PhosphoSitePlus

Other Protein References for PYROXD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Boster Bio Antibodies for PYROXD1

Domains & Families for PYROXD1 Gene

Gene Families for PYROXD1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for PYROXD1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PYROXD1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ43472 fis, clone OCBBF2037638 (B3KWN8_HUMAN)
  • cDNA FLJ60446 (B4DEW4_HUMAN)
  • Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1 (PYRD1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8WU10

UniProtKB/Swiss-Prot:

PYRD1_HUMAN :
  • Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family. PYROXD1 subfamily.
Family:
  • Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family. PYROXD1 subfamily.
genes like me logo Genes that share domains with PYROXD1: view

Function for PYROXD1 Gene

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Molecular function for PYROXD1 Gene

UniProtKB/Swiss-Prot Function:
Probable FAD-dependent oxidoreductase; involved in the cellular oxidative stress response (PubMed:27745833). Required for normal sarcomere structure and muscle fiber integrity (By similarity).

Enzyme Numbers (IUBMB) for PYROXD1 Gene

Gene Ontology (GO) - Molecular Function for PYROXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0016491 oxidoreductase activity IEA --
genes like me logo Genes that share ontologies with PYROXD1: view
genes like me logo Genes that share phenotypes with PYROXD1: view

Human Phenotype Ontology for PYROXD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PYROXD1 Gene

MGI Knock Outs for PYROXD1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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No data available for Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for PYROXD1 Gene

Localization for PYROXD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PYROXD1 Gene

Nucleus. Cytoplasm. Cytoplasm, myofibril, sarcomere.

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 PYROXD1 gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PYROXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 27745833
GO:0005737 cytoplasm IEA --
GO:0030017 sarcomere IEA,IDA 27745833
genes like me logo Genes that share ontologies with PYROXD1: view

Pathways & Interactions for PYROXD1 Gene

PathCards logo

SuperPathways for PYROXD1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PYROXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0034599 cellular response to oxidative stress IMP 27745833
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with PYROXD1: view

No data available for Pathways by source and SIGNOR curated interactions for PYROXD1 Gene

Drugs & Compounds for PYROXD1 Gene

Products:

  1. Drug

(1) Drugs for PYROXD1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
FAD Approved Pharma 0

(1) Additional Compounds for PYROXD1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid
  • 2-KDN
  • 2-keto-3-Deoxy-D-glycero-D-galacto-NONONate
  • 2-keto-3-Deoxy-D-glycero-D-galacto-NONONic acid
  • 2-oxo-3-Deoxy-D-glycero-galactononulosonate
  • 2-oxo-3-Deoxy-D-glycero-galactononulosonic acid
 22594-61-2
genes like me logo Genes that share compounds with PYROXD1: view

Transcripts for PYROXD1 Gene

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  1. CRISPR
  2. miRNA
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mRNA/cDNA for PYROXD1 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PYROXD1

Alternative Splicing Database (ASD) splice patterns (SP) for PYROXD1 Gene

No ASD Table

Relevant External Links for PYROXD1 Gene

GeneLoc Exon Structure for
PYROXD1

Expression for PYROXD1 Gene

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  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PYROXD1 Gene

mRNA expression in normal human tissues for PYROXD1 Gene
mRNA expression by GTEx for PYROXD1 GenemRNA expression by BioGPS for PYROXD1 Gene

Protein differential expression in normal tissues from HIPED for PYROXD1 Gene

This gene is overexpressed in Retina (23.3), Testis (7.6), and Islet of Langerhans (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PYROXD1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PYROXD1

SOURCE GeneReport for Unigene cluster for PYROXD1 Gene:

Hs.709545

Evidence on tissue expression from TISSUES for PYROXD1 Gene

  • Nervous system(4.3)
  • Kidney(4.3)
genes like me logo Genes that share expression patterns with PYROXD1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PYROXD1 Gene

Orthologs for PYROXD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PYROXD1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia PYROXD1 30 31
  • 99.4 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia PYROXD1 30 31
  • 89.53 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia PYROXD1 30 31
  • 89.41 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Pyroxd1 30
  • 83.43 (n)
Mouse
(Mus musculus)
 Mammalia Pyroxd1 30 17 31
  • 83.17 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia PYROXD1 31
  • 81 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 77 (a)
 OneToMany
-- 31
  • 72 (a)
 OneToMany
-- 31
  • 58 (a)
 OneToMany
Chicken
(Gallus gallus)
 Aves PYROXD1 30 31
  • 75.96 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia PYROXD1 31
  • 74 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia pyroxd1 30
  • 63.08 (n)
Str.19896 30
African clawed frog
(Xenopus laevis)
 Amphibia Xl.16405 30
Zebrafish
(Danio rerio)
 Actinopterygii ryroxd1 30 31
  • 65.2 (n)
 OneToOne
zgc73254 30
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP008042 30
  • 54.26 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta CG10721 30 31
  • 52.96 (n)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea C26D10.3 30 31
  • 45.33 (n)
 OneToOne
Sea Vase
(Ciona intestinalis)
 Ascidiacea Cin.6258 30
Species where no ortholog for PYROXD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 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 PYROXD1 Gene

ENSEMBL:
Gene Tree for PYROXD1 (if available)
TreeFam:
Gene Tree for PYROXD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PYROXD1: view image

Paralogs for PYROXD1 Gene

Paralogs for PYROXD1 Gene

Pseudogenes.org Pseudogenes for PYROXD1 Gene

genes like me logo Genes that share paralogs with PYROXD1: view

Variants for PYROXD1 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PYROXD1 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
679712 Benign: not provided 21,470,577(+) A/G THREE_PRIME_UTR_VARIANT,INTRON_VARIANT
679737 Benign: not provided 21,470,350(+) C/A THREE_PRIME_UTR_VARIANT,INTRON_VARIANT
708210 Benign: not provided 21,462,002(+) T/G INTRON_VARIANT
723435 Benign: not provided 21,467,522(+) A/C SYNONYMOUS_VARIANT
729181 Benign: not provided 21,455,198(+) C/T SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT

Additional dbSNP identifiers (rs#s) for PYROXD1 Gene

Structural Variations from Database of Genomic Variants (DGV) for PYROXD1 Gene

Variant ID Type Subtype PubMed ID
esv3628807 CNV gain 21293372
nsv1054220 CNV gain 25217958
nsv469163 CNV loss 19166990
nsv526789 CNV loss 19592680
nsv557741 CNV gain 21841781
nsv557742 CNV loss 21841781
nsv975459 CNV duplication 23825009
nsv976585 CNV duplication 23825009

Variation tolerance for PYROXD1 Gene

Residual Variation Intolerance Score: 50% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.19; 23.99% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PYROXD1 Gene

Human Gene Mutation Database (HGMD)
PYROXD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PYROXD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PYROXD1 Gene

Disorders for PYROXD1 Gene

MalaCards: The human disease database

(11) MalaCards diseases for PYROXD1 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
myopathy, myofibrillar, 8
  • mfm8
myopathy
  • muscular diseases
myofibrillar myopathy
  • myopathy, myofibrillar, desmin-related
myopathy, centronuclear, 4
  • cnm4
myopathy, centronuclear, 5
  • cnm5
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

PYRD1_HUMAN
  • Myopathy, myofibrillar, 8 (MFM8) [MIM:617258]: A form of myofibrillar myopathy, a group of chronic neuromuscular disorders characterized at ultrastructural level by disintegration of the sarcomeric Z disk and myofibrils, and replacement of the normal myofibrillar markings by small dense granules, or larger hyaline masses, or amorphous material. MFM8 is an autosomal recessive form, clinically characterized by slowly progressive symmetrical weakness affecting both proximal and distal muscles, with normal to moderately elevated creatine kinase. Mild facial weakness, a high palate, nasal speech, and swallowing difficulties are typical features, mild restrictive lung disease is common, and late-onset cardiac involvement may be present. {ECO:0000269 PubMed:27745833}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=A mutation in PYROXD1 is the cause of autosomal recessive limb-girdle muscular dystrophy. The affected individual with a homozygous recessive PYROXD1 mutation showed progressive muscle weakness with an onset at the age of 9 years. Initial symptoms included excessive falling while running, with slowly progressive weakness. Difficulty navigating stairs by the age if 18, and loss of ambulation at the age of 37 years. Neurological examination showed proximal symmetrical muscle weakness and wasting, along with calf muscle pseudohypertrophy. {ECO:0000269 PubMed:30345904}.

Additional Disease Information for PYROXD1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with PYROXD1: view

No data available for Genatlas for PYROXD1 Gene

Publications for PYROXD1 Gene

  1. Variants in the Oxidoreductase PYROXD1 Cause Early-Onset Myopathy with Internalized Nuclei and Myofibrillar Disorganization. (PMID: 27745833) O'Grady GL … Cooper ST (American journal of human genetics 2016) 2 3 4
  2. Impact of PYROXD1 deficiency on cellular respiration and correlations with genetic analyses of limb-girdle muscular dystrophy in Saudi Arabia and Sudan. (PMID: 30345904) Saha M … Kang PB (Physiological genomics 2018) 3 4
  3. 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 41
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

ExternalLinks

View latest publications for PYROXD1 gene in Mastermind

Products for PYROXD1 Gene

  • Signalway ELISA kits for PYROXD1

Sources for PYROXD1 Gene