PDYN Gene (Protein Coding)

Prodynorphin

GC20M001978
GIFtS:
43
The protein encoded by this gene is a preproprotein that is proteolytically processed to form the secreted opioid peptides beta-neoendorphin, dynorphin, leu-enkephalin, rimorphin, and leumorphin. These peptides are ligands for the kappa-type of opioid receptor. Dynorphin is involved in modulating responses to several psychoactive substances, including cocaine. Multiple alternat... See more...

Aliases for PDYN Gene

Aliases for PDYN Gene

  • Prodynorphin 2 3 5
  • Neoendorphin-Dynorphin-Enkephalin Prepropeptide 2 3
  • Beta-Neoendorphin-Dynorphin 3 4
  • Preproenkephalin B 2 3
  • Proenkephalin-B 3 4
  • Preprodynorphin 3 4
  • Leu-Enkephalin 2 3
  • Leumorphin 2 3
  • Rimorphin 2 3
  • PENKB 2 3
  • ADCA 2 3
  • Spinocerebellar Ataxia 23 2
  • Beta-Neoendorphin 2
  • Dynorphin 2
  • SCA23 3
  • PDYN 5

External Ids for PDYN Gene

Previous HGNC Symbols for PDYN Gene

  • SCA23

Previous GeneCards Identifiers for PDYN Gene

  • GC20M001947
  • GC20M001954
  • GC20M001907

Summaries for PDYN Gene

Entrez Gene Summary for PDYN Gene

  • The protein encoded by this gene is a preproprotein that is proteolytically processed to form the secreted opioid peptides beta-neoendorphin, dynorphin, leu-enkephalin, rimorphin, and leumorphin. These peptides are ligands for the kappa-type of opioid receptor. Dynorphin is involved in modulating responses to several psychoactive substances, including cocaine. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2010]

GeneCards Summary for PDYN Gene

PDYN (Prodynorphin) is a Protein Coding gene. Diseases associated with PDYN include Spinocerebellar Ataxia 23 and Drug Dependence. Among its related pathways are Signaling by GPCR and Spinocerebellar ataxia. Gene Ontology (GO) annotations related to this gene include opioid peptide activity. An important paralog of this gene is PENK.

UniProtKB/Swiss-Prot Summary for PDYN Gene

  • Leu-enkephalins compete with and mimic the effects of opiate drugs. They play a role in a number of physiologic functions, including pain perception and responses to stress (By similarity).
  • Dynorphin peptides differentially regulate the kappa opioid receptor. Dynorphin A(1-13) has a typical opiod activity, it is 700 times more potent than Leu-enkephalin (By similarity).
  • Leumorphin has a typical opiod activity and may have anti-apoptotic effect.

Additional gene information for PDYN Gene

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

Genomics for PDYN Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PDYN 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
GH20J001994 Promoter/Enhancer 0.8 EPDnew Ensembl 600.7 +0.7 684 2 FOXK2 ZFHX2 EZH2 EGR2 PDYN PDYN-AS1 SIRPA
GH20J001839 Enhancer 1.7 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 11.7 +143.8 143804 24.6 SP1 HNRNPL GATAD2A PRDM10 RFX1 NFKBIZ KDM1A RCOR2 ZNF143 RELA SIRPA PDYN SDCBP2 ZNF343 PSMF1 SIRPB2 SIRPB1 LOC107984104 ENSG00000286288 lnc-SIRPG-5
GH20J001827 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 4 +164.7 164683 4.7 HNRNPL GATAD2A TFE3 SOX13 KDM1A NFRKB RCOR2 ZNF7 PRDM1 ZIC2 lnc-SIRPA-1 ZNF343 NOP56 SIRPA SNRPB ACTG1P3 SDCBP2-AS1 PDYN SDCBP2 lnc-SIRPG-5
GH20J001808 Enhancer 1.4 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 1.8 +182.8 182751 6.6 HNRNPL GATAD2A ATF7 ZNF629 TFE3 KDM1A SP1 CEBPA EED SOX13 SIRPA SDCBP2 PDYN SIRPB2 MN297781 LOC105372501 lnc-SIRPG-5 LOC107984104 ENSG00000286288 SIRPG
GH20J001960 Enhancer 0.2 FANTOM5 3.7 +33.6 33612 0.2 PDYN SIRPA PDYN-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

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

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

Top Transcription factor binding sites by QIAGEN in the PDYN gene promoter:
  • c-Myb
  • HOXA3
  • HOXA9
  • HOXA9B
  • Meis-1
  • Meis-1b
  • Nkx2-5

Genomic Locations for PDYN Gene

Genomic Locations for PDYN Gene
chr20:1,978,756-1,994,285
(GRCh38/hg38)
Size:
15,530 bases
Orientation:
Minus strand
chr20:1,959,402-1,974,931
(GRCh37/hg19)
Size:
15,530 bases
Orientation:
Minus strand

Genomic View for PDYN Gene

Genes around PDYN on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PDYN Gene

Proteins for PDYN Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    P01213-PDYN_HUMAN
    Recommended name:
    Proenkephalin-B
    Protein Accession:
    P01213
    Secondary Accessions:
    • A8K0Q3

    Protein attributes for PDYN Gene

    Size:
    254 amino acids
    Molecular mass:
    28385 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for PDYN Gene

neXtProt entry for PDYN Gene

Protein Expression for PDYN Gene

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

Post-translational modifications for PDYN Gene

  • The N-terminal domain contains 6 conserved cysteines thought to be involved in disulfide bonding and/or processing.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PDYN Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PDYN Gene

Domains & Families for PDYN Gene

Gene Families for PDYN Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted secreted proteins
  • Transporters

Protein Domains for PDYN Gene

InterPro:
Blocks:
  • Opioid neuropeptide precursor
  • Proenkephalin B precursor signature
ProtoNet:

Suggested Antigen Peptide Sequences for PDYN Gene

GenScript: Design optimal peptide antigens:
  • Preprodynorphin (PDYN_HUMAN)
  • Preprodynorphin (Q2YEL0_HUMAN)
  • Preprodynorphin (Q2YEM6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P01213

UniProtKB/Swiss-Prot:

PDYN_HUMAN :
  • Belongs to the opioid neuropeptide precursor family.
Family:
  • Belongs to the opioid neuropeptide precursor family.
genes like me logo Genes that share domains with PDYN: view

Function for PDYN Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
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Molecular function for PDYN Gene

UniProtKB/Swiss-Prot Function:
Leu-enkephalins compete with and mimic the effects of opiate drugs. They play a role in a number of physiologic functions, including pain perception and responses to stress (By similarity).
UniProtKB/Swiss-Prot Function:
Dynorphin peptides differentially regulate the kappa opioid receptor. Dynorphin A(1-13) has a typical opiod activity, it is 700 times more potent than Leu-enkephalin (By similarity).
UniProtKB/Swiss-Prot Function:
Leumorphin has a typical opiod activity and may have anti-apoptotic effect.
GENATLAS Biochemistry:
pro-dynorphin

Phenotypes From GWAS Catalog for PDYN Gene

Gene Ontology (GO) - Molecular Function for PDYN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001515 opioid peptide activity IEA --
GO:0031628 opioid receptor binding IBA 21873635
genes like me logo Genes that share ontologies with PDYN: view
genes like me logo Genes that share phenotypes with PDYN: view

Human Phenotype Ontology for PDYN Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PDYN Gene

MGI Knock Outs for PDYN:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PDYN Gene

Localization for PDYN Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDYN Gene

Secreted.

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 PDYN gene
Compartment Confidence
plasma membrane 5
extracellular 5
nucleus 3
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
cytosol 2
peroxisome 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for PDYN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005886 plasma membrane IBA,IDA 9047294
GO:0030425 dendrite IBA 21873635
GO:0043025 neuronal cell body IBA 21873635
GO:0043679 axon terminus IBA 21873635
genes like me logo Genes that share ontologies with PDYN: view

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

Pathways & Interactions for PDYN Gene

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

Pathways by source for PDYN Gene

1 BioSystems pathway for PDYN Gene
2 GeneGo (Thomson Reuters) pathways for PDYN Gene
  • Neurophysiological process Glutamate regulation of Dopamine D1A receptor signaling
  • Transcription CREB pathway
2 Qiagen pathways for PDYN Gene
  • DREAM Repression and Dynorphin Expression
  • Neuropathic Pain-Signaling in Dorsal Horn Neurons

SIGNOR curated interactions for PDYN Gene

Activates:
Is inactivated by:

Gene Ontology (GO) - Biological Process for PDYN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007186 G protein-coupled receptor signaling pathway TAS --
GO:0007218 neuropeptide signaling pathway IBA 21873635
GO:0007268 chemical synaptic transmission IEA,IBA 21873635
GO:0007600 sensory perception IBA 21873635
genes like me logo Genes that share ontologies with PDYN: view

Drugs & Compounds for PDYN Gene

Products:

  1. Drug

(48) Drugs for PDYN Gene - From: PharmGKB and Novoseek

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

(29) Additional Compounds for PDYN Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with PDYN: view

Transcripts for PDYN Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for PDYN Gene

5 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
11 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 PDYN

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

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c ^ 5a · 5b ^ 6a · 6b · 6c · 6d · 6e · 6f
SP1: - - - - -
SP2: - - - - -
SP3: - - - -
SP4: -
SP5:
SP6: - - - - -
SP7: - - - - - -
SP8: - - -

Relevant External Links for PDYN Gene

GeneLoc Exon Structure for
PDYN

Expression for PDYN Gene

Products:

  1. Primer
  2. Gene Expression Assay

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

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

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

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x21.4), Brain - Caudate (basal ganglia) (x11.3), and Brain - Putamen (basal ganglia) (x6.4).

Protein differential expression in normal tissues from HIPED for PDYN Gene

This gene is overexpressed in Testis (25.8), Lymph node (10.6), and Ovary (9.8).

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



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

SOURCE GeneReport for Unigene cluster for PDYN Gene:

Hs.22584

Evidence on tissue expression from TISSUES for PDYN Gene

  • Nervous system(4.9)
  • Adrenal gland(2.5)
  • Blood(2.4)
  • Muscle(2.4)
  • Intestine(2.3)
  • Skin(2.2)
  • Stomach(2.1)
  • Heart(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PDYN Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • eye
  • head
Limb:
  • foot
  • lower limb
  • upper limb
General:
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with PDYN: view

No data available for Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for PDYN Gene

Orthologs for PDYN Gene

This gene was present in the common ancestor of chordates.

Orthologs for PDYN Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia PDYN 30 31
  • 98.82 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia PDYN 30 31
  • 84.91 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia PDYN 30 31
  • 82.02 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Pdyn 30
  • 76.76 (n)
Mouse
(Mus musculus)
 Mammalia Pdyn 30 17 31
  • 74.97 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia PDYN 31
  • 54 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves PDYN 30 31
  • 58.37 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia PDYN 31
  • 44 (a)
 OneToOne
Zebrafish
(Danio rerio)
 Actinopterygii pdyn 30 31 31
  • 51.8 (n)
 OneToMany
Species where no ortholog for PDYN 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)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • 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)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for PDYN Gene

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

Paralogs for PDYN Gene

Paralogs for PDYN Gene

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

Variants for PDYN Gene

Products:

  1. SNP Genotyping and Copy Number Assay

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

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
727810 Likely Benign: not provided 1,980,788(-) C/A SYNONYMOUS_VARIANT
728105 Conflicting Interpretations: Spinocerebellar ataxia type 23; not provided 1,980,506(-) G/A SYNONYMOUS_VARIANT
734141 Likely Benign: not provided 1,980,950(-) G/A SYNONYMOUS_VARIANT
739703 Likely Benign: not provided 1,980,644(-) A/G SYNONYMOUS_VARIANT
746654 Likely Benign: not provided 1,980,527(-) T/G SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for PDYN Gene

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

Variant ID Type Subtype PubMed ID
nsv470535 CNV gain 18288195

Variation tolerance for PDYN Gene

Residual Variation Intolerance Score: 51% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.68; 32.13% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDYN Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for PDYN Gene

MalaCards: The human disease database

(47) MalaCards diseases for PDYN Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
spinocerebellar ataxia 23
  • sca23
drug dependence
cocaine dependence
temporal lobe epilepsy
  • epilepsy, temporal lobe
opiate dependence
  • opioid type dependence
- elite association - COSMIC cancer census association via MalaCards
Search PDYN in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PDYN_HUMAN
  • Spinocerebellar ataxia 23 (SCA23) [MIM:610245]: Spinocerebellar ataxia is a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA23 is an adult-onset autosomal dominant form characterized by slowly progressive gait and limb ataxia, with variable additional features, including peripheral neuropathy and dysarthria. {ECO:0000269 PubMed:21035104, ECO:0000269 PubMed:21712028, ECO:0000269 PubMed:23108490, ECO:0000269 PubMed:23471613}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PDYN

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 PDYN: view

No data available for Genatlas for PDYN Gene

Publications for PDYN Gene

  1. Prodynorphin mutations cause the neurodegenerative disorder spinocerebellar ataxia type 23. (PMID: 21035104) Bakalkin G … Verbeek DS (American journal of human genetics 2010) 2 3 4
  2. Gene polymorphisms in prodynorphin (PDYN) are associated with episodic memory in the elderly. (PMID: 19468819) Kölsch H … Dichgans M (Journal of neural transmission (Vienna, Austria : 1996) 2009) 3 23 41
  3. Analysis of the prodynorphin promoter polymorphism in atopic dermatitis and disease-related pruritus. (PMID: 19486061) Greisenegger EK … Kopp T (Clinical and experimental dermatology 2009) 3 23 41
  4. A functional haplotype implicated in vulnerability to develop cocaine dependence is associated with reduced PDYN expression in human brain. (PMID: 18923396) Yuferov V … Kreek MJ (Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology 2009) 3 23 41
  5. Genetic association studies of methamphetamine use disorders: A systematic review and synthesis. (PMID: 19219857) Bousman CA … Tsuang MT (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2009) 3 23 41

ExternalLinks

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