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PEPD Gene(Protein Coding)

Peptidase D

GCID:
GC19M033386
GIFtS:
68
Genes Participants
UDN Logo

Aliases for PEPD Gene

Aliases for PEPD Gene

  • Peptidase D 2 3 4 5
  • Proline Dipeptidase 3 4
  • X-Pro Dipeptidase 3 4
  • Imidodipeptidase 3 4
  • PROLIDASE 3 4
  • Testicular Tissue Protein Li 138 3
  • Aminoacyl-L-Proline Hydrolase 3
  • EC 3.4.13.9 4
  • Prolidase 2
  • PRD 4

External Ids for PEPD Gene

Previous GeneCards Identifiers for PEPD Gene

  • GC19M034495
  • GC19M034326
  • GC19M038553
  • GC19M038569
  • GC19M033877
  • GC19M030378

Summaries for PEPD Gene

Entrez Gene Summary for PEPD Gene

  • This gene encodes a member of the peptidase family. The protein forms a homodimer that hydrolyzes dipeptides or tripeptides with C-terminal proline or hydroxyproline residues. The enzyme serves an important role in the recycling of proline, and may be rate limiting for the production of collagen. Mutations in this gene result in prolidase deficiency, which is characterized by the excretion of large amount of di- and tri-peptides containing proline. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]

GeneCards Summary for PEPD Gene

PEPD (Peptidase D) is a Protein Coding gene. Diseases associated with PEPD include Prolidase Deficiency and Sexual Sadism. GO annotations related to this gene include peptidase activity and aminopeptidase activity.

UniProtKB/Swiss-Prot for PEPD Gene

  • Splits dipeptides with a prolyl or hydroxyprolyl residue in the C-terminal position. Plays an important role in collagen metabolism because the high level of iminoacids in collagen.

Gene Wiki entry for PEPD Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PEPD Gene

Genomics for PEPD Gene

Products:

  1. Regulatory Element

Regulatory Elements for PEPD Gene

Enhancers for PEPD Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PEPD on UCSC Golden Path with GeneCards custom track

Promoters for PEPD Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PEPD on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the PEPD gene promoter:

Genomic Location for PEPD Gene

Chromosome:
19
Start:
33,386,949 bp from pter
End:
33,521,893 bp from pter
Size:
134,945 bases
Orientation:
Minus strand

Genomic View for PEPD Gene

Genes around PEPD on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PEPD Gene

Proteins for PEPD Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    P12955-PEPD_HUMAN
    Recommended name:
    Xaa-Pro dipeptidase
    Protein Accession:
    P12955
    Secondary Accessions:
    • A8K3Z1
    • A8K416
    • A8K696
    • A8MX47
    • B4DDB7
    • B4DGJ1
    • E9PCE8
    • Q8TBN9
    • Q9BT75

    Protein attributes for PEPD Gene

    Size:
    493 amino acids
    Molecular mass:
    54548 Da
    Cofactor:
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PEPD Gene

    Alternative splice isoforms for PEPD Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PEPD Gene

Proteomics data for PEPD Gene at MOPED

Protein Expression for PEPD Gene

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

Post-translational modifications for PEPD Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PEPD Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PEPD Gene

Domains & Families for PEPD Gene

Protein Domains for PEPD Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for PEPD Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P12955

UniProtKB/Swiss-Prot:

PEPD_HUMAN :
  • Belongs to the peptidase M24B family. Eukaryotic-type prolidase subfamily.
Family:
  • Belongs to the peptidase M24B family. Eukaryotic-type prolidase subfamily.
genes like me logo Genes that share domains with PEPD: view

No data available for Gene Families for PEPD Gene

Function for PEPD Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for PEPD Gene

GENATLAS Biochemistry:
peptidase D
UniProtKB/Swiss-Prot CatalyticActivity:
Hydrolysis of Xaa- -Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on Pro- -Pro.
UniProtKB/Swiss-Prot Function:
Splits dipeptides with a prolyl or hydroxyprolyl residue in the C-terminal position. Plays an important role in collagen metabolism because the high level of iminoacids in collagen.

Enzyme Numbers (IUBMB) for PEPD Gene

Gene Ontology (GO) - Molecular Function for PEPD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004181 metallocarboxypeptidase activity TAS 1972707
GO:0016787 hydrolase activity IEA --
GO:0030145 manganese ion binding IEA --
GO:0102009 proline dipeptidase activity IEA --
genes like me logo Genes that share ontologies with PEPD: view

Phenotypes for PEPD Gene

MGI mutant phenotypes for PEPD:
inferred from 1 alleles
GenomeRNAi human phenotypes for PEPD:
genes like me logo Genes that share phenotypes with PEPD: view

Human Phenotype Ontology for PEPD Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for PEPD Gene

miRTarBase miRNAs that target PEPD

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for PEPD Gene

Localization for PEPD Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PEPD Gene COMPARTMENTS Subcellular localization image for PEPD gene
Compartment Confidence
extracellular 5
cytosol 3
nucleus 2
endoplasmic reticulum 1
lysosome 1
mitochondrion 1
peroxisome 1
plasma membrane 1
vacuole 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for PEPD Gene

Pathways & Interactions for PEPD Gene

SuperPathways for PEPD Gene

PathCards logoMore details on SuperPathways for PEPD
No Data Available

Gene Ontology (GO) - Biological Process for PEPD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008152 metabolic process IEA --
genes like me logo Genes that share ontologies with PEPD: view

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

Drugs & Compounds for PEPD Gene

Products:

  1. Drug

(25) Drugs for PEPD Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Manganese Pharma 32

(13) Additional Compounds for PEPD Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Glycylproline
  • 1-(Aminoacetyl)proline
  • 1-Glycyl-L-Proline
  • 1-Glycylproline
  • GLY-pro
  • N-Glycyl-L-proline
 704-15-4
genes like me logo Genes that share compounds with PEPD: view

Transcripts for PEPD Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for PEPD Gene

(3) REFSEQ mRNAs :
(13) Additional mRNA sequences :
(455) Selected AceView cDNA sequences:
(13) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PEPD Gene

Peptidase D:
Representative Sequences:

Flow Cytometry Products

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

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17a · 17b
SP1: - - -
SP2: -
SP3: - - - - - -
SP4: -
SP5:
SP6:

Relevant External Links for PEPD Gene

GeneLoc Exon Structure for
PEPD
ECgene alternative splicing isoforms for
PEPD

Expression for PEPD Gene

Products:

  1. Primer

mRNA expression in normal human tissues for PEPD Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Kidney - Cortex (x5.5).

Protein differential expression in normal tissues from HIPED for PEPD Gene

This gene is overexpressed in Serum (11.8) and Pancreatic juice (7.4).

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



SOURCE GeneReport for Unigene cluster for PEPD Gene Hs.36473

genes like me logo Genes that share expression patterns with PEPD: view

Protein tissue co-expression partners for PEPD Gene

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for PEPD Gene

Orthologs for PEPD Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PEPD Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
 Mammalia PEPD 35
  • 89.32 (n)
  • 91.68 (a)
PEPD 36
  • 92 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia PEPD 35
  • 89.93 (n)
  • 92.7 (a)
PEPD 36
  • 93 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Pepd 35
  • 84.18 (n)
  • 89.05 (a)
Pepd 16
Pepd 36
  • 89 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia PEPD 35
  • 99.1 (n)
  • 98.84 (a)
PEPD 36
  • 97 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Pepd 35
  • 84.96 (n)
  • 89.23 (a)
oppossum
(Monodelphis domestica)
 Mammalia PEPD 36
  • 84 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia PEPD 36
  • 79 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves PEPD 35
  • 74.78 (n)
  • 79.11 (a)
PEPD 36
  • 78 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia PEPD 36
  • 69 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia pepd 35
  • 71.6 (n)
  • 77.57 (a)
Str.5139 35
zebrafish
(Danio rerio)
 Actinopterygii -- 35
pepd 35
  • 71.55 (n)
  • 74.43 (a)
pepd 36
  • 72 (a)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta Dip-C 37
  • 50 (a)
Dip-C 35
  • 59.83 (n)
  • 53.35 (a)
Dip-C 36
  • 50 (a)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP004775 35
  • 57.49 (n)
  • 56.36 (a)
worm
(Caenorhabditis elegans)
 Secernentea K12C11.1 37
  • 52 (a)
K12C11.1 35
  • 56.62 (n)
  • 54.78 (a)
K12C11.1 36
  • 52 (a)
 OneToOne
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes -- 36
  • 27 (a)
 OneToOne
-- 38
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT4G29490 35
  • 56.88 (n)
  • 58.75 (a)
Alicante grape
(Vitis vinifera)
 eudicotyledons Vvi.1123 35
rice
(Oryza sativa)
 Liliopsida Os.27534 35
Os02g0224400 35
  • 55.74 (n)
  • 57.2 (a)
corn
(Zea mays)
 Liliopsida Zm.3239 35
sea squirt
(Ciona savignyi)
 Ascidiacea -- 36
  • 48 (a)
 OneToMany
CSA.8389 36
  • 50 (a)
 OneToMany
Species with no ortholog for PEPD:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 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)
  • wheat (Triticum aestivum)

Evolution for PEPD Gene

ENSEMBL:
Gene Tree for PEPD (if available)
TreeFam:
Gene Tree for PEPD (if available)

Paralogs for PEPD Gene

Pseudogenes.org Pseudogenes for PEPD Gene

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

No data available for Paralogs for PEPD Gene

Variants for PEPD Gene

Sequence variations from dbSNP and Humsavar for PEPD Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
VAR_004404 Prolidase deficiency (PD)
VAR_004405 Prolidase deficiency (PD)
VAR_011614 Prolidase deficiency (PD)
VAR_011615 Prolidase deficiency (PD)
rs17570 - 33,387,931(-) CCTTC(C/T)TTAAC reference, missense

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

Variant ID Type Subtype PubMed ID
dgv1073e1 CNV Complex 17122850
nsv911597 CNV Loss 21882294
nsv828526 CNV Loss 20364138
dgv3845n71 CNV Loss 21882294
dgv3846n71 CNV Loss 21882294
nsv470138 CNV Gain 18288195
dgv3847n71 CNV Loss 21882294
nsv522571 CNV Loss 19592680
dgv139e55 CNV Gain 17911159
nsv525549 CNV Gain 19592680
nsv828527 CNV Gain 20364138
nsv911608 CNV Loss 21882294
nsv513524 CNV Insertion 21212237
esv2469451 CNV Insertion 19546169
nsv819550 CNV Insertion 19587683
esv2718472 CNV Deletion 23290073
esv2677046 CNV Deletion 23128226

Variation tolerance for PEPD Gene

Residual Variation Intolerance Score: 74.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.60; 89.03% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PEPD Gene

Human Gene Mutation Database (HGMD)
PEPD

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

Disorders for PEPD Gene

MalaCards: The human disease database

(6) MalaCards diseases for PEPD Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
prolidase deficiency
  • hyperimidodipeptiduria
sexual sadism
  • sadism
hypermobility syndrome
  • benign joint hypermobility
legg-calve-perthes disease
  • calve - perthes' disease
diabetic foot ulcers
  • diabetic foot
- elite association - COSMIC cancer census association via MalaCards
Search PEPD in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PEPD_HUMAN
  • Prolidase deficiency (PD) [MIM:170100]: A multisystem disorder associated with massive iminodipeptiduria and lack of or reduced prolidase activity in erythrocytes, leukocytes, or cultured fibroblasts. Clinical features include skin ulcers, developmental delay, recurrent infections, and a characteristic facies. {ECO:0000269 PubMed:12384772, ECO:0000269 PubMed:2365824, ECO:0000269 PubMed:8198124, ECO:0000269 PubMed:8900231}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for PEPD Gene

prolidase deficiency,with variable expression from no manifestation to severe progressive skin ulceration,decreased resistance to infection,impaired cognitive development

Relevant External Links for PEPD

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

Publications for PEPD Gene

  1. Primary structure and gene localization of human prolidase. (PMID: 2925654) Endo F. … Matsuda I. (J. Biol. Chem. 1989) 2 3 4 67
  2. Structural organization of the gene for human prolidase (peptidase D) and demonstration of a partial gene deletion in a patient with prolidase deficiency. (PMID: 1972707) Tanoue A. … Matsuda I. (J. Biol. Chem. 1990) 2 3 23
  3. Prolidase activity and oxidative status in patients with thalassemia major. (PMID: 20087956) Cakmak A. … Aksoy N. (J. Clin. Lab. Anal. 2010) 3 23
  4. Dilatation of the ascending aorta is associated with low serum prolidase activity. (PMID: 20383038) Akcakoyun M. … Esen A.M. (Tohoku J. Exp. Med. 2010) 3 23
  5. Characterization of prolidase I and II purified from normal human erythrocytes: comparison with prolidase in erythrocytes from a patient with prolidase deficiency. (PMID: 19263194) Uramatsu S. … Kodama H. (Amino Acids 2009) 3 23

Products for PEPD Gene

  • Addgene plasmids for PEPD

Sources for PEPD Gene

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