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Aliases for PEPD Gene

Aliases for PEPD Gene

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

Regulatory Elements for PEPD Gene

Enhancers for PEPD Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19F033472 1 Ensembl ENCODE 23.8 +48.4 48441 2.3 PKNOX1 INSM2 ZNF76 KLF17 FEZF1 ZNF2 RAD21 ZEB1 GLIS2 ZNF366 PEPD GPATCH1 LSM14A KIAA0355 GC19P033457 GC19M033516
GH19F033532 0.2 ENCODE 22.1 -11.4 -11377 0.8 CBX3 ZNF610 AEBP2 ZNF133 KLF8 ZNF518A PEPD LOC105372370 LOC100996681
GH19F033485 1.2 FANTOM5 ENCODE 21.7 +35.0 35037 2.0 GLIS2 SCRT2 GLIS1 ZIC2 PEPD SLC7A10 GC19P033457 GC19M033516
GH19F033388 1.7 FANTOM5 Ensembl ENCODE 14.4 +128.6 128573 10.5 MLX ZFP64 ARID4B FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP5 GPATCH1 CHST8 AKR1B1P7 LOC100996681 RPL21P131 PEPD WDR88 CEBPG LSM14A CEBPA
GH19F033415 0.8 Ensembl ENCODE 11.3 +105.4 105443 1.1 PKNOX1 KLF17 ZNF2 RAD21 GLIS2 ZNF366 ZNF143 ZNF391 FOS EGR2 CHST8 PEPD GC19P033418 CEBPG
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

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
ENSR00000043967 293 2001 ARID4B SIN3A DMAP1 ZNF2 YY1 FOS ZNF548 SP3 SP5 MXD4

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 StructureGene Density

RefSeq DNA sequence for PEPD Gene

Proteins for PEPD Gene

  • 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

Post-translational modifications for PEPD Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

No data available for DME Specific Peptides for PEPD Gene

Domains & Families for PEPD Gene

Suggested Antigen Peptide Sequences for PEPD Gene

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

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:0004177 aminopeptidase activity IEA --
GO:0004181 metallocarboxypeptidase activity TAS 1972707
GO:0005515 protein binding IPI 21044950
GO:0008233 peptidase activity IEA --
GO:0008237 metallopeptidase activity IEA --
genes like me logo Genes that share ontologies with PEPD: view
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 Models for PEPD Gene

MGI Knock Outs for PEPD:
  • Pepd tm1a(KOMP)Wtsi

Animal Model Products

miRNA for PEPD Gene

miRTarBase miRNAs that target PEPD

Flow Cytometry Products

No data available for 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

Gene Ontology (GO) - Cellular Components for PEPD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with PEPD: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PEPD Gene

Pathways & Interactions for PEPD Gene

SuperPathways for PEPD Gene

No Data Available

Gene Ontology (GO) - Biological Process for PEPD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0006520 cellular amino acid metabolic process TAS 1972707
GO:0030574 collagen catabolic 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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Manganese Approved Nutra 34

(12) 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

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

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for PEPD Gene



Protein tissue co-expression partners for PEPD Gene

NURSA nuclear receptor signaling pathways regulating expression of PEPD Gene:

PEPD

SOURCE GeneReport for Unigene cluster for PEPD Gene:

Hs.36473
genes like me logo Genes that share expression patterns with PEPD: view

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
chimpanzee
(Pan troglodytes)
Mammalia PEPD 34 35
  • 99.1 (n)
dog
(Canis familiaris)
Mammalia PEPD 34 35
  • 89.93 (n)
cow
(Bos Taurus)
Mammalia PEPD 34 35
  • 89.32 (n)
rat
(Rattus norvegicus)
Mammalia Pepd 34
  • 84.96 (n)
mouse
(Mus musculus)
Mammalia Pepd 34 16 35
  • 84.18 (n)
oppossum
(Monodelphis domestica)
Mammalia PEPD 35
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PEPD 35
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves PEPD 34 35
  • 74.78 (n)
lizard
(Anolis carolinensis)
Reptilia PEPD 35
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pepd 34
  • 71.6 (n)
Str.5139 34
zebrafish
(Danio rerio)
Actinopterygii pepd 34 35
  • 71.55 (n)
-- 34
fruit fly
(Drosophila melanogaster)
Insecta Dip-C 36 34 35
  • 59.83 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004775 34
  • 57.49 (n)
worm
(Caenorhabditis elegans)
Secernentea K12C11.1 36 34 35
  • 56.62 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 35
  • 27 (a)
OneToOne
-- 37
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G29490 34
  • 56.88 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.1123 34
rice
(Oryza sativa)
Liliopsida Os02g0224400 34
  • 55.74 (n)
Os.27534 34
corn
(Zea mays)
Liliopsida Zm.3239 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8389 35
  • 50 (a)
OneToMany
-- 35
  • 48 (a)
OneToMany
Species where no ortholog for PEPD was found in the sources mined by GeneCards:
  • 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
rs121917721 Prolidase deficiency (PD) [MIM:170100], Pathogenic 33,401,862(-) TGTTC(A/G)ACATG reference, missense
rs121917722 Prolidase deficiency (PD) [MIM:170100], Pathogenic 33,464,060(-) AAGCC(A/G)AGTGT intron-variant, reference, missense
rs121917723 Prolidase deficiency (PD) [MIM:170100], Pathogenic 33,401,855(-) CATGG(A/G)CGGTG reference, missense
rs121917724 Prolidase deficiency (PD) [MIM:170100], Pathogenic 33,387,892(-) TTGGC(A/G)GGGTG reference, missense
rs121917725 Pathogenic 33,411,697(-) ACGAC(C/G/T)GAACG reference, missense, stop-gained

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

Variant ID Type Subtype PubMed ID
dgv139e55 CNV gain 17911159
dgv2009e59 CNV duplication 20981092
esv2469451 CNV insertion 19546169
esv2677046 CNV deletion 23128226
esv2718472 CNV deletion 23290073
esv2758755 CNV gain 17122850
esv3412309 CNV duplication 20981092
esv3556302 CNV deletion 23714750
esv3556305 CNV deletion 23714750
esv3644189 CNV loss 21293372
esv3644190 CNV loss 21293372
esv3644191 CNV loss 21293372
esv3644192 CNV loss 21293372
nsv1111169 CNV tandem duplication 24896259
nsv1134784 CNV deletion 24896259
nsv470138 CNV gain 18288195
nsv473132 CNV novel sequence insertion 20440878
nsv473839 CNV novel sequence insertion 20440878
nsv513524 CNV insertion 21212237
nsv522571 CNV loss 19592680
nsv525549 CNV gain 19592680
nsv819550 CNV insertion 19587683
nsv828526 CNV loss 20364138
nsv828527 CNV gain 20364138
nsv978804 CNV duplication 23825009

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
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PEPD

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

Disorders for PEPD Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
prolidase deficiency
  • hyperimidodipeptiduria
bacterial vaginosis
  • vaginosis, bacterial
hypermobility syndrome
  • benign joint hypermobility
legg-calve-perthes disease
  • calve - perthes' disease
sexual sadism
  • sadism
- 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. Mutation analysis of five new patients affected by prolidase deficiency: the lack of enzyme activity causes necrosis-like cell death in cultured fibroblasts. (PMID: 12384772) Forlino A. … Cetta G. (Hum. Genet. 2002) 3 4 22 64
  2. Expression and molecular analysis of mutations in prolidase deficiency. (PMID: 8900231) Ledoux P. … Hechtman P. (Am. J. Hum. Genet. 1996) 3 4 22 64
  3. Four novel PEPD alleles causing prolidase deficiency. (PMID: 8198124) Ledoux P. … Hechtman P. (Am. J. Hum. Genet. 1994) 3 4 22 64
  4. 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 22 64
  5. A single nucleotide change in the prolidase gene in fibroblasts from two patients with polypeptide positive prolidase deficiency. Expression of the mutant enzyme in NIH 3T3 cells. (PMID: 2365824) Tanoue A. … Matsuda I. (J. Clin. Invest. 1990) 3 4 22 64

Products for PEPD Gene

Sources for PEPD Gene

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