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PEPD Gene

protein-coding   GIFtS: 62
GCID: GC19M033877

Peptidase D

  See PEPD-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Peptidase D1 2 3     imidodipeptidase2
Proline Dipeptidase2 3     Xaa-Pro Dipeptidase2
X-Pro Dipeptidase2 3     EC 3.4.13.93
prolidase1     Imidodipeptidase3
PROLIDASE2     PRD3
Aminoacyl-L-Proline Hydrolase2     Prolidase3

External Ids:    HGNC: 88401   Entrez Gene: 51842   Ensembl: ENSG000001242997   OMIM: 6132305   UniProtKB: P129553   

Export aliases for PEPD gene to outside databases

Previous GC identifers: GC19M034495 GC19M034326 GC19M038553 GC19M038569 GC19M030378


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 metallocarboxypeptidase activity and manganese ion binding.

UniProtKB/Swiss-Prot: PEPD_HUMAN, P12955
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

Gene Wiki entry for PEPD Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000019.9  NC_018930.2  NT_011109.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the PEPD gene promoter:
         PPAR-gamma1   IRF-7A   RelA   Nkx2-5   PPAR-gamma2   HNF-3beta   NF-kappaB   NF-kappaB1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for PEPD

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PEPD


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.11   Ensembl cytogenetic band:  19q13.11   HGNC cytogenetic band: 19q13.11

PEPD Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PEPD gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M033877:  view genomic region     (about GC identifiers)

Start:
33,877,855 bp from pter      End:
34,012,799 bp from pter
Size:
134,945 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: PEPD_HUMAN, P12955 (See protein sequence)
Recommended Name: Xaa-Pro dipeptidase  
Size: 493 amino acids; 54548 Da
Cofactor: Binds 2 manganese ions per subunit
Subunit: Homodimer
Mass spectrometry: Mass=54251.73; Method=MALDI; Range=2-493; Source=PubMed:11840567;
2 PDB 3D structures from and Proteopedia for PEPD:
2IW2 (3D)        2OKN (3D)    
Secondary accessions: A8K3Z1 A8K416 A8K696 A8MX47 B4DDB7 B4DGJ1 E9PCE8 Q8TBN9 Q9BT75
Alternative splicing: 3 isoforms:  P12955-1   P12955-2   P12955-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PEPD: NX_P12955

Explore proteomics data for PEPD at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See PEPD Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_000276.2  NP_001159528.1  NP_001159529.1  

    ENSEMBL proteins: 
     ENSP00000244137   ENSP00000380226   ENSP00000391890   ENSP00000468516   ENSP00000476514  
     ENSP00000476667   ENSP00000476869  

    PEPD Human Recombinant Protein Products:

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    Novus Biologicals PEPD Proteins
    Novus Biologicals PEPD Lysates
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    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for PEPD

     
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    antibodies-online proteins for PEPD (6 products) 

     
    antibodies-online peptides for PEPD

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    antibodies-online antibodies for PEPD (32 products) 

    PEPD Assay Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR007865 Aminopep_P_N
     IPR000994 Pept_M24_structural-domain
     IPR001131 Peptidase_M24B_aminopep-P_CS

    Graphical View of Domain Structure for InterPro Entry P12955

    ProtoNet protein and cluster: P12955

    1 Blocks protein domain: IPB007865 Aminopeptidase P

    UniProtKB/Swiss-Prot: PEPD_HUMAN, P12955
    Similarity: Belongs to the peptidase M24B family. Eukaryotic-type prolidase subfamily


    Find genes that share domains with PEPD           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PEPD_HUMAN, P12955
    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
    Catalytic activity: Hydrolysis of Xaa- -Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action
    on Pro- -Pro

         Genatlas biochemistry entry for PEPD:
    peptidase D

         Enzyme Number (IUBMB): EC 3.4.13.91

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004177aminopeptidase activity IEA--
    GO:0004181metallocarboxypeptidase activity TAS1972707
    GO:0008233peptidase activity ----
    GO:0016805dipeptidase activity IEA--
    GO:0030145manganese ion binding IEA--
         
    Find genes that share ontologies with PEPD           About GenesLikeMe


    Phenotypes:
         3 GenomeRNAi human phenotypes for PEPD:
     Decreased influenza A/WSN/33 r  Increased cell number in G2M,   Increased gamma-H2AX phosphory 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for PEPD

    miRNA
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    miRTarBase miRNAs that target PEPD:
    hsa-mir-423-3p (MIRT042567)

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    SwitchGear 3'UTR luciferase reporter plasmidPEPD 3' UTR sequence
    Inhib. RNA
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    Sino Biological Human cDNA Clone for PEPD
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    extracellular2
    nucleus2
    endoplasmic reticulum1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0070062extracellular vesicular exosome IDA19056867

    Find genes that share ontologies with PEPD           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PEPD
    Interactions:

        GeneGlobe Interaction Network for PEPD

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for PEPD (P129552, 3 ENSP000002441374) via UniProtKB, MINT, STRING, and/or I2D (see all 82)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4BP628053, ENSP000003665814I2D: score=4 STRING: ENSP00000366581
    HIST1H4CP628053, ENSP000003670344I2D: score=4 STRING: ENSP00000367034
    HIST1H4DP628053, ENSP000003432824I2D: score=4 STRING: ENSP00000343282
    HIST1H4EP628053, ENSP000003536244I2D: score=4 STRING: ENSP00000353624
    HIST1H4HP628053, ENSP000002893524I2D: score=4 STRING: ENSP00000289352
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006508proteolysis TAS1972707
    GO:0006520cellular amino acid metabolic process TAS1972707
    GO:0030574collagen catabolic process IEA--

    Find genes that share ontologies with PEPD           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PEPD

    2 HMDB Compounds for PEPD    About this table
    CompoundSynonyms CAS #PubMed Ids
    Glycylproline1-(Aminoacetyl)proline (see all 6)704-15-416642978
    Manganesemanganese 7439-96-5--

    Selected Novoseek inferred chemical compound relationships for PEPD gene (see all 38)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    glycylproline 93.2 14 15530480 (2), 9972056 (1), 10582130 (1), 1536787 (1) (see all 7)
    proline 85.7 151 15696600 (5), 11820612 (4), 1437403 (3), 9581474 (3) (see all 70)
    acetylproline 85.4 2 2246246 (1), 1545347 (1)
    pepq 81.2 3 12859771 (1), 8633861 (1), 10075426 (1)
    anthraquinone-2-carboxylic acid 79.7 3 9972056 (3)
    hydroxyproline 76.4 33 8031960 (2), 9112701 (1), 17999410 (1), 18806117 (1) (see all 24)
    melphalan 52.8 31 14572862 (4), 10697434 (3), 17377743 (3), 15804176 (3) (see all 8)
    chlorambucil 50.1 9 9581474 (3), 11338665 (3), 15178351 (1)
    tripeptide s 48.1 1 9879669 (1)
    6-phosphogluconate 36.7 1 7810807 (1)



    Find genes that share compounds with PEPD           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for PEPD gene (3 alternative transcripts): 
    NM_000285.3  NM_001166056.1  NM_001166057.1  

    Unigene Cluster for PEPD:

    Peptidase D
    Hs.36473  [show with all ESTs]
    Unigene Representative Sequence: NM_000285
    13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000593085 ENST00000244137(uc002nur.4) ENST00000589598 ENST00000591968
    ENST00000397032(uc010xrr.2) ENST00000436370(uc002nuq.4 uc010xrs.2)
    ENST00000588328 ENST00000590731 ENST00000609145 ENST00000593163 ENST00000588719
    ENST00000590755 ENST00000590408
    miRNA
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat PEPD
      QuantiTect SYBR Green Assays in human, mouse, rat PEPD
      QuantiFast Probe-based Assays in human, mouse, rat PEPD

    Additional mRNA sequence: 

    AK057538.1 AK225037.1 AK290756.1 AK290781.1 AK291561.1 AK293126.1 AK294619.1 BC004305.1 
    BC015027.1 BC028295.1 BT006692.1 CR541669.1 J04605.1 

    19 DOTS entries:

    DT.447692  DT.100793949  DT.100793951  DT.121501050  DT.91772559  DT.100732650  DT.100793956  DT.121501026 
    DT.100793952  DT.40315802  DT.100793964  DT.100804841  DT.100810995  DT.120978751  DT.121500975  DT.121500988 
    DT.121500996  DT.100810001  DT.95256615 

    455 AceView cDNA sequences (see top 24):

    CR626494 BI756568 BM756066 BQ006951 BF432095 CB216666 BG767493 BM755925 
    BQ720584 CA445150 AA906251 BG770634 BE396008 CA397698 BQ021219 CA429295 
    CF272305 BF476206 N33079 BM023632 AW271523 BX113786 BM920899 CF264855 
    BX351818 R40821 CA434047 BF001803 BQ004285 BF725508 BE891587 BM708006 
    CR541669 CR598964 BM547809 BC004305 BM545128 BP377763 BU728217 BI823930 
    BF592046 BF197597 CR619095 BU733181 BF205206 BP342120 BU185278 AU142553 
    CR617814 BM805597 BI758133 BC015027 CB144900 BQ227979 CR609932 CR590409 
    AW137119 CR617788 BI756190 BP376008 CB155686 CA309899 AL548325 CR619694 
    BI835706 BT006692 BM759634 BM708323 BM802530 AI570481 BQ009575 BM827716 
    CR590549 AA907732 CR626035 BM707768 CA307020 BI766836 CA428447 BM548769 
    AK057538 BX335686 BM921594 BI769993 BI771066 BX351497 BM801583 AL545922 
    BM783717 CD608000 BM783513 BG284561 BE906470 BM783225 BM972341 J04605 
    BQ020528 BM759728 BI523891 AU142238 BV198160 AL037857 CA748931 BU678168 
    AI002530 AI239630 BF969160 BG249011 BM772985 BG765767 AL575072 AW163438 
    AL547859 BI907127 AL550515 BG576639 AI391680 CD608006 AA309013 AL044197 
    BC028295 BM835978 BM783554 BM783305 BM783056 AU135980 BP370524 CA308844 
    AU139389 BQ109436 AL553115 CD608011 AW157563 BG399504 AL037877 BM470852 
    BI771810 AL547991 BP381219 CA305974 BF974316 BI524649 BM707630 CD607998 
    AL578055 BQ893884 N26271 BM970941 BI906211 AL037120 BQ722991 AL549514 
    AU142398 CB127536 BM546376 AI086909 BM783578 BM129572 BP372359 BM548753 
    BX365041 BI258702 BU732091 BU731409 BM747905 CD608001 AA309012 BF036137 
    AA587397 BU601735 BI768311 BM750066 BX402581 BI518972 AL554651 BM007362 
    AI377395 AW614439 BQ433590 BE313138 BM013662 BQ015873 AI801877 AW073906 
    BU625763 CK816203 N40982 BU159319 AL551533 AL574352 BM783756 BM563248 
    BM546492 AL571458 BM818598 CD369458 AL572649 BM783753 AA481608 BE247390 
    BX324796 BP357785 BX365042 AL551304 BI832642 AW051391 CA314479 BM739667 
    BM799058 AU133724 BX459592 BM509177 AI376407 AU135033 CA429972 BI831156 
    BI906786 BI827565 CD607996 BF975309 BF568581 BM783791 CA424881 BQ425767 
    AI826928 BM835971 BM783547 BX422608 BI832641 BM919612 BM737673 NM_000285 
    BM745203 BF431252 BI861676 AL555595 AL535726 AL552148 AI743667 BM042015 
    BG675861 CB164372 BP382729 AW512991 AA331480 AW170299 AI954487 AA910929 
    BE742723 BI824347 AA308859 AL575528 BM747941 AI927926 AW269137 AI088125 
    BF195721 CF455910 BM835972 AW771628 AA349301 AW050954 CB140181 AW303466 
    T29275 AL576213 BI519573 AL577383 CA488560 AI184869 BE899614 BV198161 
    AA999885 AI149407 BF594699 BI908851 BG338844 AI890522 BF796068 CA441599 
    BM509423 N73889 BM150276 BF947731 AW243253 BE674446 BG927863 BI910748 
    AW589225 BI092233 BM906463 AI935569 AA594457 AU076795 AI635763 CD608013 
    AU141439 BX404119 AW007820 AW264151 AW418749 BM046125 AI219531 BV198559 
    AI985372 AA632749 CD675216 AI767124 BF001232 BF128859 AA993213 BQ073100 
    BM821812 AW028406 AA923708 BI596983 BM990002 AA722605 BF115206 AW044238 
    T93736 AA968732 BM706895 BF591389 T15666 AA678384 BG433189 H51150 
    AW368957 AI274166 AW300047 AA368360 AI539734 BM737721 AI871271 BP377838 
    T96243 CD608015 AU100450 AW614144 AI565438 AU159845 AL575048 R98789 
    AW236451 BE879205 AI347232 BX351694 AL572926 AU159595 AI569148 R52141 
    BE260593 BE904708 BP365540 AL566028 BG432638 AU155778 CD608008 BF002134 
    BI759829 AA318150 CD608010 AL520619 N38843 AA295464 BQ372768 BP347680 
    BG314676 BG705421 BM042588 N39906 AA857825 BE892712 AA459105 AI918565 
    AA155717 AA883949 BQ677538 BF196722 AI261451 AI887091 BI909372 AI862526 
    R39141 AI985817 BM887670 AA459325 BX331774 H14822 BQ316077 BF737643 
    R42220 BG286740 BF061674 BG680398 AU159733 AI094074 CD608003 BI824879 
    AI811857 AI268068 AW242936 AI245535 BM149780 AI198290 R50988 AA155718 
    R54933 BF873381 R98788 AA600969 BQ640703 AU123356 W29072 AI702012 
    AA135558 N44991 AA011097 R54744 R15321 W03950 AI349556 N44650 
    AL570896 R14018 H51114 BG762396 BI771565 AI214367 AW662890 R14806 
    AI361219 AL520620 BI862585 AA135654 AW516488 AW615176 AA626134 BI909102 
    BX372580 R61669 AA883615 AW772139 AA496567 BE392295 H22871 R61002 
    AL573695 BM768987 CK904526 AI249362 R20394 H14865 BE149428 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for PEPD (see all 6)    About this scheme

    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:                                                                                                                        


    ECgene alternative splicing isoforms for PEPD

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    PEPD expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCAGGCTGTG
    PEPD Expression
    About this image


    PEPD expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 9) fully expand
     
     Eye (Sensory Organs)
             Mature Horizontal Cells Inner Nuclear Layer
     
     Neurons
             Mature Horizontal Cells Inner Nuclear Layer
     
     Kidney (Urinary System)
     
     Thyroid (Endocrine System)
     
     Adipose (Muscoskeletal System)
    PEPD Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PEPD Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.36473
        Custom PCR Arrays for PEPD
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PEPD

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for PEPD gene from Selected species (see all 23)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pepd1 , 5 peptidase D1, 5 84.18(n)1
    89.05(a)1
      7 (20.70 cM)5
    186241  NM_008820.21  NP_032846.21 
     349123795 
    chicken
    (Gallus gallus)
    Aves PEPD1 peptidase D 74.78(n)
    79.11(a)
      415776  NM_001079717.1  NP_001073185.1 
    lizard
    (Anolis carolinensis)
    Reptilia PEPD6
    peptidase D
    69(a)
    1 ↔ 1
    GL343508.1(517939-630186)
    African clawed frog
    (Xenopus laevis)
    Amphibia BC054994.12   -- 74.32(n)    BC054994.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BC055252.12   -- 75.46(n)   337498  BC055252.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Dip-C1 , 3 dipeptidyl-peptidase3
    Dipeptidase C1
    50(a)3
    59.83(n)1
    53.35(a)1
      87B93
    477691  NM_141935.31  NP_650192.11 
    worm
    (Caenorhabditis elegans)
    Secernentea K12C11.11 , 3 K12C11.11 52(a)3
    56.62(n)1
    54.78(a)1
      I(1341234-1342265)3
    1717041  NM_058442.31  NP_490843.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes (YFR006W)4 Putative X-Pro aminopeptidase; green fluorescent protein more   --   6(156145-157752) 850556  NP_116661.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT4G294901 AT4G29490 56.88(n)
    58.75(a)
      829070  NM_119094.4  NP_194678.2 
    rice
    (Oryza sativa)
    Liliopsida Os.275342 Oryza sativa (japonica cultivar-group) cDNA clone0 more 71.33(n)    AK064268.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PEPD gene

    Find genes that share paralogs with PEPD           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for PEPD
    PGOHUM00000237113


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
    About This Section

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    Selected SNPs for PEPD (see all 3143)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0116154
    Prolidase deficiency (PD)4--see VAR_0116152 G D mis40--------
    VAR_0044044
    Prolidase deficiency (PD)4--see VAR_0044042 D N mis40--------
    VAR_0116144
    Prolidase deficiency (PD)4--see VAR_0116142 R Q mis40--------
    VAR_0044054
    Prolidase deficiency (PD)4--see VAR_0044052 G R mis40--------
    rs1219177251,2
    Cpathogenic134060009(-) ACGACC/TGAACG 6 R * stg10--------
    rs1408421,2
    C--33877912(+) GACAG-/AAAGT 
            
    AAAGT
    3 -- ut310--------
    rs106596041,2
    C--33877913(+) AAGTA-/AAAG  
     T
    /AAGTA
    TCAGA
    6 -- ut310--------
    rs794865191,2
    C--33878074(+) ATTAA-/TTAA  
            
    AAAAG
    3 -- ut310--------
    rs1113760441,2
    C--33880403(+) GGGCTC/-TCCCC 3 -- int11Minor allele frequency- -:0.50CSA 2
    rs785214731,2
    C,F--33881647(+) GCCAAC/GGGGCC 3 -- int17Minor allele frequency- G:0.22WA NA CSA EA 365

    HapMap Linkage Disequilibrium report for PEPD (33877855 - 34012799 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for PEPD (see all 17):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2718472CNV Deletion23290073
    esv2677046CNV Deletion23128226
    nsv819550CNV Insertion19587683
    esv2469451CNV Insertion19546169
    nsv513524CNV Insertion21212237
    nsv522571CNV Loss19592680
    nsv911597CNV Loss21882294
    nsv911608CNV Loss21882294
    dgv3846n71CNV Loss21882294
    dgv3847n71CNV Loss21882294

    Human Gene Mutation Database (HGMD): PEPD
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PEPD
    DNA2.0 Custom Variant and Variant Library Synthesis for PEPD

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 613230   
    OMIM disorders: 170100  
    UniProtKB/Swiss-Prot: PEPD_HUMAN, P12955
  • 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. Note=The disease is
    caused by mutations affecting the gene represented in this entry

  • 3 diseases for PEPD:    
    About MalaCards
    prolidase deficiency    bacterial vaginosis    legg-calve-perthes disease

    2 diseases from the University of Copenhagen DISEASES database for PEPD:
    Intellectual disability     Bacterial vaginosis

    Find genes that share disorders with PEPD           About GenesLikeMe

    Selected Novoseek inferred disease relationships for PEPD gene (see all 26)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    skin ulcer 73.2 11 1437403 (1), 18806117 (1), 8408817 (1), 12452876 (1) (see all 10)
    mental retardation 61 22 1437403 (1), 12000488 (1), 12646727 (1), 15309682 (1) (see all 18)
    bacterial vaginosis 53.8 5 12388968 (2), 17714681 (1), 12517887 (1), 12023767 (1)
    leg ulcer 53.2 10 11116849 (2), 18855790 (2), 1301685 (1), 9411652 (1) (see all 8)
    skin lesion 52.1 18 12384772 (2), 2010534 (2), 15309682 (1), 19415262 (1) (see all 13)
    splenomegaly 49 5 8408817 (1), 9587929 (1), 17459310 (1), 19937054 (1) (see all 5)
    osteogenesis imperfecta 47.8 3 15802041 (2), 11277941 (1)
    respiratory tract infections 30.4 4 12000488 (1), 15309682 (1), 19415262 (1)
    connective tissue diseases 28 3 19415262 (1), 17142620 (1)
    enzyme deficiency 27 1 8919529 (1)

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

    Genetic Association Database (GAD): PEPD
    Human Genome Epidemiology (HuGE) Navigator: PEPD (2 documents)

    Export disorders for PEPD gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PEPD gene, integrated from 10 sources (see all 224):
    (articles sorted by number of sources associating them with PEPD)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Primary structure and gene localization of human prolidase. (PubMed id 2925654)1, 2, 3 Endo F.... Matsuda I. (J. Biol. Chem. 1989)
    2. Structural organization of the gene for human prolidase (peptidase D) and demonstration of a partial gene deletion in a patient with prolidase deficiency. (PubMed id 1972707)1, 3, 9 Tanoue A....Matsuda I. (J. Biol. Chem. 1990)
    3. Four novel PEPD alleles causing prolidase deficiency. (PubMed id 8198124)1, 2, 9 Ledoux P.... Hechtman P. (Am. J. Hum. Genet. 1994)
    4. Mutation analysis of five new patients affected by prolidase deficiency: the lack of enzyme activity causes necrosis-like cell death in cultured fibroblasts. (PubMed id 12384772)1, 2, 9 Forlino A.... Cetta G. (Hum. Genet. 2002)
    5. Expression and molecular analysis of mutations in prolidase deficiency. (PubMed id 8900231)1, 2, 9 Ledoux P.... Hechtman P. (Am. J. Hum. Genet. 1996)
    6. 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. (PubMed id 2365824)1, 2, 9 Tanoue A.... Matsuda I. (J. Clin. Invest. 1990)
    7. Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals. (PubMed id 22479202)1, 4 Dastani Z....Kathiresan S. (PLoS Genet. 2012)
    8. Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians. (PubMed id 22158537)1, 4 Cho Y.S....Seielstad M. (Nat. Genet. 2012)
    9. Confirmation of multiple risk Loci and genetic impacts by a genome-wide association study of type 2 diabetes in the Japanese population. (PubMed id 19401414)1, 4 Takeuchi F....Kato N. (Diabetes 2009)
    10. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 5184 HGNC: 8840 AceView: PEPD Ensembl:ENSG00000124299 euGenes: HUgn5184
    ECgene: PEPD H-InvDB: PEPD

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PEPD Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PEPD gene:
    Search GeneIP for patents involving PEPD

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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