Human Gene PEPD (uc010xrs.2)
  Description: Homo sapiens peptidase D (PEPD), transcript variant 3, mRNA.
RefSeq Summary (NM_001166057): 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].
Transcript (Including UTRs)
   Position: hg19 chr19:33,877,855-34,012,799 Size: 134,945 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr19:33,878,250-34,012,666 Size: 134,417 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:33,877,855-34,012,799)mRNA (may differ from genome)Protein (429 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: E9PCE8_HUMAN
DESCRIPTION: SubName: Full=Xaa-Pro dipeptidase;
COFACTOR: Binds 2 manganese ions per subunit (By similarity).
SIMILARITY: Belongs to the peptidase M24B family.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PEPD
CDC HuGE Published Literature: PEPD
Positive Disease Associations: Adiponectin , Diabetes Mellitus, Type 2 , Stroke , Triglycerides
Related Studies:
  1. Adiponectin
    Zari Dastani et al. PLoS genetics 2012, Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals., PLoS genetics. [PubMed 22479202]
  2. Adiponectin
    Zari Dastani et al. PLoS genetics 2012, Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals., PLoS genetics. [PubMed 22479202]
  3. Diabetes Mellitus, Type 2
    Yoon Shin Cho et al. Nature genetics 2012, Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians., Nature genetics. [PubMed 22158537]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PEPD
Diseases sorted by gene-association score: prolidase deficiency* (1702), bacterial vaginosis (31), hypermobility syndrome (16), legg-calve-perthes disease (13), sexual sadism (11), osteogenesis imperfecta, type i (8), cutaneous solitary mastocytoma (7), griscelli syndrome, type 1 (7), osteogenesis imperfecta, type iii (3)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 87.64 RPKM in Small Intestine - Terminal Ileum
Total median expression: 1173.61 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -56.60133-0.426 Picture PostScript Text
3' UTR -110.86395-0.281 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007865 - Aminopep_P_N
IPR000994 - Pept_M24_structural-domain
IPR001131 - Peptidase_M24B_aminopep-P_CS

Pfam Domains:
PF00557 - Metallopeptidase family M24

SCOP Domains:
53092 - Creatinase/prolidase N-terminal domain
55920 - Creatinase/aminopeptidase

ModBase Predicted Comparative 3D Structure on E9PCE8
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  BC004305 - Homo sapiens peptidase D, mRNA (cDNA clone MGC:10905 IMAGE:3626134), complete cds.
AK225037 - Homo sapiens mRNA for Xaa-Pro dipeptidase variant, clone: adKA01621.
E02334 - cDNA sequence coding for human prolytase.
J04605 - Human prolidase (imidodipeptidase) mRNA, complete cds.
BC028295 - Homo sapiens peptidase D, mRNA (cDNA clone MGC:24893 IMAGE:4470066), complete cds.
BC015027 - Homo sapiens peptidase D, mRNA (cDNA clone MGC:9000 IMAGE:3920275), complete cds.
AK290756 - Homo sapiens cDNA FLJ75447 complete cds, highly similar to Homo sapiens peptidase D, mRNA.
AK294619 - Homo sapiens cDNA FLJ58179 complete cds, highly similar to Xaa-Pro dipeptidase (EC 3.4.13.9).
AK293126 - Homo sapiens cDNA FLJ57945 complete cds, highly similar to Xaa-Pro dipeptidase (EC 3.4.13.9).
AK291561 - Homo sapiens cDNA FLJ78243 complete cds, highly similar to Homo sapiens peptidase D, mRNA.
AK290781 - Homo sapiens cDNA FLJ78212 complete cds, highly similar to Human prolidase (imidodipeptidase) mRNA.
HM005451 - Homo sapiens clone HTL-T-138 testicular tissue protein Li 138 mRNA, complete cds.
DQ891114 - Synthetic construct clone IMAGE:100003744; FLH169444.01X; RZPDo839C0596D peptidase D (PEPD) gene, encodes complete protein.
BT006692 - Homo sapiens peptidase D mRNA, complete cds.
CR541669 - Homo sapiens full open reading frame cDNA clone RZPDo834G1027D for gene PEPD, peptidase D; complete cds, incl. stopcodon.
KJ891778 - Synthetic construct Homo sapiens clone ccsbBroadEn_01172 PEPD gene, encodes complete protein.
KJ901047 - Synthetic construct Homo sapiens clone ccsbBroadEn_10441 PEPD-like gene, encodes complete protein.
KR709341 - Synthetic construct Homo sapiens clone CCSBHm_00000717 PEPD (PEPD) mRNA, encodes complete protein.
KR709342 - Synthetic construct Homo sapiens clone CCSBHm_00000718 PEPD (PEPD) mRNA, encodes complete protein.
KR709343 - Synthetic construct Homo sapiens clone CCSBHm_00000720 PEPD (PEPD) mRNA, encodes complete protein.
KR709344 - Synthetic construct Homo sapiens clone CCSBHm_00000723 PEPD (PEPD) mRNA, encodes complete protein.
DQ894294 - Synthetic construct Homo sapiens clone IMAGE:100008754; FLH169440.01L; RZPDo839C0595D peptidase D (PEPD) gene, encodes complete protein.
CU677179 - Synthetic construct Homo sapiens gateway clone IMAGE:100020716 5' read PEPD mRNA.
AK057538 - Homo sapiens cDNA FLJ32976 fis, clone TESTI2014036, highly similar to XAA-PRO DIPEPTIDASE (EC 3.4.13.9).
JD208493 - Sequence 189517 from Patent EP1572962.
JD102393 - Sequence 83417 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: E9PCE8, E9PCE8_HUMAN, NM_001166057, NP_001159529
UCSC ID: uc010xrs.2
RefSeq Accession: NM_001166057
Protein: E9PCE8 CCDS: CCDS54244.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PEPD:
prolidase-def (Prolidase Deficiency)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001166057.1
exon count: 13CDS single in 3' UTR: no RNA size: 1827
ORF size: 1290CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2661.00frame shift in genome: no % Coverage: 99.51
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.