Human Gene PGA4 (uc001nqy.3) Description and Page Index
  Description: Homo sapiens pepsinogen 4, group I (pepsinogen A) (PGA4), mRNA.
RefSeq Summary (NM_001079808): This gene encodes a protein precursor of the digestive enzyme pepsin, a member of the peptidase A1 family of endopeptidases. The encoded precursor is secreted by gastric chief cells and undergoes autocatalytic cleavage in acidic conditions to form the active enzyme, which functions in the digestion of dietary proteins. This gene is found in a cluster of related genes on chromosome 11, each of which encodes one of multiple pepsinogens. Pepsinogen levels in serum may serve as a biomarker for atrophic gastritis and gastric cancer. [provided by RefSeq, Jul 2015]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AK291864.1, ERR279867.573.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1966682, SAMEA1968540 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr11:60,989,821-60,999,179 Size: 9,359 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr11:60,989,873-60,999,003 Size: 9,131 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:60,989,821-60,999,179)mRNA (may differ from genome)Protein (388 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCHPRDLynxMGIneXtProtOMIM
PubMedReactomeStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: PEPA4_HUMAN
DESCRIPTION: RecName: Full=Pepsin A-4; EC=3.4.23.1; AltName: Full=Pepsinogen-4; Flags: Precursor;
FUNCTION: Shows particularly broad specificity; although bonds involving phenylalanine and leucine are preferred, many others are also cleaved to some extent.
CATALYTIC ACTIVITY: Preferential cleavage: hydrophobic, preferably aromatic, residues in P1 and P1' positions. Cleaves 1-Phe-|-Val-2, 4-Gln-|-His-5, 13-Glu-|-Ala-14, 14-Ala-|-Leu-15, 15-Leu-|-Tyr-16, 16-Tyr-|-Leu-17, 23-Gly-|-Phe-24, 24-Phe-|-Phe-25 and 25-Phe-|- Tyr-26 bonds in the B chain of insulin.
SUBCELLULAR LOCATION: Secreted.
SIMILARITY: Belongs to the peptidase A1 family.

-  MalaCards Disease Associations
  MalaCards Gene Search: PGA4
Diseases sorted by gene-association score: atrophic gastritis (6), gastritis (5), amyotrophic lateral sclerosis 1 (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 368.71 RPKM in Stomach
Total median expression: 369.52 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 -14.9052-0.287 Picture PostScript Text
3' UTR -45.00176-0.256 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
IPR001461 - Peptidase_A1
IPR021109 - Peptidase_aspartic
IPR001969 - Peptidase_aspartic_AS
IPR009007 - Peptidase_aspartic_catalytic
IPR012848 - Propep_A1

Pfam Domains:
PF00026 - Eukaryotic aspartyl protease
PF07966 - A1 Propeptide
PF14543 - Xylanase inhibitor N-terminal

SCOP Domains:
50630 - Acid proteases

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1FLH
- X-ray

1PSN
- X-ray MuPIT

1PSO
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
1QRP - X-ray 3UTL - X-ray


ModBase Predicted Comparative 3D Structure on P0DJD7
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004190 aspartic-type endopeptidase activity
GO:0008233 peptidase activity
GO:0016787 hydrolase activity

Biological Process:
GO:0006508 proteolysis
GO:0006914 autophagy
GO:0007586 digestion
GO:0030163 protein catabolic process
GO:0044267 cellular protein metabolic process

Cellular Component:
GO:0005576 extracellular region
GO:0070062 extracellular exosome
GO:0097486 multivesicular body lumen


-  Descriptions from all associated GenBank mRNAs
  AK301286 - Homo sapiens cDNA FLJ60006 complete cds, highly similar to Pepsin A precursor (EC 3.4.23.1).
AK312941 - Homo sapiens cDNA, FLJ93393, highly similar to Homo sapiens pepsinogen 5, group I (pepsinogen A) (PGA5), mRNA.
AK301305 - Homo sapiens cDNA FLJ58952 complete cds, highly similar to Pepsin A precursor (EC 3.4.23.1).
AK291864 - Homo sapiens cDNA FLJ77962 complete cds.
AK225669 - Homo sapiens mRNA for Pepsin A precursor variant, clone: STM08122.
AK125628 - Homo sapiens cDNA FLJ43640 fis, clone STOMA2000168, highly similar to PEPSIN A PRECURSOR (EC 3.4.23.1).
AK225679 - Homo sapiens mRNA for Pepsin A precursor variant, clone: STM08066.
BC150659 - Homo sapiens pepsinogen 4, group I (pepsinogen A), mRNA (cDNA clone MGC:183570 IMAGE:9057030), complete cds.
BC171808 - Homo sapiens pepsinogen 4, group I (pepsinogen A), mRNA (cDNA clone MGC:198523 IMAGE:9054462), complete cds.
BC171814 - Homo sapiens pepsinogen 4, group I (pepsinogen A), mRNA (cDNA clone MGC:198529 IMAGE:9054468), complete cds.
BC171815 - Homo sapiens pepsinogen 3, group I (pepsinogen A), mRNA (cDNA clone MGC:198530 IMAGE:9054469), complete cds.
BC171910 - Homo sapiens pepsinogen 4, group I (pepsinogen A), mRNA (cDNA clone MGC:198625 IMAGE:9054564), complete cds.
BC171920 - Homo sapiens pepsinogen 4, group I (pepsinogen A), mRNA (cDNA clone MGC:198635 IMAGE:9054574), complete cds.
KX856064 - Homo sapiens pregnancy-associated glycoprotein mRNA, complete cds.
BC152844 - Synthetic construct Homo sapiens clone IMAGE:100016085, MGC:184199 pepsinogen 4, group I (pepsinogen A) (PGA4) mRNA, encodes complete protein.
BC160184 - Synthetic construct Homo sapiens clone IMAGE:100064216, MGC:193299 pepsinogen 3, group I (pepsinogen A) (PGA3) mRNA, encodes complete protein.
AB528778 - Synthetic construct DNA, clone: pF1KE0243, Homo sapiens PGA4 gene for pepsinogen 4, group I, without stop codon, in Flexi system.
JD194045 - Sequence 175069 from Patent EP1572962.
JD450690 - Sequence 431714 from Patent EP1572962.
AL832946 - Homo sapiens mRNA; cDNA DKFZp666J2410 (from clone DKFZp666J2410).
JD035985 - Sequence 17009 from Patent EP1572962.
JD020735 - Sequence 1759 from Patent EP1572962.
JD033527 - Sequence 14551 from Patent EP1572962.
JD019271 - Sequence 295 from Patent EP1572962.
JD022843 - Sequence 3867 from Patent EP1572962.
JD308988 - Sequence 290012 from Patent EP1572962.
JD182965 - Sequence 163989 from Patent EP1572962.
JD411014 - Sequence 392038 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P0DJD7 (Reactome details) participates in the following event(s):

R-HSA-5684864 NAPSA, CTSH, PGA3-5 cleave pro-SFTPB
R-HSA-5685902 NAPSA, CTSH, PGA3-5 cleave pro-SFTPC
R-HSA-5683826 Surfactant metabolism
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A8K749, B7ZW75, NM_001079808, NP_001073276, P00790, P0DJD7, PEPA4_HUMAN, Q7M4R0, Q8N1E3
UCSC ID: uc001nqy.3
RefSeq Accession: NM_001079808
Protein: P0DJD7 (aka PEPA4_HUMAN)
CCDS: CCDS31575.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001079808.1
exon count: 9CDS single in 3' UTR: no RNA size: 1395
ORF size: 1167CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2114.00frame shift in genome: no % Coverage: 100.00
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.