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    PGLYRP4 peptidoglycan recognition protein 4 [ Homo sapiens (human) ]

    Gene ID: 57115, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PGLYRP4provided by HGNC
    Official Full Name
    peptidoglycan recognition protein 4provided by HGNC
    Primary source
    HGNC:HGNC:30015
    See related
    Ensembl:ENSG00000163218 MIM:608198; AllianceGenome:HGNC:30015
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PGRPIB; SBBI67; PGRP-Ibeta; PGLYRPIbeta
    Summary
    Summary: This gene encodes a peptidoglycan recognition protein, which belongs to the N-acetylmuramoyl-L-alanine amidase 2 family. These proteins are part of the innate immune system and recognize peptidoglycan, a ubiquitous component of bacterial cell walls. This antimicrobial protein binds to murein peptidoglycans of Gram-positive bacteria. [provided by RefSeq, Oct 2014]
    Expression
    Biased expression in skin (RPKM 2.9) and esophagus (RPKM 1.0) See more
    Orthologs
    mouse all
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    Genomic context

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    See PGLYRP4 in Genome Data Viewer
    Location:
    1q21.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (153330120..153348841, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (152467338..152486071, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (153302596..153321317, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1338 Neighboring gene loricrin cornified envelope precursor protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1740 Neighboring gene peptidoglycan recognition protein 3 Neighboring gene RNA, U6 small nuclear 160, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1340 Neighboring gene S100 calcium binding protein A9 Neighboring gene S100 calcium binding protein A12

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Peptidoglycan Recognition Protein 4 Limits Bacterial Clearance and Inflammation in Lungs by Control of the Gut Microbiota. Dabrowski AN, et al. Front Immunol, 2019. PMID 31616404, Free PMC Article
    2. Peptidoglycan recognition protein genes and risk of Parkinson's disease. Goldman SM, et al. Mov Disord, 2014 Aug. PMID 24838182, Free PMC Article
    3. Peptidoglycan recognition proteins Pglyrp3 and Pglyrp4 are encoded from the epidermal differentiation complex and are candidate genes for the Psors4 locus on chromosome 1q21. Sun C, et al. Hum Genet, 2006 Mar. PMID 16362825
    4. A Novel Innate Response of Human Corneal Epithelium to Heat-killed Candida albicans by Producing Peptidoglycan Recognition Proteins. Hua X, et al. PLoS One, 2015. PMID 26039076, Free PMC Article
    5. Structural insights into the bactericidal mechanism of human peptidoglycan recognition proteins. Cho S, et al. Proc Natl Acad Sci U S A, 2007 May 22. PMID 17502600, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Peptidoglycan Recognition Protein 4 Limits Bacterial Clearance and Inflammation in Lungs by Control of the Gut Microbiota.
      Title: Peptidoglycan Recognition Protein 4 Limits Bacterial Clearance and Inflammation in Lungs by Control of the Gut Microbiota.
    2. a significant induction of three PGLYRPs 2-4 in primary human corneal epithelial cells (HCECs) exposed to live or heat-killed Candida albicans, is reported.
      Title: A Novel Innate Response of Human Corneal Epithelium to Heat-killed Candida albicans by Producing Peptidoglycan Recognition Proteins.
    3. This study demonistrated that PGLYRP4 single-nucleotide polymorphisms is risk of Parkinson's disease.
      Title: Peptidoglycan recognition protein genes and risk of Parkinson's disease.
    4. Results describe the function of mammalian antimicrobial peptidoglycan recognition proteins 3 and 4, and show that they are a new class of bactericidal and bacteriostatic proteins.
      Title: Peptidoglycan recognition proteins are a new class of human bactericidal proteins.
    5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    7. Data are consistent with previous reports of association of psoriasis with genes on 1q21, and suggest a role for Pglyrp4 in skin biology.
      Title: Peptidoglycan recognition proteins Pglyrp3 and Pglyrp4 are encoded from the epidermal differentiation complex and are candidate genes for the Psors4 locus on chromosome 1q21.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120-treated vaginal epithelial cells show upregulation of peptidoglycan recognition protein 4 (PGLYRP4) expression as compared to untreated control PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables N-acetylmuramoyl-L-alanine amidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptidoglycan binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables peptidoglycan immune receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in antimicrobial humoral immune response mediated by antimicrobial peptide IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in defense response to Gram-positive bacterium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in defense response to bacterium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in detection of bacterium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in innate immune response NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in killing of cells of another organism IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in peptidoglycan catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    peptidoglycan recognition protein 4
    Names
    PGRP-I-beta
    peptidoglycan recognition protein I-beta
    peptidoglycan recognition protein intermediate beta

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_020393.4 → NP_065126.2  peptidoglycan recognition protein 4 precursor

      See identical proteins and their annotated locations for NP_065126.2

      Status: REVIEWED

      Source sequence(s)
      AF242518, AK292203, BC142636
      Consensus CDS
      CCDS30871.1
      UniProtKB/Swiss-Prot
      A8K838, Q3B822, Q3B823, Q5SY63, Q5SY64, Q96LB8, Q9HD75
      Related
      ENSP00000352672.5, ENST00000359650.10
      Conserved Domains (1) summary
      smart00701
      Location:211 → 351
      PGRP; Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      153330120..153348841 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011509791.3 → XP_011508093.1  peptidoglycan recognition protein 4 isoform X2

      UniProtKB/Swiss-Prot
      Q96LB8
      Related
      ENSP00000357728.3, ENST00000368739.3
      Conserved Domains (1) summary
      smart00701
      Location:207 → 347
      PGRP; Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme

    2. XM_011509792.1 → XP_011508094.1  peptidoglycan recognition protein 4 isoform X3

      Conserved Domains (1) summary
      smart00701
      Location:53 → 194
      PGRP; Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme

    3. XM_011509789.3 → XP_011508091.1  peptidoglycan recognition protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011508091.1

      UniProtKB/Swiss-Prot
      A8K838, Q3B822, Q3B823, Q5SY63, Q5SY64, Q96LB8, Q9HD75
      Conserved Domains (1) summary
      smart00701
      Location:211 → 351
      PGRP; Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme

    4. XM_011509793.2 → XP_011508095.1  peptidoglycan recognition protein 4 isoform X4

      Conserved Domains (1) summary
      smart00701
      Location:43 → 183
      PGRP; Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme

    5. XM_011509790.1 → XP_011508092.1  peptidoglycan recognition protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011508092.1

      UniProtKB/Swiss-Prot
      A8K838, Q3B822, Q3B823, Q5SY63, Q5SY64, Q96LB8, Q9HD75
      Conserved Domains (1) summary
      smart00701
      Location:211 → 351
      PGRP; Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme

    RNA

    1. XR_921897.3 RNA Sequence

    2. XR_007062001.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      152467338..152486071 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337789.1 → XP_054193764.1  peptidoglycan recognition protein 4 isoform X2

    2. XM_054337790.1 → XP_054193765.1  peptidoglycan recognition protein 4 isoform X3

    3. XM_054337787.1 → XP_054193762.1  peptidoglycan recognition protein 4 isoform X1

    4. XM_054337791.1 → XP_054193766.1  peptidoglycan recognition protein 4 isoform X4

    5. XM_054337788.1 → XP_054193763.1  peptidoglycan recognition protein 4 isoform X1

    RNA

    1. XR_008486116.1 RNA Sequence

    2. XR_008486115.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96LB8.2 GenPept UniProtKB/Swiss-Prot:Q96LB8

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