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PADI4 peptidyl arginine deiminase 4 [ Homo sapiens (human) ]

Gene ID: 23569, updated on 3-Feb-2021

Summary

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Official Symbol
PADI4provided by HGNC
Official Full Name
peptidyl arginine deiminase 4provided by HGNC
Primary source
HGNC:HGNC:18368
See related
Ensembl:ENSG00000159339 MIM:605347
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
PAD; PAD4; PDI4; PDI5; PADI5
Summary
This gene is a member of a gene family which encodes enzymes responsible for the conversion of arginine residues to citrulline residues. This gene may play a role in granulocyte and macrophage development leading to inflammation and immune response. [provided by RefSeq, Jul 2008]
Expression
Restricted expression toward bone marrow (RPKM 64.4) See more
Orthologs
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Genomic context

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See PADI4 in Genome Data Viewer
Location:
1p36.13
Exon count:
18
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (17308195..17364004)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (17634692..17690499)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene peptidyl arginine deiminase 1 Neighboring gene peptidyl arginine deiminase 3 Neighboring gene microRNA 3972 Neighboring gene peptidyl arginine deiminase 6 Neighboring gene RCC2 antisense RNA 1 Neighboring gene regulator of chromosome condensation 2

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
  • 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. Protein arginine deiminase 4 antagonizes methylglyoxal-induced histone glycation. Zheng Q, et al. Nat Commun, 2020 Jun 26. PMID 32591537, Free PMC Article
  2. PADI4 modulates the invasion and migration of osteosarcoma cells by down-regulation of epithelial-mesenchymal transition. Zhai Q, et al. Life Sci, 2020 Sep 1. PMID 32544462
  3. Peptidylarginine Deiminase IV Regulates Breast Cancer Stem Cells via a Novel Tumor Cell-Autonomous Suppressor Role. Moshkovich N, et al. Cancer Res, 2020 Jun 1. PMID 32265227
  4. NETosis proceeds by cytoskeleton and endomembrane disassembly and PAD4-mediated chromatin decondensation and nuclear envelope rupture. Thiam HR, et al. Proc Natl Acad Sci U S A, 2020 Mar 31. PMID 32170015, Free PMC Article
  5. PADI4‑mediated epithelial‑mesenchymal transition in lung cancer cells. Liu M, et al. Mol Med Rep, 2019 Apr. PMID 30816464, Free PMC Article

See all (171) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Peptidylarginine Deiminase Isozyme-Specific PAD2, PAD3 and PAD4 Inhibitors Differentially Modulate Extracellular Vesicle Signatures and Cell Invasion in Two Glioblastoma Multiforme Cell Lines.
    Title: Peptidylarginine Deiminase Isozyme-Specific PAD2, PAD3 and PAD4 Inhibitors Differentially Modulate Extracellular Vesicle Signatures and Cell Invasion in Two Glioblastoma Multiforme Cell Lines.
  2. Peptidylarginine Deiminase IV Regulates Breast Cancer Stem Cells via a Novel Tumor Cell-Autonomous Suppressor Role.
    Title: Peptidylarginine Deiminase IV Regulates Breast Cancer Stem Cells via a Novel Tumor Cell-Autonomous Suppressor Role.
  3. PAD enzymes in rheumatoid arthritis: pathogenic effectors and autoimmune targets.
    Title: PAD enzymes in rheumatoid arthritis: pathogenic effectors and autoimmune targets.
  4. Protein arginine deiminase 4 antagonizes methylglyoxal-induced histone glycation.
    Title: Protein arginine deiminase 4 antagonizes methylglyoxal-induced histone glycation.
  5. PADI4 modulates the invasion and migration of osteosarcoma cells by down-regulation of epithelial-mesenchymal transition.
    Title: PADI4 modulates the invasion and migration of osteosarcoma cells by down-regulation of epithelial-mesenchymal transition.
  6. NETosis proceeds by cytoskeleton and endomembrane disassembly and PAD4-mediated chromatin decondensation and nuclear envelope rupture.
    Title: NETosis proceeds by cytoskeleton and endomembrane disassembly and PAD4-mediated chromatin decondensation and nuclear envelope rupture.
  7. This study shows that ubiquitous or nervous system expression of human PAD2 or PAD4 in Drosophila melanogaster have minimal impact on Drosophila melanogaster lifespan, fecundity, and the response to acute heat stress.
    Title: In vivo expression of peptidylarginine deiminase in Drosophila melanogaster.
  8. PAD4 exacerbates ischemic acute kidney injury and inflammation by promoting renal tubular NF-kappaB activity and inflammation via NEMO citrullination.
    Title: Peptidyl arginine deiminase-4 exacerbates ischemic AKI by finding NEMO.
  9. This study identifies for the first time an immunomodulatory protein, Gal-9, that triggers activation of granulocytes leading to increased PAD-4 expression and generation of citrullinated autoantigens. This pathway may represent a potentially important mechanism for development of Rheumatoid Arthritis.
    Title: Galectin-9 Is a Possible Promoter of Immunopathology in Rheumatoid Arthritis by Activation of Peptidyl Arginine Deiminase 4 (PAD-4) in Granulocytes.
  10. PADI4 expression levels, but not PADI4 polymorphisms, are associated with ICU mortality in septic shock patients.
    Title: Peptidylarginine deiminase 4 concentration, but not PADI4 polymorphisms, is associated with ICU mortality in septic shock patients.
Submit: New GeneRIF Correction See all GeneRIFs (141)

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

Associated conditions

Description Tests
Common variants on 1p36 and 1q42 are associated with cutaneous basal cell carcinoma but not with melanoma or pigmentation traits.
GeneReviews: Not available
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
GeneReviews: Not available
Genome-wide association study of rheumatoid arthritis in Koreans: population-specific loci as well as overlap with European susceptibility loci.
GeneReviews: Not available
Rheumatoid arthritis
MedGen: C0003873 OMIM: 180300 GeneReviews: Not available
Compare labs
The human AIRE gene at chromosome 21q22 is a genetic determinant for the predisposition to rheumatoid arthritis in Japanese population.
GeneReviews: Not available

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

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
arginine binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
calcium ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
calcium ion binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
protein-arginine deiminase activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
protein-arginine deiminase activity IDA
Inferred from Direct Assay
more info
 PubMed 
protein-arginine deiminase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
cellular protein modification process TAS
Traceable Author Statement
more info
 PubMed 
chromatin organization ISS
Inferred from Sequence or Structural Similarity
more info
  
chromatin organization TAS
Traceable Author Statement
more info
  
chromatin remodeling ISS
Inferred from Sequence or Structural Similarity
more info
  
histone H3-R26 citrullination IDA
Inferred from Direct Assay
more info
 PubMed 
histone citrullination IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
histone citrullination IDA
Inferred from Direct Assay
more info
 PubMed 
innate immune response IEA
Inferred from Electronic Annotation
more info
  
nucleosome assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
protein citrullination IDA
Inferred from Direct Assay
more info
 PubMed 
protein citrullination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
stem cell population maintenance ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
cytosol TAS
Traceable Author Statement
more info
  
nucleoplasm TAS
Traceable Author Statement
more info
  
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
protein-containing complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
protein-arginine deiminase type-4
Names
HL-60 PAD
PADI-H protein
peptidyl arginine deiminase, type IV
peptidyl arginine deiminase, type V
protein-arginine deiminase type IV
NP_036519.2
XP_011539452.1
XP_011539453.1
XP_011539454.1
XP_011539455.1
XP_011539456.1
XP_011539457.1
XP_011539458.1
XP_011539459.1

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.

Genomic

  1. NG_023261.2 RefSeqGene

    Range
    5009..60815
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_012387.3 → NP_036519.2  protein-arginine deiminase type-4

    See identical proteins and their annotated locations for NP_036519.2

    Status: REVIEWED

    Source sequence(s)
    AB017919, AC004824, AK314839
    Consensus CDS
    CCDS180.1
    UniProtKB/Swiss-Prot
    Q9UM07
    Related
    ENSP00000364597.4, ENST00000375448.4
    Conserved Domains (3) summary
    pfam03068
    Location:286 → 660
    PAD; Protein-arginine deiminase (PAD)
    pfam08526
    Location:1 → 111
    PAD_N; Protein-arginine deiminase (PAD) N-terminal domain
    pfam08527
    Location:113 → 272
    PAD_M; Protein-arginine deiminase (PAD) middle domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    17308195..17364004
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541151.1 → XP_011539453.1  protein-arginine deiminase type-4 isoform X2

    See identical proteins and their annotated locations for XP_011539453.1

    Conserved Domains (3) summary
    pfam03068
    Location:286 → 560
    PAD; Protein-arginine deiminase (PAD)
    pfam08526
    Location:1 → 111
    PAD_N; Protein-arginine deiminase (PAD) N-terminal domain
    pfam08527
    Location:113 → 272
    PAD_M; Protein-arginine deiminase (PAD) middle domain

  2. XM_011541156.1 → XP_011539458.1  protein-arginine deiminase type-4 isoform X6

    See identical proteins and their annotated locations for XP_011539458.1

    Conserved Domains (3) summary
    pfam03068
    Location:286 → 383
    PAD; Protein-arginine deiminase (PAD)
    pfam08526
    Location:1 → 111
    PAD_N; Protein-arginine deiminase (PAD) N-terminal domain
    pfam08527
    Location:113 → 272
    PAD_M; Protein-arginine deiminase (PAD) middle domain

  3. XM_011541154.2 → XP_011539456.1  protein-arginine deiminase type-4 isoform X4

    See identical proteins and their annotated locations for XP_011539456.1

    Conserved Domains (3) summary
    pfam03068
    Location:286 → 395
    PAD; Protein-arginine deiminase (PAD)
    pfam08526
    Location:1 → 111
    PAD_N; Protein-arginine deiminase (PAD) N-terminal domain
    pfam08527
    Location:113 → 272
    PAD_M; Protein-arginine deiminase (PAD) middle domain

  4. XM_011541153.1 → XP_011539455.1  protein-arginine deiminase type-4 isoform X4

    See identical proteins and their annotated locations for XP_011539455.1

    Conserved Domains (3) summary
    pfam03068
    Location:286 → 395
    PAD; Protein-arginine deiminase (PAD)
    pfam08526
    Location:1 → 111
    PAD_N; Protein-arginine deiminase (PAD) N-terminal domain
    pfam08527
    Location:113 → 272
    PAD_M; Protein-arginine deiminase (PAD) middle domain

  5. XM_011541155.1 → XP_011539457.1  protein-arginine deiminase type-4 isoform X5

    See identical proteins and their annotated locations for XP_011539457.1

    Conserved Domains (3) summary
    pfam03068
    Location:286 → 383
    PAD; Protein-arginine deiminase (PAD)
    pfam08526
    Location:1 → 111
    PAD_N; Protein-arginine deiminase (PAD) N-terminal domain
    pfam08527
    Location:113 → 272
    PAD_M; Protein-arginine deiminase (PAD) middle domain

  6. XM_011541150.1 → XP_011539452.1  protein-arginine deiminase type-4 isoform X1

    See identical proteins and their annotated locations for XP_011539452.1

    Conserved Domains (3) summary
    pfam03068
    Location:224 → 598
    PAD; Protein-arginine deiminase (PAD)
    pfam08526
    Location:1 → 111
    PAD_N; Protein-arginine deiminase (PAD) N-terminal domain
    pfam08527
    Location:114 → 210
    PAD_M; Protein-arginine deiminase (PAD) middle domain

  7. XM_011541157.1 → XP_011539459.1  protein-arginine deiminase type-4 isoform X7

    See identical proteins and their annotated locations for XP_011539459.1

    Conserved Domains (1) summary
    pfam03068
    Location:1 → 363
    PAD; Protein-arginine deiminase (PAD)

  8. XM_011541152.1 → XP_011539454.1  protein-arginine deiminase type-4 isoform X3

    See identical proteins and their annotated locations for XP_011539454.1

    Conserved Domains (2) summary
    pfam03068
    Location:107 → 481
    PAD; Protein-arginine deiminase (PAD)
    pfam08527
    Location:1 → 93
    PAD_M; Protein-arginine deiminase (PAD) middle domain

Reference GRCh38.p13 PATCHES

Genomic

  1. NW_011332688.1 Reference GRCh38.p13 PATCHES

    Range
    153421..209227
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UM07.2 GenPept UniProtKB/Swiss-Prot:Q9UM07

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