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

Gene ID: 23569, updated on 14-Nov-2024

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; AllianceGenome:HGNC:18368
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
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (17308197..17364004)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (17122255..17177953)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (17634692..17690499)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17536705-17537206 Neighboring gene peptidyl arginine deiminase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17585529-17586030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17586031-17586530 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:17597192-17597435 Neighboring gene peptidyl arginine deiminase 3 Neighboring gene NANOG hESC enhancer GRCh37_chr1:17600492-17600993 Neighboring gene microRNA 3972 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:17621951-17622120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17631014-17631874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17642404-17642961 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17685053-17685772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17703685-17704186 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:17707761-17708960 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:17720217-17721416 Neighboring gene peptidyl arginine deiminase 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17727331-17728267 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 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. PADI4 polymorphisms and the functional haplotype are associated with increased rheumatoid arthritis susceptibility: A replication study in a Southern Mexican population. Baños-Hernández CJ, et al. Hum Immunol, 2017 Sep. PMID 28551357
  2. The role of peptidylarginine deiminase 4 in ovarian cancer cell tumorigenesis and invasion. Cui YY, et al. Tumour Biol, 2016 Apr. PMID 26563365
  3. A novel PAD4/SOX4/PU.1 signaling pathway is involved in the committed differentiation of acute promyelocytic leukemia cells into granulocytic cells. Song G, et al. Oncotarget, 2016 Jan 19. PMID 26673819, Free PMC Article
  4. Association between the PADI4 -94G/A polymorphism and rheumatoid arthritis: a meta-analysis in the Chinese population. Chang HX. Genet Mol Res, 2016 Mar 31. PMID 27051025
  5. Anti-PAD4 autoantibodies in rheumatoid arthritis: levels in serum over time and impact on PAD4 activity as measured with a small synthetic substrate. Pollmann S, et al. Rheumatol Int, 2012 May. PMID 21267570, Free PMC Article

See all (212) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Involvement of peptidylarginine deiminase 4 in eosinophil extracellular trap formation and contribution to citrullinated histone signal in thrombi.
    Title: Involvement of peptidylarginine deiminase 4 in eosinophil extracellular trap formation and contribution to citrullinated histone signal in thrombi.
  2. Citrullinating enzyme PADI4 and transcriptional repressor RING1B bind in cancer cells.
    Title: Citrullinating enzyme PADI4 and transcriptional repressor RING1B bind in cancer cells.
  3. Polymorphic Analysis of Genes PADI4 (rs2240340, rs1748033) and HLA-DRB1 (rs2395175) in Arthritis Patients in Pakistani Population.
    Title: Polymorphic Analysis of Genes PADI4 (rs2240340, rs1748033) and HLA-DRB1 (rs2395175) in Arthritis Patients in Pakistani Population.
  4. hRpn13 shapes the proteome and transcriptome through epigenetic factors HDAC8, PADI4, and transcription factor NF-kappaB p50.
    Title: hRpn13 shapes the proteome and transcriptome through epigenetic factors HDAC8, PADI4, and transcription factor NF-κB p50.
  5. Molecular Factors in PAD2 (PADI2) and PAD4 (PADI4) Are Associated with Interstitial Lung Disease Susceptibility in Rheumatoid Arthritis Patients.
    Title: Molecular Factors in PAD2 (PADI2) and PAD4 (PADI4) Are Associated with Interstitial Lung Disease Susceptibility in Rheumatoid Arthritis Patients.
  6. New insights into cancer: MDM2 binds to the citrullinating enzyme PADI4.
    Title: New insights into cancer: MDM2 binds to the citrullinating enzyme PADI4.
  7. An African-Specific Variant of TP53 Reveals PADI4 as a Regulator of p53-Mediated Tumor Suppression.
    Title: An African-Specific Variant of TP53 Reveals PADI4 as a Regulator of p53-Mediated Tumor Suppression.
  8. Implications of Peptidyl Arginine Deiminase 4 gene transcription and polymorphisms in susceptibility to rheumatoid arthritis in an Iranian population.
    Title: Implications of Peptidyl Arginine Deiminase 4 gene transcription and polymorphisms in susceptibility to rheumatoid arthritis in an Iranian population.
  9. PADI4 and IL-33 gene polymorphisms with susceptibility to systemic lupus erythematosus and juvenile idiopathic arthritis, a systematic review and meta-analysis.
    Title: PADI4 and IL-33 gene polymorphisms with susceptibility to systemic lupus erythematosus and juvenile idiopathic arthritis, a systematic review and meta-analysis.
  10. Neutrophil PAD4: how does it function in cancer beyond promoting NETosis?
    Title: Neutrophil PAD4: how does it function in cancer beyond promoting NETosis?
Submit: New GeneRIF Correction See all GeneRIFs (178)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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 calcium ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H1R54 arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H2AR3 arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3R17 arginine deiminase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3R2 arginine deiminase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3R26 arginine deiminase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3R8 arginine deiminase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H4R3 arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone arginine deiminase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone arginine deiminase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-arginine deiminase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein-arginine deiminase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein-arginine deiminase activity TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
involved_in chromatin organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in chromatin organization TAS
Traceable Author Statement
more info
  
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chromatin remodeling ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in nucleosome assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in post-translational protein modification IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in post-translational protein modification IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein modification process TAS
Traceable Author Statement
more info
 PubMed 
involved_in stem cell population maintenance ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of 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_047272566.1
XP_054187638.1
XP_054187639.1
XP_054187640.1
XP_054187641.1
XP_054187642.1
XP_054187643.1
XP_054187644.1
XP_054187645.1
XP_054191687.1
XP_054191688.1
XP_054191689.1
XP_054191690.1
XP_054191691.1
XP_054191692.1
XP_054191693.1

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_023261.3 RefSeqGene

    Range
    5002..60809
    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
    A8K392, B2RBW0, Q5VTZ8, Q70SX4, 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: 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
    17308197..17364004
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541151.2 → 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_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

  3. XM_011541156.2 → 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

  4. XM_011541154.3 → 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

  5. XM_011541153.2 → 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

  6. XM_011541155.2 → 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

  7. 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

  8. XM_047416610.1 → XP_047272566.1  protein-arginine deiminase type-4 isoform X7

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332688.1 Reference GRCh38.p14 PATCHES

    Range
    153421..209227
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331664.1 → XP_054187639.1  protein-arginine deiminase type-4 isoform X2

  2. XM_054331663.1 → XP_054187638.1  protein-arginine deiminase type-4 isoform X1

  3. XM_054331669.1 → XP_054187644.1  protein-arginine deiminase type-4 isoform X6

  4. XM_054331667.1 → XP_054187642.1  protein-arginine deiminase type-4 isoform X4

  5. XM_054331666.1 → XP_054187641.1  protein-arginine deiminase type-4 isoform X4

  6. XM_054331668.1 → XP_054187643.1  protein-arginine deiminase type-4 isoform X5

  7. XM_054331665.1 → XP_054187640.1  protein-arginine deiminase type-4 isoform X3

  8. XM_054331670.1 → XP_054187645.1  protein-arginine deiminase type-4 isoform X7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    17122255..17177953
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054335713.1 → XP_054191688.1  protein-arginine deiminase type-4 isoform X2

  2. XM_054335712.1 → XP_054191687.1  protein-arginine deiminase type-4 isoform X1

  3. XM_054335717.1 → XP_054191692.1  protein-arginine deiminase type-4 isoform X6

  4. XM_054335716.1 → XP_054191691.1  protein-arginine deiminase type-4 isoform X4

  5. XM_054335715.1 → XP_054191690.1  protein-arginine deiminase type-4 isoform X4

  6. XM_054335714.1 → XP_054191689.1  protein-arginine deiminase type-4 isoform X3

  7. XM_054335718.1 → XP_054191693.1  protein-arginine deiminase type-4 isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UM07.2 GenPept UniProtKB/Swiss-Prot:Q9UM07

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