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

    Gene ID: 23569, updated on 5-Mar-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
    mouse all
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (17308197..17364004)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (17122255..17177953)
    105.20220307 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
    • 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. Implications of Peptidyl Arginine Deiminase 4 gene transcription and polymorphisms in susceptibility to rheumatoid arthritis in an Iranian population. Bagheri-Hosseinabadi Z, et al. BMC Med Genomics, 2023 May 16. PMID 37193992, Free PMC Article
    2. Neutrophil PAD4: how does it function in cancer beyond promoting NETosis? Garcia-Gerique L, et al. Oncotarget, 2023 Mar 24. PMID 36961884, Free PMC Article
    3. A common missense variant rs874881 of PADI4 gene and rheumatoid arthritis: Genetic association study and in-silico analysis. Bashir M, et al. Gene, 2023 Feb 20. PMID 36535460
    4. The Role of Peptidyl Arginine Deiminase IV(PADI4) in Cancers. Wu X, et al. Anticancer Agents Med Chem, 2023. PMID 35702765
    5. PADI4 Polymorphisms Confer Risk of Anti-CCP-Positive Rheumatoid Arthritis in Synergy With HLA-DRB1*04 and Smoking. Massarenti L, et al. Front Immunol, 2021. PMID 34733271, Free PMC Article

    See all (204) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. New insights into cancer: MDM2 binds to the citrullinating enzyme PADI4.
      Title: New insights into cancer: MDM2 binds to the citrullinating enzyme PADI4.
    4. 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.
    5. 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.
    6. 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.
    7. Neutrophil PAD4: how does it function in cancer beyond promoting NETosis?
      Title: Neutrophil PAD4: how does it function in cancer beyond promoting NETosis?
    8. The Role of Peptidyl Arginine Deiminase IV(PADI4) in Cancers.
      Title: The Role of Peptidyl Arginine Deiminase IV(PADI4) in Cancers.
    9. The armadillo-repeat domain of Plakophilin 1 binds to human enzyme PADI4.
      Title: The armadillo-repeat domain of Plakophilin 1 binds to human enzyme PADI4.
    10. A common missense variant rs874881 of PADI4 gene and rheumatoid arthritis: Genetic association study and in-silico analysis.
      Title: A common missense variant rs874881 of PADI4 gene and rheumatoid arthritis: Genetic association study and in-silico analysis.
    Submit: New GeneRIF Correction See all GeneRIFs (175)

    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

    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)

    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
    enables calcium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 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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    NEW Try the new Transcript table

    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_2023_10

    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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