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PADI3 Gene

protein-coding   GIFtS: 50
GCID: GC01P017575

Peptidyl Arginine Deiminase, Type III

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Peptidyl Arginine Deiminase, Type III1 2     EC 3.5.3.153 8
Peptidylarginine Deiminase III2 3     PAD32
Protein-Arginine Deiminase Type III2 3     Protein-Arginine Deiminase Type-32
PDI32 3     

External Ids:    HGNC: 183371   Entrez Gene: 517022   Ensembl: ENSG000001426197   OMIM: 6067555   UniProtKB: Q9ULW83   

Export aliases for PADI3 gene to outside databases

Previous GC identifers: GC01P017313 GC01P016616 GC01P016956 GC01P017320 GC01P017448 GC01P015819


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PADI3 Gene:
This gene encodes a member of the peptidyl arginine deiminase family of enzymes, which catalyze the
post-translational deimination of proteins by converting arginine residues into citrullines in the presence of
calcium ions. The family members have distinct substrate specificities and tissue-specific expression patterns.
The type III enzyme modulates hair structural proteins, such as filaggrin in the hair follicle and trichohyalin
in the inner root sheath, during hair follicle formation. Together with the type I enzyme, this enzyme may also
play a role in terminal differentiation of the epidermis. This gene exists in a cluster with four other
paralogous genes. (provided by RefSeq, Jul 2008)

GeneCards Summary for PADI3 Gene:
PADI3 (peptidyl arginine deiminase, type III) is a protein-coding gene. Diseases associated with PADI3 include pulmonary function, and breast and colorectal cancer. GO annotations related to this gene include protein-arginine deiminase activity and calcium ion binding. An important paralog of this gene is PADI2.

UniProtKB/Swiss-Prot: PADI3_HUMAN, Q9ULW8
Function: Catalyzes the deimination of arginine residues of proteins

Gene Wiki entry for PADI3 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000001.11  NT_032977.10  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the PADI3 gene promoter:
         Oct-B1   HOXA3   MyoD   Olf-1   CUTL1   XBP-1   Ik-3   NF-kappaB   AREB6   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPADI3 promoter sequence
   Search Chromatin IP Primers for PADI3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PADI3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p36.13   Ensembl cytogenetic band:  1p36.13   HGNC cytogenetic band: 1p36.13

PADI3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PADI3 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P017575:  view genomic region     (about GC identifiers)

Start:
17,575,593 bp from pter      End:
17,610,728 bp from pter
Size:
35,136 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: PADI3_HUMAN, Q9ULW8 (See protein sequence)
Recommended Name: Protein-arginine deiminase type-3  
Size: 664 amino acids; 74743 Da
Cofactor: Calcium (By similarity)
Secondary accessions: Q58EY7 Q70SX5

Explore the universe of human proteins at neXtProt for PADI3: NX_Q9ULW8

Explore proteomics data for PADI3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for PADI3 (Q9ULW8) (see all 12)
     APWIMTP  VVMNSPSN  VNMLVLGK  FPYKRILG 


    See PADI3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_057317.2  
    ENSEMBL proteins: 
     ENSP00000364609  

    PADI3 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    PADI: Peptidyl arginine deiminases

    Selected InterPro protein domains (see all 6):
     IPR013733 Prot_Arg_deaminase_cen_dom
     IPR013732 PAD_N
     IPR008972 Cupredoxin
     IPR004303 PAD
     IPR016296 Protein-arginine_deiminase_sub

    Graphical View of Domain Structure for InterPro Entry Q9ULW8

    ProtoNet protein and cluster: Q9ULW8

    1 Blocks protein domain: IPB004303 Protein-arginine deiminase

    UniProtKB/Swiss-Prot: PADI3_HUMAN, Q9ULW8
    Similarity: Belongs to the protein arginine deiminase family


    PADI3 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PADI3_HUMAN, Q9ULW8
    Function: Catalyzes the deimination of arginine residues of proteins
    Catalytic activity: Protein L-arginine + H(2)O = protein L-citrulline + NH(3)

         Enzyme Number (IUBMB): EC 3.5.3.151 2

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004668protein-arginine deiminase activity IEA--
    GO:0005509calcium ion binding IEA--
         
    PADI3 for ontologies           About GeneDecksing


    Phenotypes:
         1 MGI phenotypic allele for Padi3 (no phenotypes)

    PADI3 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PADI3
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    SwitchGear 3'UTR luciferase reporter plasmidPADI3 3' UTR sequence
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PADI3_HUMAN, Q9ULW8: Cytoplasm
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus4
    cytosol3
    extracellular2
    mitochondrion2
    peroxisome1
    plasma membrane1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ----
    GO:0005737cytoplasm IEA--

    PADI3 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for PADI3 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1protein citrullination
    protein citrullination


    1 BioSystems Pathway for PADI3
        protein citrullination


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PADI3
    Interactions:

        GeneGlobe Interaction Network for PADI3

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0018101protein citrullination IEA--

    PADI3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PADI3

    5 HMDB Compounds for PADI3    About this table
    CompoundSynonyms CAS #PubMed Ids
    AmmoniaNH3 (see all 31)7664-41-7--
    CalciumCa (see all 2)7440-70-2--
    Citrulline(2S)-2-amino-5-(carbamoylamino)pentanoic acid (see all 55)372-75-8--
    L-Arginine(S)-2-Amino-5-[(aminoiminomethyl)amino]pentanoate (see all 14)74-79-3--
    WaterDihydrogen oxide (see all 2)7732-18-5--

    1 DrugBank Compound for PADI3    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    L-Citrulline2-Amino-5-uredovaleric acid (see all 8)372-75-8target--16671893 11069618 15150696



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for PADI3 gene: 
    NM_016233.2  

    Unigene Cluster for PADI3:

    Peptidyl arginine deiminase, type III
    Hs.149195  [show with all ESTs]
    Unigene Representative Sequence: BC041592
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000375460(uc001bai.3)
    miRNA
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    5 qRT-PCR Assays for microRNAs that regulate PADI3:
    hsa-miR-3678-3p hsa-miR-4251 hsa-miR-589* hsa-miR-330-3p hsa-miR-589
    SwitchGear 3'UTR luciferase reporter plasmidPADI3 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat PADI3
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      QuantiTect SYBR Green Assays in human, mouse, rat PADI3
      QuantiFast Probe-based Assays in human, mouse, rat PADI3

    Additional mRNA sequence: 

    AB026831.1 BC041592.1 BC109091.1 BC109092.1 

    1 DOTS entry:

    DT.75150995 

    20 AceView cDNA sequences:

    BM908529 BM549909 BM018564 BC041592 BE182919 BI085442 AI246243 BE735575 
    BM016595 NM_016233 BI085444 BM020359 AL710699 BM019318 BM908844 BE563328 
    AB026831 BX283443 BM016592 BM017129 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PADI3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTTGACTATG
    PADI3 Expression
    About this image

    PADI3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PADI3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.149195

    UniProtKB/Swiss-Prot: PADI3_HUMAN, Q9ULW8
    Tissue specificity: Hair follicles, and epidermis at very low levels

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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for PADI3 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Padi31 , 5 peptidyl arginine deiminase, type III1, 5 84.69(n)1
    87.2(a)1
      4 (72.50 cM)5
    186011  NM_011060.41  NP_035190.31 
     1407853655 
    chicken
    (Gallus gallus)
    Aves PADI31 peptidyl arginine deiminase, type III 64.54(n)
    58.12(a)
      395910  NM_205043.1  NP_990374.1 
    lizard
    (Anolis carolinensis)
    Reptilia PADI36
    peptidyl arginine deiminase, type III
    47(a)
    1 ↔ 1
    GL344803.1(6947-18633)
    zebrafish
    (Danio rerio)
    Actinopterygii padi26
    peptidyl arginine deiminase, type II
    46(a)
    1 → many
    6(47784349-47806450) ENSDARG00000044167


    ENSEMBL Gene Tree for PADI3 (if available)
    TreeFam Gene Tree for PADI3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PADI3 gene
    PADI22  PADI42  PADI12  
    4 SIMAP similar genes for PADI3 using alignment to 1 protein entry:     PADI3_HUMAN:
    PADI1    PADI2    PADI4    PADI6

    PADI3 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PADI3 (see all 909)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0355024
    A breast cancer sample4--see VAR_0355022 G R mis40--------
    rs37635871,2
    C,F,H--17573614(+) TCTGTG/CCTCAC 1 -- us2k17Minor allele frequency- C:0.02EA NS NA 2146
    rs1148278091,2
    C,F--17573626(+) AGAAGG/CCTAGG 1 -- us2k11Minor allele frequency- C:0.03WA 118
    rs586209511,2
    C,F--17573965(+) GGTGCG/ATCTTC 1 -- us2k13Minor allele frequency- A:0.09NA WA 240
    rs1471177181,2
    --17573982(+) ATCTCC/TGCCAG 1 -- us2k10--------
    rs30034191,2
    C,F,O,H--17573988(+) GCCAGA/GGCCAG 1 -- us2k130Minor allele frequency- N:0.00NS EA NA WA 3392
    rs1385216361,2
    --17574055(+) GACACC/TCAAGG 1 -- us2k10--------
    rs121278981,2
    C,F--17574153(+) ATGCCC/TCTCTG 1 -- us2k14Minor allele frequency- T:0.07WA NA 242
    rs1406907051,2
    C--17574347(+) AGGCC-/TCACAG 1 -- us2k10--------
    rs30034201,2
    C,H--17574369(+) cagacG/Aagaaa 1 -- us2k16Minor allele frequency- A:0.00NS EA NA 422

    HapMap Linkage Disequilibrium report for PADI3 (17575593 - 17610728 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for PADI3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv508958CNV Insertion20534489
    nsv4076CNV Insertion18451855
    nsv521814CNV Loss19592680
    nsv470700CNV Loss18288195
    nsv516116CNV Gain19592680
    nsv834291CNV Gain17160897

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 606755    OMIM disorders: --

    3 diseases for PADI3:    About MalaCards
    pulmonary function    breast and colorectal cancer    colorectal cancer


    PADI3 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PADI3

    Export disorders for PADI3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PADI3 gene, integrated from 10 sources (see all 22):
    (articles sorted by number of sources associating them with PADI3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Human peptidylarginine deiminase type III: molecular cloning and nucleotide sequence of the cDNA, properties of the recombinant enzyme, and immunohistochemical localization in human skin. (PubMed id 11069618)1, 2, 3, 7, 9 Kanno T.... Takahara H. (J. Invest. Dermatol. 2000)
    2. NF-Y and Sp1/Sp3 are involved in the transcriptional regulation of the peptidylarginine deiminase type III gene (PADI3) in human keratinocytes. (PubMed id 16671893)1, 7, 9 Dong S....Takahara H. (Biochem. J. 2006)
    3. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
    4. Comparative analysis of the mouse and human peptidylarginine deiminase gene clusters reveals highly conserved non-coding segments and a new human gene, PADI6. (PubMed id 15087120)1, 2 Chavanas S.... Simon M. (Gene 2004)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    6. Identification of 45 novel SNPs in the 83-kb region containing peptidylarginine deiminase types 1 and 3 loci on chromosomal band 1p36.13. (PubMed id 15150696)1, 7 Iida A. and Nakamura Y. (J. Hum. Genet. 2004)
    7. Long-range enhancer associated with chromatin looping allows AP-1 regulation of the peptidylarginine deiminase 3 gene in differentiated keratinocyte. (PubMed id 18923650)1, 9 Chavanas S....Simon M. (PLoS ONE 2008)
    8. Autophagy negatively regulates cancer cell proliferation via selectively targeting VPRBP. (PubMed id 22963397)1 Wang B.S....Wang M.R. (Clin. Sci. 2013)
    9. Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. (PubMed id 23284291)1 Hancock D.B....London S.J. (PLoS Genet. 2012)
    10. Crystallization and preliminary X-ray crystallographic analysis of human peptidylarginine deiminase type III. (PubMed id 22684066)1 Unno M....Takahara H. (Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 51702 HGNC: 18337 AceView: PADI3 Ensembl:ENSG00000142619 euGenes: HUgn51702
    ECgene: PADI3 H-InvDB: PADI3

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PADI3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for PADI3 gene:
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