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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

PADI6 Gene

protein-coding   GIFtS: 47
GCID: GC01P017698

Peptidyl Arginine Deiminase, Type VI

  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)
About This Section

Aliases
Peptidyl Arginine Deiminase, Type VI1 2     Peptidylarginine Deiminase Type 62
Peptidyl Arginine Deiminase-Like Protein2 3     Protein-Arginine Deiminase Type-62
hPADVI2 3     Peptidylarginine Deiminase VI3
EC 3.5.3.153 8     Protein-Arginine Deiminase Type VI3

External Ids:    HGNC: 204491   Entrez Gene: 3532382   Ensembl: ENSG000002560497   OMIM: 6103635   UniProtKB: Q6TGC43   

Export aliases for PADI6 gene to outside databases

Previous GC identifers: GC00U911624 GC01U901038 GC01P017444 GC01P017571 GC01P015944


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for PADI6 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.
This protein may play a role in cytoskeletal reorganization in the egg and in early embryo development. (provided
by RefSeq, Sep 2012)

GeneCards Summary for PADI6 Gene: 
PADI6 (peptidyl arginine deiminase, type VI) is a protein-coding gene. Diseases associated with PADI6 include basal cell carcinoma, and melanoma. GO annotations related to this gene include protein-arginine deiminase activity and calcium ion binding.

UniProtKB/Swiss-Prot: PADI6_HUMAN, Q6TGC4
Function: Catalyzes the deimination of arginine residues of proteins. May be involved in cytoskeletal
reorganization in the egg and early embryo (By similarity)




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.2  NT_004610.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PADI6 gene promoter:
         CUTL1   HNF-4alpha2   GATA-2   C/EBPalpha   HNF-4alpha1   CHOP-10   CBF-A   POU2F1   POU2F1a   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPADI6 promoter sequence
   Search SABiosciences Chromatin IP Primers for PADI6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PADI6


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

PADI6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PADI6 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P017698:  view genomic region     (about GC identifiers)

Start:
17,698,691 bp from pter      End:
17,728,195 bp from pter
Size:
29,505 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: PADI6_HUMAN, Q6TGC4 (See protein sequence)
Recommended Name: Protein-arginine deiminase type-6  
Size: 694 amino acids; 77727 Da
Cofactor: Calcium (By similarity)
Subcellular location: Cytoplasm (By similarity). Nucleus (By similarity)
2 PDB 3D structures from and Proteopedia for PADI6:
4DAT (3D)        4DAU (3D)    
Secondary accessions: Q330K5 Q70SX3

Explore the universe of human proteins at neXtProt for PADI6: NX_Q6TGC4

Explore proteomics data for PADI6 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q6TGC4

  • 4 DME Specific Peptides for PADI6 (Q6TGC4)
     LASPSAC  AQQVQAPV  GKEYPLGR  LGIPKPFGP 

    PADI6 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PADI6 Protein Expression
    REFSEQ proteins: NP_997304.3  
    Human Recombinant Protein Products for PADI6: 
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    Cloud-Clone Corp. Proteins for PADI6 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

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

    PADI6 for ontologies           About GeneDecksing



    PADI6 Antibody Products: 
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    PADI: Peptidyl arginine deiminases

    5/6 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 Q6TGC4

    ProtoNet protein and cluster: Q6TGC4

    1 Blocks protein domain: IPB004303 Protein-arginine deiminase

    UniProtKB/Swiss-Prot: PADI6_HUMAN, Q6TGC4
    Similarity: Belongs to the protein arginine deiminase family


    PADI6 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PADI6_HUMAN, Q6TGC4
    Function: Catalyzes the deimination of arginine residues of proteins. May be involved in cytoskeletal
    reorganization in the egg and early embryo (By similarity)
    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 (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004668protein-arginine deiminase activity IEA--
    GO:0005509calcium ion binding IEA--
         
    PADI6 for ontologies           About GeneDecksing


    Phenotypes:
         3 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Padi6):
     embryogenesis  no phenotypic analysis  reproductive system 

    PADI6 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Padi6tm1.1Jgo for PADI6

       inGenious Targeting Laboratory - Custom generated mouse model solutions for PADI6 
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PADI6


    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for PADI6 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1protein citrullination
    protein citrullination


    1 BioSystems Pathway for PADI6
        protein citrullination


    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PADI6

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

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

    PADI6 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PADI6

    1 HMDB Compound for PADI6    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    1 DrugBank Compound for PADI6    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    L-Citrulline2-Amino-5-uredovaleric acid (see all 8)372-75-8target--17139284 17016423

    Search CenterWatch for drugs/clinical trials and news about PADI6

    (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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PADI6 gene: 
    NM_207421.3  

    Unigene Cluster for PADI6:

    Peptidyl arginine deiminase, type VI
    Hs.531598  [show with all ESTs]
    Unigene Representative Sequence: AY443100
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000434762 ENST00000358481(uc001bak.1)
    miRNA
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    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
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                         Customized lentivirus expression plasmids for stable overexpression of PADI6 
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    Additional mRNA sequence: 

    AY422079.1 AY443100.1 

    2 DOTS entries:

    DT.102819972  DT.121442582 

    2 AceView cDNA sequences:

    NM_207421 AY422079 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    PADI6 expression in normal human tissues (normalized intensities)      PADI6 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATTCTTTGCC
    PADI6 Expression
    About this image


    PADI6 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/1 selected tissues (see all 1) fully expand
     
     Ovary (Reproductive System)    fully expand to see all 4 entries
             Pre-Granulosa Cells Primordial Follicle
             Secondary follicles
             oocyte   

     -- (Integumentary System)
             skin   

    See PADI6 Protein Expression from SPIRE MOPED and PaxDB
    SOURCE GeneReport for Unigene cluster: Hs.531598

    UniProtKB/Swiss-Prot: PADI6_HUMAN, Q6TGC4
    Tissue specificity: Ovary, testis and peripheral blood leukocytes

        SABiosciences Custom PCR Arrays for PADI6
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PADI6

    (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)
    About This Section

    This gene was present in the common ancestor of human and mouse.

    Orthologs for PADI6 gene from 1/5 species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Padi61 , 5 peptidyl arginine deiminase, type VI1, 5 74.54(n)1
    67.74(a)1
      4 (72.26 cM)5
    2427261  NM_153106.21  NP_694746.21 
     1407273555 


    ENSEMBL Gene Tree for PADI6 (if available)
    TreeFam Gene Tree for PADI6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PADI6 gene
    4 SIMAP similar genes for PADI6 using alignment to 1 protein entry:     PADI6_HUMAN:
    PADI3    PADI4    PADI1    PADI2

    PADI6 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1128 SNPs in PADI6 are shown (see all 1128)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1995116101,2
    C--15949372(+) TTGTT-/TTGT  
      TTTGTC
    TTGTT
    1 -- int10--------
    rs1430828331,2
    --15949379(+) GTTTT-/GTCTTGTT 1 -- int10--------
    rs66643211,2
    C--15953762(+) ACCCCC/TGACAC 1 -- int10--------
    rs67033921,2
    C,F,A,H--15953763(+) CCCCCG/CACACC 1 -- int16Minor allele frequency- C:0.29WA NA EA 366
    rs2018772411,2
    --15953763(+) CCCCC-/GACACC 1 -- int10--------
    rs768864471,2
    C--15966697(+) GGGGGA/GGGGGA 1 -- int10--------
    rs106904731,2
    C--17699379(+) AGCAA-/ACACACA 1 -- int11Minor allele frequency- AC:0.50CSA 2
    rs716726131,2
    C--17699380(+) GCAAA-/ACCACAG 1 -- int10--------
    rs23082301,2
    C--17699509(-) AACAC-/CAC   
      T
    /TCAC
    CTTCT
    1 -- int15EU NA EA CSA 344
    rs717205861,2
    C--17699510(+) GAAGG-/GTGA  
            
    TGTTT
    1 -- int10--------

    HapMap Linkage Disequilibrium report for PADI6 (17698691 - 17728195 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for PADI6:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2214804CNV Deletion18987734
    esv2590404CNV Deletion19546169
    esv2626551CNV Deletion19546169

    SABiosciences Cancer Mutation PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing PADI6
    DNA2.0 Custom Variant and Variant Library Synthesis for PADI6

    (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.)
    About This Section
    OMIM gene information: 610363    OMIM disorders: --

    2 diseases for PADI6:    About MalaCards
    basal cell carcinoma    melanoma


    PADI6 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PADI6
    Human Genome Epidemiology (HuGE) Navigator: PADI6 (1 document)

    Export disorders for PADI6 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)
    About This Section

    PubMed articles for PADI6 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with PADI6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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, 3, 9 Chavanas S.... Simon M. (2004)
    2. cDNA cloning, gene organization and expression analysis of human peptidylarginine deiminase type VI. (PubMed id 15625577)1, 2, 9 Zhang J.... Mao Y. (2004)
    3. Common variants on 1p36 and 1q42 are associated with cutaneous basal cell carcinoma but not with melanoma or pigmentation traits. (PubMed id 18849993)1, 4 Stacey S.N....Stefansson K. (2008)
    4. Identification and structural characterization of two 14-3-3 binding sites in the human peptidylarginine deiminase type VI. (PubMed id 22634725)1 Rose R.... Ottmann C. (2012)
    5. How many drug targets are there? (PubMed id 17139284)7 Overington J.P....Hopkins A.L. (2006)
    6. Drugs, their targets and the nature and number of dru g targets. (PubMed id 17016423)7 Imming P....Meyer A. (2006)
    7. PAD, a growing family of citrullinating enzymes: genes, features and involvement in disease. (PubMed id 14579251)1 Vossenaar E.R....Pruijn G.J. (2003)
    8. Use of proteomics to identify highly abundant materna l factors that drive the egg-to-embryo transition. (PubMed id 20106898)9 Yurttas P....Coonrod S.A. (2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 353238 HGNC: 20449 AceView: PADI6 Ensembl:ENSG00000256049 euGenes: HUgn353238
    ECgene: PADI6 H-InvDB: PADI6

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for PADI6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PADI6 gene:
    Search GeneIP for patents involving PADI6

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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