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

PADI6 Gene

protein-coding   GIFtS: 46
GCID: GC01P017698

peptidyl arginine deiminase, type VI
 Explore 3 diseases affiliated with
PADI6 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for PADI6    

Aliases
for PADI6 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
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
HPADVI1     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


Summaries
for PADI6 gene

(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:
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)

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)




Genomic Views
for PADI6 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.1  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 plasmid: PADI6 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

Proteins
for PADI6 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q6TGC4

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

    PADI6 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_997304.3  
    Human Recombinant Protein Products: 
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    Uscn 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



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    Uscn ELISAs and CLIAs for PADI6

    Protein Domains /
    Families
    for PADI6 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    PADI6 for domains           About GeneDecksing

    5/6 InterPro domains/families (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 family: IPB004303 Protein-arginine deiminase

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


    Function
    for PADI6 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         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)
    Catalytic activity: Protein L-arginine + H(2)O = protein L-citrulline + NH(3)

    Enzyme Number (IUBMB): EC 3.5.3.151 2

    miRNA
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    Inhib. RNA
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    Gene Editing
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    Clone
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    Search LifeMap BioReagents cell lines for PADI6

    In Situ Assay
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    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


    Animal Models:
         Mouse knock-out Padi6tm1.1Jgo for PADI6
         3 MGI mutant phenotypes (inferred from 2 alleles) (MGI details for Padi6):
     embryogenesis  no phenotypic analysis  reproductive system 

    PADI6 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for PADI6 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1protein citrullination
    		protein citrullination1.00


    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:0018101peptidyl-citrulline biosynthetic process from peptidyl-arginine IEA--


    PADI6 for ontologies           About GeneDecksing



    Drugs & Compounds
    for PADI6 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 

    Transcripts
    for PADI6 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    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, 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
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    OriGene shRNA RFP: PADI6
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    Clone
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    Primer
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    Additional cDNA sequence: 

    AY422079.1 AY443100.1 

    2 DOTS entries:

    DT.102819972  DT.121442582 

    2 AceView cDNA sequences:

    AY422079 NM_207421 

    GeneLoc Exon Structure


    Expression
    for PADI6 gene

    (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)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ATTCTTTGCC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    PADI6 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    2 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    OvaryPrimary FollicleGranulosa CellsOvary
    OvaryPrimordial FolliclePre-Granulosa CellsOvary
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Secondary follicles (Primary Cell)Ovary, Reproductive System

    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:     
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    Orthologs
    for PADI6 gene

    (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
    for PADI6 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    		  --

    Genomic Variants
    for PADI6 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/882 NCBI SNPs in PADI6 are shown (see all 882)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 1 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs782740331,2
    		--15942844(+) GAAAAG/CAGCAA 1 -- us2k12Minor allele frequency- C:0.04CSA WA 120
    rs740587451,2
    		C,--15942854(+) AAAGCG/ACCCCG 1 -- us2k13Minor allele frequency- A:0.06WA CSA 121
    rs12048801,2
    		C,F,A,H,--15943049(-) CCTTCG/AAGGTT 1 -- us2k19Minor allele frequency- A:0.04NS EA NA WA 776
    rs729187221,2
    		C,--15943672(+) GGCTCC/TGCTGA 1 -- us2k11Minor allele frequency- T:0.50WA 2
    rs112033741,2
    		C,H,--15943857(+) ACAAGC/TACCCT 1 -- us2k15Minor allele frequency- T:0.01NS EA WA 516
    rs112033751,2
    		C,H,--15943887(+) CAGAGG/AGTTAA 1 -- us2k14Minor allele frequency- A:0.02NS EA WA 390
    rs75409251,2
    		C,--15944055(+) atggtG/Agtgca 1 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs168259901,2
    		C,F,--15944224(+) CCTTCG/ATCAAT 1 -- us2k14Minor allele frequency- A:0.02NA CSA 142
    rs12048751,2
    		C,F,O,A,H,--15944346(-) CTGTCG/AGGGCA 1 -- us2k119Minor allele frequency- A:0.10NS EA NA CSA WA 2356
    rs716440481,2
    		C,F,--15945115(+) AAACCA/CTGGGG 1 -- int13Minor allele frequency- C:0.04NA 124

    HapMap Linkage Disequilibrium report for PADI6 (17698691 - 17728195 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for PADI6
         2 Indels: 97305 44472

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    DNA2.0 Custom Variant and Variant Library Synthesis for PADI6

    Disorders / Diseases
    for PADI6 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    PADI6 for disorders           About GeneDecksing

    OMIM gene information: 610363    OMIM disorders: --

    3 diseases for PADI6:    About MalaCards
    basal cell carcinoma    melanoma    carcinoma

    Human Genome Epidemiology (HuGE) Navigator: PADI6 (1 document)

    Export disorders for PADI6 gene to outside databases

    Publications
    for PADI6 gene

    (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. 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)
    4. Common variants on 1p36 and 1q42 are associated with cutaneous basal cell carcinoma but not with melanoma or pigmentation traits. (PubMed id 18849993)1 Stacey S.N....Stefansson K. (2008)
    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)

    External Searches for PADI6 gene

    (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)

    Genome Databases showing PADI6 gene

    (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

    Other Databases showing PADI6 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing PADI6 gene

    (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

    Intellectual Property
    for PADI6 gene

    (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



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    In Situ Hybridization Assays from
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    About This Section

     
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     PADI6 Proteins, Antibodies, CLIAs, and ELISAs
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