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PADI4 Gene

protein-coding   GIFtS: 54

GC01P017507
peptidyl arginine deiminase, type IV
(Previous names: peptidyl arginine deiminase, type V )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: PADI5)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
EC 3.5.3.15 3
OTTHUMP00000002482 2
PAD 1, 2, 5
PAD4 2
PADI5 2, 3, 5
PDI4 1, 2
PDI5 1, 2, 3
Descriptions
HL-60 PAD 2, 3
PADI-H protein 2
Peptidylarginine deiminase IV 3
Protein-arginine deiminase type IV 3
peptidyl arginine deiminase, type IV 2
peptidyl arginine deiminase, type V 1, 2
protein-arginine deiminase 2
External Ids
HGNC: 183681
Entrez Gene: 235692
UniProtKB: Q9UM073
Ensembl: ENSG000001593397
Search outside databases for aliases for PADI4 gene

Previous GC identifers: GC00U991184 GC01P016675 GC01P017015 GC01P017379

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

EntrezGene summary for PADI4:
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]

UniProtKB/Swiss-Prot: PADI4_HUMAN, Q9UM07
Function: Catalyzes the citrullination/deimination of arginine residues of proteins. Citrullinates
histone H3 at 'Arg-8' and/or 'Arg-17' and histone H4 at 'Arg-3', which prevents their methylation
by CARM1 and HRMT1L2/PRMT1 and represses transcription. Citrullinates EP300/P300 at 'Arg-2142',
which favors its interaction with NCOA2/GRIP1

Gene Wiki entry for PADI4

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the PADI4 gene  

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

PADI4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P017507:     (about GC identifiers)

Start:
17,507,277 bp from pter
End:
17,563,082 bp from pter
Size:
55,806 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000001.9  NT_004610.18  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: PADI4_HUMAN, Q9UM07 (See protein sequence)
Recommended Name: Protein-arginine deiminase type-4  
Size: 663 amino acids; 74095 Da
Cofactor: Binds 5 calcium ions per subunit
Subcellular location: Cytoplasm. Nucleus. Cytoplasmic granule. Note=Cytoplasmic granules of
eosinophils and neutrophils
PDB structures from and Proteopedia :
1WD8 (3D)    1WD9 (3D)    1WDA (3D)    2DEW (3D)    2DEX (3D)    2DEY (3D)    2DW5 (3D)    
Secondary accessions: Q5VTZ8 Q70SX4

REFSEQ proteins: NP_036519.2  

ENSEMBL proteins: 
ENSP00000364602 ENSP00000351690 ENSP00000364597 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Browse Human Recombinant Proteins at Sigma-Aldrich  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (PADI4 / PAD4)
Human Recombinant Proteins from Abnova (PADI4)
              OriGene Purified Recombinant Human Protein: PADI4 

2 Gene Ontology (GO) cellular component terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005634 nucleus IEA--
GO:0005737 cytoplasm IEA--
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Antibodies for PADI4: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Sigma-Aldrich Antibody Arrays and Antibodies for PADI4
Browse R&D Systems for Antibodies
Antibodies from Abcam (PADI4 / PAD4), each with their AbpromiseSM
Monoclonal and Polyclonal Antibodies from Abnova (PADI4)
Novus Biologicals Antibodies for PADI4

Assays for PADI4: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

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

5 InterPro domains/families:
 IPR013732 PAD_N
 IPR004303 PAD
 IPR016296 Protein-arginine_deiminase_sub
 IPR013530 PAD_C
 IPR013733 PAD_central


   GeneDecks  PADI4 for the domains selected above  
About GeneDecksing

Graphical View of Domain Structure for InterPro Entry Q9UM07

ProtoNet protein and cluster: Q9UM07

1 Blocks protein family: IPB004303 Protein-arginine deiminase

UniProtKB/Swiss-Prot: PADI4_HUMAN, Q9UM07
Similarity: Belongs to the protein arginine deiminase family

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (PADI4)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (PADI4)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_012387

              Applied Biosystems Silencer® siRNAs for PADI4

              Sigma-Aldrich siRNA for PADI4  
                     Sigma-Aldrich shRNA for PADI4  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Invitrogen Clones for PADI4
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_012387
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_012387
                                 untagged cDNA clones in CMV expression vector (see all 3): AF229067 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_012387

UniProtKB/Swiss-Prot: PADI4_HUMAN, Q9UM07
Function: Catalyzes the citrullination/deimination of arginine residues of proteins. Citrullinates
histone H3 at 'Arg-8' and/or 'Arg-17' and histone H4 at 'Arg-3', which prevents their methylation
by CARM1 and HRMT1L2/PRMT1 and represses transcription. Citrullinates EP300/P300 at 'Arg-2142',
which favors its interaction with NCOA2/GRIP1
Catalytic activity: Protein L-arginine + H(2)O = protein L-citrulline + NH(3)
Biophysicochemical properties: Kinetic parameters: KM=0.055 mM for fibrinogen; KM=0.064 mM for
filaggrin; Vmax=33.2 umol/h/mg enzyme toward fibrinogen; Vmax=8.0 umol/h/mg enzyme toward
filaggrin; pH dependence: Optimum pH is 6.5-9.0;
Enzyme Number (IUBMB): EC 3.5.3.15 

1 MGI phenotypic allele for Padi4 (no phenotypes)


3 Gene Ontology (GO) molecular function terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0004668 protein-arginine deiminase activity TAS10488123
GO:0005509 calcium ion binding IEA--
GO:0016787 hydrolase activity IEA--
About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section


 Gene Network CentralTM Interacting Genes and Proteins Network for  PADI4 


5/7 Interacting proteins for PADI4 (ENSP000003645973) via UniProtKB, MINT, and/or STRING (see all 7 )
InteractantInteraction Details
GeneCardExternal ID(s)
PTPN22ENSP000003528333STRING (score=.887)
TP53ENSP000002693053STRING (score=.845)
CARM1ENSP000003256903STRING (score=.814)
RUNX1ENSP000003003053STRING (score=.795)
FCRL3ENSP000003571693STRING (score=.742)
About this table

5 Gene Ontology (GO) biological process terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0006350 transcription IEA--
GO:0006355 regulation of transcription, DNA-dependent IEA--
GO:0006464 protein modification process TAS10488123
GO:0016568 chromatin modification IEA--
GO:0018101 peptidyl-citrulline biosynthetic process from peptidyl-arginine IEA--
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for PADI4
4 Novoseek chemical compound relationships for PADI4 gene
Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
acpa 76.34 2 18476880 (2)
baee 73.50 3 11017707 (2)
fibrinogen 22.32 1 16892136 (1)
calcium 10.72 4 12586539 (1), 16892136 (1), 15625577 (1), 19004619 (1)
About this table


(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (PADI4)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (PADI4)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_012387

              Sigma-Aldrich siRNA for PADI4  
                     Sigma-Aldrich shRNA for PADI4  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_012387  

REFSEQ mRNAs for PADI4 gene: 

NM_012387.2   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_012387  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_012387
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_012387
                                 untagged cDNA clones in CMV expression vector (see all 3): AF229067 

Additional cDNA sequence: 

AB017919.1 AF229067.1 AK290507.1 AK309637.1 AK314839.1 BC025718.1 

6 DOTS entries:

DT.200682  DT.92424921  DT.91944157  DT.95097226  DT.95154884  DT.95218477 

24/56 AceView cDNA sequences (see all 56 ):

BF942697 CB241171 BM676574 BX280830 BM713957 AA682801 BU502414 BX492929 
BI021411 BX492994 BI836729 AB017919 NM_012387 BI019938 BC025718 BI905950 
BX493079 BI025762 CB146134 BI020543 BU600065 AI766115 AW467231 BI910127 

highest scoring ESTs for PADI4:

AA682801 AB017919 AI766115 AW084484 AW467326 BC025718 BF895958 BF896009 BF896025 BF896041 

Unigene Cluster for PADI4:

Peptidyl arginine deiminase, type IV
Hs.522969  [show with all ESTs]
Unigene Representative Sequence: BC025718


GeneLoc Exon Structure

3 Ensembl transcripts including schematic representations:
ENST00000375453  ENST00000358829  ENST00000375448  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

PADI4 expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for PADI4

1 / 2 / 3

8 probe-sets matching PADI4 gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

86508_at2, 3 U95-D 2 1.00 0.94 0.93 1.15 T92118 0.80 1.00 0.91 1
75941_at2, 3 U95-D 4 1.00 0.89 0.99 0.86 AA682801 1.00 1.00 1.00 1

220001_at2, 3 U133-A 1 1.00 1.00 -- -- NM_012387 0.60 1.00 0.82 1

211413_s_at2, 3 U133-A 1 1.00 1.00 -- -- AF229067 0.40 1.00 0.76 1

211412_at2, 3 U133-A 1 0.82 1.00 -- -- AF229067 0.40 1.00 0.76 1

220001_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

211413_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

211412_at2 U133Plus2 1 0.82 1.00 -- -- -- -- -- -- --
GeneDecks  PADI4 for binary patterns associated with the probe-sets selected above  
About GeneDecksing
About this table    
Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: GTGCCCTGAG

SOURCE GeneReport for Unigene cluster: Hs.522969

UniProtKB/Swiss-Prot: PADI4_HUMAN, Q9UM07
Tissue specificity: Expressed in eosinophils and neutrophils, not expressed in peripheral monocytes
or lymphocytes

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for PADI4 gene from 5 species
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
PADI41   -- peptidyl arginine deiminase, type IV 83.61(n)
76.85(a)
606921  XM_843401.1  XP_848494.1 
chimpanzee
(Pan troglodytes)
PADI41   -- peptidyl arginine deiminase, type IV 95.34(n)
94.21(a)
456530  XM_513116.2  XP_513116.2 
cow
(Bos taurus)
PADI41   -- peptidyl arginine deiminase, type IV 83.03(n)
74.32(a)
508161  XM_584904.3  XP_584904.3 
rat
(Rattus norvegicus)
Padi41   -- peptidyl arginine deiminase, type IV 80.01(n)
74.62(a)
29512  NM_017227.1  NP_058923.1 
mouse
(Mus musculus)
Padi41, 5 4 (71.00 cM)5
peptidyl arginine deiminase, type IV1, 5 80.16(n)1
73.87(a)1
186021  NM_011061.11  NP_035191.11 
 AB0138505  AB1216925  (see all 10)
About this table        Species with no ortholog for PADI4

ENSEMBL Gene Tree for PADI4
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for PADI4 gene
PADI22  PADI12  PADI62  PADI32  

(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/604 NCBI SNPs in PADI4 are shown (see all 604 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 226)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 1 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs14084221,2
A,C,F,H,O17563502(-) CCATCA/GAGTTT 1 -- ng3111Minor allele frequency- G:0.04EU EA WA NA 978
rs25017951,2
A,C,F,H17506086(+) CAAACA/GCAAGA 1 -- ng518Minor allele frequency- G:0.10EU EA WA 832
rs112033671,2
A,C,F,H17530203(+) GAAAGC/TGGCCA 1 A/V mis117Minor allele frequency- T:0.47EU EA WA NA 1740
rs25017961,2
A,C,F,H17506109(+) GAAACA/GCTCTA 1 -- ng518Minor allele frequency- G:0.09EU EA WA 838
rs17480201,2
A,C,F,H17541196(-) GGTTGG/AACGTG 1 F/S mis1 ese39Minor allele frequency- A:0.07EU EA WA NA 914
rs8748811,2
A,C,F,H17533086(+) CACCGC/GGGTGG 1 A/G mis1 ese310Minor allele frequency- G:0.43EA EU WA NA 2414
rs112033661,2
A,C,F,H17530121(+) CCCACA/GGCCCT 1 S/G mis19Minor allele frequency- G:0.47EU EA WA NA 906
rs24771341,2
A,C,F,H17506159(-) CCCAAA/CAAGGA 1 -- ng514Minor allele frequency- C:0.28EU EA WA 418
rs24771331,2
A,C,F,H17506479(-) GCTTAG/TTATTA 1 -- ng514Minor allele frequency- T:0.06EU EA WA 420
rs115795041,2
A,C,F,H17505833(+) GATAAA/GTTTTG 1 -- ng517Minor allele frequency- G:0.21EU EA WA NA 554
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HapMap Linkage Disequilibrium images for PADI4 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 605347   disorders: 180300  

UniProtKB/Swiss-Prot: PADI4_HUMAN, Q9UM07

  • PADI4 is thought to be a rheumatoid arthritis susceptibility locus [MIM:180300]. Could
    have an important role in the pathogenesis of rheumatoid arthritis by increasing citrullination of
    proteins in rheumatoid arthritis synovial tissues, leading, in a cytokine-rich milieu, to a break
    in tolerance to citrullinated peptides processed and presented in the appropriate HLA context
  • 10 Novoseek disease relationships for PADI4 gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    rheumatoid arthritis 78.84 38 15485997 (4), 17216583 (2), 15077293 (2), 15814578 (2) (see all 24)
    rheumatic diseases 59.86 2 17968335 (1), 16134727 (1)
    autoimmunity 47.82 2 18645041 (2)
    lupus erythematosus systemic 38.66 2 17968335 (1), 15080264 (1)
    autoimmune diseases 38.03 1 17868046 (1)
    multiple sclerosis 35.61 4 16828881 (2), 15080264 (1), 18476880 (1)
    inflammation 28.20 4 16245073 (2), 15814578 (1), 18645041 (1)
    osteoarthritis 21.54 2 17968929 (1)
    arthritis 8.51 3 17968929 (2)
    leukemia 0.00 3 17216583 (1), 16502257 (1)
    About this table

    Genetic Association Database: PADI4
    Human Genome Epidemiology Navigator: PADI4 (31 documents)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/99 PubMed articles for PADI4 gene (see all 99 ):
    (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, and/or H-InvDB)
    About This Section

    Entrez Gene: 23569 HGNC: 18368 AceView: PADI4 Ensembl:ENSG00000159339 euGenes: HUgn23569
    ECgene: PADI4 H-InvDB: PADI4
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

      --
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for PADI4:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for PADI4 Antibodies for PADI4
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for PADI4 Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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     shRNA in GFP-retroviral vector
     Search Tocris compounds for PADI4




     Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
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