Aliases &
Descriptions
for PADI4 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase)
About This Section
|
| Aliases & Descriptions |
|---|
| peptidyl arginine deiminase, type IV1 2 | | HL-60 PAD2 3 | | PDI51 2 3 | | PADI-H protein2 | | PAD1 2 5 | | protein-arginine deiminase type-42 | | PADI52 3 5 | | PAD42 | | PDI41 2 | | Peptidylarginine deiminase IV3 | | peptidyl arginine deiminase, type V1 2 | | EC 3.5.3.153 | | Protein-arginine deiminase type IV2 3 | | |
Export aliases for PADI4 gene to outside databasesPrevious GC identifers: GC00U991184 GC01P016675 GC01P017015 GC01P017379 GC01P017507 GC01P017634 |
Summaries
for PADI4 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for PADI4:
This gene is a member of a gene family which encodes enzymes responsible for the conversion of arginine residues tocitrulline residues. This gene may play a role in granulocyte and macrophage development leading to inflammation andimmune response. (provided by RefSeq)
UniProtKB/Swiss-Prot: PADI4_HUMAN, Q9UM07Function: 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 andrepresses transcription. Citrullinates EP300/P300 at 'Arg-2142', which favors its interaction with NCOA2/GRIP1
Gene Wiki entry for PADI4 |
Genomic Views
for PADI4 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 60),
Regulatory elements and Epigenetics data according to
Qiagen and/or
SABiosciences)
About This Section
|
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the PADI4 gene promoter:
NF-kappaB1 NF-kappaB JunD AP-1 c-Fos Fra-1 JunB c-Jun NF-E2 p45 NF-E2
Other transcription factors
Search SABiosciences Chromatin IP Primers for PADI4
Epigenetics:
|  | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays  |
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: 1p36.13PADI4 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 GC01P015882: view genomic region
(about GC identifiers)
Start:
|
15,880,966 bp from pter |
End:
|
15,936,461 bp from pter |
Size:
|
55,496 bases |
Orientation:
|
plus strand |
1 alternative location:
| Chr1+ 17,634,690-17,690,499 |
RefSeq DNA sequence:- NC_000001.10 NT_004610.19
|
Proteins
for PADI4 gene
(According to
1UniProtKB,
neXtProt,
and/or Ensembl,
Phosphorylation sites according to 2Phosphosite,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological, and/or
ProSpec,
Biochemical Assays by
Millipore,
Sigma-Aldrich,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Dec 2010 and
Entrez Gene,
Antibodies by
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals, and/or
Epitomics)
About This Section
|
UniProtKB/Swiss-Prot: PADI4_HUMAN, Q9UM07 (See
protein sequence)Recommended Name: Protein-arginine deiminase type-4 Size: 663 amino acids; 74079 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 Q70SX4Explore the universe of human proteins at neXtProt for PADI4: NX_Q9UM07
REFSEQ proteins: NP_036519.2
ENSEMBL proteins: ENSP00000351690 ENSP00000364602 ENSP00000364597
Human Recombinant Proteins
2 Gene Ontology (GO) cellular component terms (GO ID links to tree view): About this table
PADI4 for ontologies About GeneDecksing
Antibodies for PADI4:
Assays for PADI4: |
Protein
Domains/
Families
for PADI4 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
PADI4 for domains About GeneDecksing
5/6 InterPro domains/families (see all 6):Graphical View of Domain Structure for InterPro Entry Q9UM07ProtoNet protein and cluster: Q9UM07 1 Blocks protein family: IPB004303 Protein-arginine deiminase
UniProtKB/Swiss-Prot: PADI4_HUMAN, Q9UM07Similarity: Belongs to the protein arginine deiminase family |
Gene Function
for PADI4 gene
(According to UniProtKB,
IUBMB,and/or
Genatlas, Animal models from MGI Dec 24 2010,
shRNA from
OriGene,
Sigma-Aldrich,
RNAi from
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Clones from Millipore,
Sigma-Aldrich,
OriGene,
GenScript,
Sino Biological,
Cell Lines from GenScript,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene.)
About This Section
|
UniProtKB/Swiss-Prot: PADI4_HUMAN, Q9UM07Function: 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 andrepresses transcription. Citrullinates EP300/P300 at 'Arg-2142', which favors its interaction with NCOA2/GRIP1Catalytic 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=33.2umol/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
3 Gene Ontology (GO) molecular function terms (GO ID links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0004668 | protein-arginine deiminase activity |
IEA | -- | | GO:0005509 | calcium ion binding |
IEA | -- | | GO:0016787 | hydrolase activity |
IEA | -- |
About this table
PADI4 for ontologies About GeneDecksing
Animal Models: 1 MGI phenotypic allele  for Padi4 (no phenotypes)
PADI4 for phenotypes About GeneDecksing
|
Pathways & Interactions
for PADI4 gene
(Pathways according to
Millipore,
Cell Signaling Technology,
Sigma-Aldrich,
KEGG
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
PCR Arrays from
SABiosciences,
Proteins Network according to
SABiosciences,
Sigma-Aldrich,
Interactions according to 1UniProtKB,
2MINT, and/or
3STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene).
About This Section
|
SABiosciences Custom Pathway-Focused PCR Arrays for PADI4
SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for PADI4
4 Gene Ontology (GO) biological process terms (GO ID links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0006464 | protein modification process |
IEA | -- | | GO:0016568 | chromatin modification |
IEA | -- | | GO:0018101 | peptidyl-citrulline biosynthetic process from peptidyl-arginine |
IEA | -- | | GO:0045449 | regulation of transcription |
IEA | -- |
About this table
PADI4 for ontologies About GeneDecksing
|
Drugs & Compounds
for PADI4 gene(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
|
PADI4 for compounds About GeneDecksing
 Browse Tocris compounds for PADI4
6  Novoseek chemical compound relationships for PADI4 gene
| Compound |
-log (P-Val) |
Hits |
PubMed IDs for Articles with Shared Sentences (# sentences) |
| citrulline |
91 |
35 |
10027703 (2), 16539813 (2), 12586539 (1), 17216583 (1) (see all 27) |
| acpa |
83.8 |
2 |
18476880 (2) |
| arginine |
74.6 |
33 |
15832289 (2), 15339660 (2), 19246161 (2), 12586539 (1) (see all 29) |
| baee |
71.7 |
3 |
11017707 (2) |
| fibrinogen |
26.3 |
2 |
16892136 (1), 20450789 (1) |
| calcium |
11.2 |
4 |
12586539 (1), 16892136 (1), 15625577 (1), 19004619 (1) |
About this table
|
Transcripts
for PADI4 gene(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
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
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from
Sigma-Aldrich,
OriGene,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Tagged/untagged cDNA clones from
OriGene,
Sigma-Aldrich,
GenScript,
Primers from
OriGene and/or
SABiosciences)
About This Section
|
REFSEQ mRNAs for PADI4 gene: NM_012387.2 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 BM676574 CB241171 BM713957 BX280830 BX493079 NM_012387 AI766115 BI019938 BI910127 BI836729 AB017919 BI905950 AW467231 BX492929 BU600065 BI020543 BI021411 BU502414 BI025762 BI752751 AA682801 BC025718 BX492994
 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
6 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000358829 ENST00000467001 ENST00000468945 ENST00000375453 ENST00000487048
ENST00000375448(uc009vpc.2 uc001baj.2)
|
Expression
for PADI4 gene
(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 228 Homo sapiens),
SAGE tags according to
CGAP,
plus additional links to
SOURCE, and/or
GNF
BioGPS, and/or
EXPOLDB, and/or
UniProtKB,
Primers from
OriGene and/or
SABiosciences
)
About This Section
| PADI4 expression in normal and diseased human tissues
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 |
1 |
0.75 |
1.00 |
0.93 |
1.15 |
T92118 |
0.80 |
1.00 |
0.91 |
1 |
| 75941_at2, 3
|
U95-D |
3 |
0.69 |
0.91 |
0.99 |
0.86 |
AA682801 |
1.00 |
1.00 |
1.00 |
1 |
| 220001_at2, 3
|
U133-A |
1 |
0.82 |
1.00 |
-- |
-- |
NM_012387 |
0.60 |
1.00 |
0.82 |
1 |
| 211413_s_at2, 3
|
U133-A |
1 |
0.73 |
1.00 |
-- |
-- |
AF229067 |
0.40 |
1.00 |
0.76 |
1 |
| 211412_at2, 3
|
U133-A |
1 |
0.36 |
1.00 |
-- |
-- |
AF229067 |
0.40 |
1.00 |
0.76 |
1 |
| 220001_at2
|
U133Plus2 |
1 |
0.82 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 211413_s_at2
|
U133Plus2 |
1 |
0.73 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 211412_at2
|
U133Plus2 |
1 |
0.36 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
About this table
PADI4 for expression About GeneDecksing
Data from
Genenote
(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, Q9UM07Tissue specificity: Expressed in eosinophils and neutrophils, not expressed in peripheral monocytes or lymphocytes
SABiosciences Custom PCR Arrays for PADI4
|
Orthologs
for PADI4 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
and/or
5MGI Dec 24 2010,
with possible further links to
Flybase
and/or
WormBase,
Gene Trees according to Ensembl)
About This Section
|
Orthologs for PADI4 gene from 5 species
About this table Species with no ortholog for PADI4
ENSEMBL Gene Tree for PADI4 (if available) |
Paralogs
for PADI4 gene(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section
| Paralogs for PADI4 gene
- PADI22 PADI12 PADI32
PADI4 for paralogs About GeneDecksing
|
Genomic Variants
for PADI4 gene(SNPs according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Chr 1 pos | Sequence | Recs | AA
Chg | Type | More | Recs | Allele
freq | Pop | Total
sample | More |
|---|
About this tableHapMap Linkage Disequilibrium images for PADI4 (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 4 variations for PADI4
4 CNVs: 68142 43389 68143 6799 | | QIAGEN SeqTarget long-range PCR primers for resequencing PADI4 |
|
Disorders & Mutations
for PADI4 gene
(in which this Gene is Involved, According to
OMIM, UniProtKB,
Novoseek, PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
LSDB, HGMD, GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
PADI4 for disorders About GeneDecksing
OMIM: 605347 disorders: 180300 UniProtKB/Swiss-Prot: PADI4_HUMAN, Q9UM07
Genetic variations in PADI4 are a cause of susceptibility to rheumatoid arthritis (RA) [MIM:180300]. It is asystemic inflammatory disease with autoimmune features and a complex genetic component. It primarily affects thejoints and is characterized by inflammatory changes in the synovial membranes and articular structures, widespreadfibrinoid degeneration of the collagen fibers in mesenchymal tissues, and by atrophy and rarefaction of bonystructures. Note=Could have an important role in the pathogenesis of rheumatoid arthritis by increasing citrullinationof proteins in rheumatoid arthritis synovial tissues, leading, in a cytokine-rich milieu, to a break in tolerance tocitrullinated peptides processed and presented in the appropriate HLA context
10 Novoseek disease relationships for PADI4 gene
| Disease |
-log (P-Val) |
Hits |
PubMed IDs for Articles with Shared Sentences (# sentences) |
| rheumatoid arthritis |
80.4 |
41 |
15485997 (4), 17216583 (2), 15077293 (2), 15814578 (2) (see all 26) |
| rheumatic diseases |
57.3 |
2 |
17968335 (1), 16134727 (1) |
| autoimmunity |
50.7 |
2 |
18645041 (2) |
| autoimmune diseases |
46.2 |
2 |
17868046 (1), 19892302 (1) |
| multiple sclerosis |
36.2 |
5 |
16828881 (2), 19540364 (1), 15080264 (1), 18476880 (1) |
| lupus erythematosus systemic |
35.7 |
2 |
17968335 (1), 15080264 (1) |
| osteoarthritis |
30.5 |
2 |
17968929 (1) |
| inflammation |
28.8 |
4 |
16245073 (2), 15814578 (1), 18645041 (1) |
| arthritis |
4.84 |
3 |
17968929 (2) |
| leukemia |
0 |
3 |
17216583 (1), 16502257 (1) |
About this table
Genetic Association Database (GAD): PADI4
Human Genome Epidemiology (HuGE) Navigator: PADI4 (37 documents)
Export disorders and mutations for PADI4 gene to outside databases
|
Medical News
for PADI4 gene(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications
for PADI4 gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6UniProtKB/TrEMBL, and/or
7Novoseek)
About This Section
|
10/125 PubMed articles for PADI4 gene, integrated from 7 sources (see all 125):
(articles sorted by number of sources associating them with PADI4)- High variability of peptidylarginine deiminase 4 (PADI4) in a healthy white population: characterization of six new variants of PADI4 exons 2-4 by a novel haplotype-specific sequencing-based approach. (PubMed id 15338034)1, 2, 4, 7 Hoppe B....Salama A. (2004)
- Molecular characterization of peptidylarginine deiminase in HL-60 cells induced by retinoic acid and 1alpha,25-dihydroxyvitamin D(3). (PubMed id 10488123)1, 2, 3, 7 Nakashima K.... Yamada M. (1999)
- Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. (PubMed id 12833157)1, 2, 4 Suzuki A.... Yamamoto K. (2003)
- Genetic and genomic studies of PADI4 in rheumatoid arthritis. (PubMed id 15814578)1, 4, 7 Harney S.M....Brown M.A. (2005)
- A functional haplotype of the PADI4 gene associated with increased rheumatoid arthritis susceptibility in Koreans. (PubMed id 16385500)1, 4, 7 Kang C.P....Bae S.C. (2006)
- Association between PADI4 and rheumatoid arthritis: a replication study. (PubMed id 16200584)1, 4, 7 Ikari K....Kamatani N. (2005)
- Investigation of polymorphisms in the PADI4 gene in determining severity of inflammatory polyarthritis. (PubMed id 15731287)1, 4, 7 Barton A....Silman A. (2005)
- Histone deimination antagonizes arginine methylation. (PubMed id 15339660)1, 2, 7 Cuthbert G.L.... Kouzarides T. (2004)
- A functional haplotype of the PADI4 gene associated with rheumatoid arthritis in a Japanese population is not associated in a United Kingdom population. (PubMed id 15077293)1, 4, 7 Barton A....Worthington J. (2004)
- PADI4 polymorphisms are not associated with rheumatoid arthritis in the Spanish population. (PubMed id 15998632)1, 4, 7 Martinez A....Urcelay E. (2005)
|
External Searches for PADI4 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing PADI4 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing PADI4 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing PADI4 gene(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
|
|
About This Section
| Patent Information for PADI4 gene:
Search GeneIP for patents involving PADI4
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for PADI4 gene(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or
Enzo Life Sciences)
About This Section
|
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| | | |
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 |  |  |  | |
| |  | Search Tocris compounds for PADI4 |
| |  |  |  |  | | | | |
 | | | ELISAs and CLIAs for PADI4 |
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