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Aliases for PYDC1 Gene

Aliases for PYDC1 Gene

  • Pyrin Domain Containing 1 2 3 5
  • PYD (Pyrin Domain) Containing 1 2 3
  • Pyrin-Only Protein 1 3 4
  • PAAD-Only Protein 1 3 4
  • Cellular POP1 3 4
  • CPOP1 3 4
  • POP1 3 4
  • ASC2 3 4
  • PYC1 3 4
  • Pyrin Domain-Containing Protein 1 3
  • ASCI 4

External Ids for PYDC1 Gene

Previous GeneCards Identifiers for PYDC1 Gene

  • GC16M031135
  • GC16M028788

Summaries for PYDC1 Gene

GeneCards Summary for PYDC1 Gene

PYDC1 (Pyrin Domain Containing 1) is a Protein Coding gene. Diseases associated with PYDC1 include Black Piedra and Listeriosis. Among its related pathways are Toll-Like receptor Signaling Pathways. An important paralog of this gene is PYCARD.

UniProtKB/Swiss-Prot for PYDC1 Gene

  • Associates with PYCARD/ASC and modulates its ability to collaborate with MEFV/pyrin and NLRP3/cryopyrin in NF-kappa-B and pro-caspase-1 activation. Suppresses kinase activity of NF-kappa-B inhibitor kinase (IKK) complex, expression of NF-kappa-B inducible genes and inhibits NF-kappa-B activation by cytokines and LPS.

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PYDC1 Gene

Genomics for PYDC1 Gene

Regulatory Elements for PYDC1 Gene

Enhancers for PYDC1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16G031252 1.6 FANTOM5 Ensembl ENCODE 31.1 -36.5 -36540 1.8 PKNOX1 ATF1 ARNT E2F7 TCF12 ZNF766 FOS JUNB NCOA1 ZNF592 PYDC1 PYCARD TRIM72 PRSS36 ITGAM ITGAX ZNF646 ZNF668 STX4 KAT8
GH16G031264 1 Ensembl ENCODE 32.8 -48.3 -48275 2.1 HDGF CTCF PKNOX1 BACH1 EBF1 RELA POLR2A EED FOS RELB PYDC1 PYCARD PRSS36 HSD3B7 ITGAM ITGAX
GH16G031243 1.1 Ensembl ENCODE 29.6 -27.0 -26958 1.0 BCOR HDAC1 PKNOX1 ATF1 TAL1 ETV1 ZMYM3 GATA2 NCOR1 EED PYDC1 PYCARD TRIM72 FUS PRSS8 ZNF764 GC16P031242 ITGAM
GH16G031349 1.5 FANTOM5 Ensembl ENCODE dbSUPER 15.8 -133.1 -133057 1.2 BCOR ZNF146 ZMYM3 MAX EGR2 ITGAX STX4 PYDC1 KAT8 ITGAM ZNF646 ARMC5 HSD3B7 ZNF668 FUS
GH16G031247 0.6 ENCODE 33.2 -31.1 -31112 1.1 ZNF3 GATAD2B ZFHX2 IKZF1 PRDM10 ETV6 IKZF2 SP7 EGR2 PYDC1 TRIM72 PYCARD FUS PRSS36 STX4 STX1B LOC730183 GC16P031242 ITGAM
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PYDC1 on UCSC Golden Path with GeneCards custom track

Promoters for PYDC1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000085317 1759 401 PKNOX1 SIN3A GLIS2 GATA2 KLF7 SP3 REST ZNF579 ZNF610 SMARCA4

Genomic Location for PYDC1 Gene

Chromosome:
16
Start:
31,215,962 bp from pter
End:
31,217,359 bp from pter
Size:
1,398 bases
Orientation:
Minus strand

Genomic View for PYDC1 Gene

Genes around PYDC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PYDC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PYDC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PYDC1 Gene

Proteins for PYDC1 Gene

  • Protein details for PYDC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WXC3-PYDC1_HUMAN
    Recommended name:
    Pyrin domain-containing protein 1
    Protein Accession:
    Q8WXC3
    Secondary Accessions:
    • B2R8L4
    • Q8NFP8

    Protein attributes for PYDC1 Gene

    Size:
    89 amino acids
    Molecular mass:
    10107 Da
    Quaternary structure:
    • Interacts with PYCARD/ASC (via pyrin domain).

    Three dimensional structures from OCA and Proteopedia for PYDC1 Gene

neXtProt entry for PYDC1 Gene

Post-translational modifications for PYDC1 Gene

Other Protein References for PYDC1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PYDC1 Gene

Domains & Families for PYDC1 Gene

Gene Families for PYDC1 Gene

Protein Domains for PYDC1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PYDC1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PYDC1: view

No data available for UniProtKB/Swiss-Prot for PYDC1 Gene

Function for PYDC1 Gene

Molecular function for PYDC1 Gene

UniProtKB/Swiss-Prot Function:
Associates with PYCARD/ASC and modulates its ability to collaborate with MEFV/pyrin and NLRP3/cryopyrin in NF-kappa-B and pro-caspase-1 activation. Suppresses kinase activity of NF-kappa-B inhibitor kinase (IKK) complex, expression of NF-kappa-B inducible genes and inhibits NF-kappa-B activation by cytokines and LPS.

Gene Ontology (GO) - Molecular Function for PYDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12656673
genes like me logo Genes that share ontologies with PYDC1: view

Phenotypes for PYDC1 Gene

GenomeRNAi human phenotypes for PYDC1:
genes like me logo Genes that share phenotypes with PYDC1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PYDC1 Gene

Localization for PYDC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PYDC1 Gene

Cytoplasm. Note=Recruited to specks formed by PYCARD within the cytoplasm. {ECO:0000269 PubMed:17178784}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PYDC1 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 2
mitochondrion 2
extracellular 1

Gene Ontology (GO) - Cellular Components for PYDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 12656673
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA 12656673
GO:0008385 IkappaB kinase complex IDA 12656673
genes like me logo Genes that share ontologies with PYDC1: view

Pathways & Interactions for PYDC1 Gene

genes like me logo Genes that share pathways with PYDC1: view

Pathways by source for PYDC1 Gene

1 KEGG pathway for PYDC1 Gene

Gene Ontology (GO) - Biological Process for PYDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006469 negative regulation of protein kinase activity IDA 12656673
GO:0009968 negative regulation of signal transduction IEA --
GO:0010804 negative regulation of tumor necrosis factor-mediated signaling pathway IMP 24871464
GO:0032088 NOT negative regulation of NF-kappaB transcription factor activity IMP,IDA 24871464
GO:0033209 tumor necrosis factor-mediated signaling pathway IDA 12656673
genes like me logo Genes that share ontologies with PYDC1: view

No data available for SIGNOR curated interactions for PYDC1 Gene

Transcripts for PYDC1 Gene

mRNA/cDNA for PYDC1 Gene

(1) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(11) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PYDC1 Gene

PYD (pyrin domain) containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PYDC1 Gene

No ASD Table

Relevant External Links for PYDC1 Gene

GeneLoc Exon Structure for
PYDC1
ECgene alternative splicing isoforms for
PYDC1

Expression for PYDC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PYDC1 Gene

mRNA differential expression in normal tissues according to GTEx for PYDC1 Gene

This gene is overexpressed in Skin - Sun Exposed (Lower leg) (x7.5), Brain - Cerebellar Hemisphere (x7.3), Brain - Cerebellum (x6.4), Skin - Not Sun Exposed (Suprapubic) (x5.9), Brain - Amygdala (x5.6), and Brain - Nucleus accumbens (basal ganglia) (x5.3).

Protein differential expression in normal tissues from HIPED for PYDC1 Gene

This gene is overexpressed in Breast (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PYDC1 Gene



Protein tissue co-expression partners for PYDC1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PYDC1 Gene:

PYDC1

SOURCE GeneReport for Unigene cluster for PYDC1 Gene:

Hs.58314

mRNA Expression by UniProt/SwissProt for PYDC1 Gene:

Q8WXC3-PYDC1_HUMAN
Tissue specificity: Predominantly expressed in monocytes, macrophages and granulocytes.

Evidence on tissue expression from TISSUES for PYDC1 Gene

  • Nervous system(4.3)
  • Heart(4)
genes like me logo Genes that share expression patterns with PYDC1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for PYDC1 Gene

Orthologs for PYDC1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PYDC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PYDC1 34 35
  • 98.88 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 25 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 23 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 17 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii pycard 35
  • 12 (a)
OneToMany
Species where no ortholog for PYDC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PYDC1 Gene

ENSEMBL:
Gene Tree for PYDC1 (if available)
TreeFam:
Gene Tree for PYDC1 (if available)

Paralogs for PYDC1 Gene

Paralogs for PYDC1 Gene

(3) SIMAP similar genes for PYDC1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PYDC1: view

Variants for PYDC1 Gene

Sequence variations from dbSNP and Humsavar for PYDC1 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs1000961838 -- 31,216,457(+) AAAAA(C/T)CCAAC intron-variant
rs1002294610 -- 31,215,490(+) CGCTC(A/G)CATTC intron-variant
rs1003355331 -- 31,219,064(+) GGCAT(A/C)CCCAT intron-variant, upstream-variant-2KB
rs1003471655 -- 31,218,571(+) CAGCT(A/G)CTTGG intron-variant, upstream-variant-2KB
rs1005139861 -- 31,216,840(+) GCGTA(C/G)TCCTC intron-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for PYDC1 Gene

Variant ID Type Subtype PubMed ID
dgv4990n54 CNV gain 21841781

Variation tolerance for PYDC1 Gene

Residual Variation Intolerance Score: 46.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.23; 5.14% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PYDC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PYDC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PYDC1 Gene

Disorders for PYDC1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PYDC1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
black piedra
listeriosis
  • infection by listeria monocytogenes
peptic ulcer perforation
  • acute peptic ulcer with perforation
atrial septal defect 4
  • atrial heart septal defect 4
- elite association - COSMIC cancer census association via MalaCards
Search PYDC1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for PYDC1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PYDC1
genes like me logo Genes that share disorders with PYDC1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PYDC1 Gene

Publications for PYDC1 Gene

  1. Structure and dynamics of ASC2, a pyrin domain-only protein that regulates inflammatory signaling. (PMID: 16905547) Natarajan A. … Hill J.M. (J. Biol. Chem. 2006) 2 3 4 64
  2. The CLRX.1/NOD24 (NLRP2P) pseudogene codes a functional negative regulator of NF-I_B, pyrin-only protein 4. (PMID: 24871464) Porter K.A. … Harton J.A. (Genes Immun. 2014) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. The PAAD/PYRIN-only protein POP1/ASC2 is a modulator of ASC-mediated nuclear-factor-kappa B and pro-caspase-1 regulation. (PMID: 12656673) Stehlik C. … Reed J.C. (Biochem. J. 2003) 3 4 64
  5. PYPAF1: a PYRIN-containing APAF1-like protein that assembles with ASC and activates NF-kB. (PMID: 11786556) Manji G.A. … Bertin J. (J. Biol. Chem. 2002) 2 4 64

Products for PYDC1 Gene

Sources for PYDC1 Gene

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