This gene belongs to the pentraxin superfamily, whose members encode highly conserved multifunctional proteins. The encoded protein, like other members of this family, contains a conserved pentraxin domain at the C-terminus. The highest levels of expression of the protein were observed in bone marrow, small intestine and testes. [provided by RefSeq, Jun 2016] See more...

Aliases for PTX4 Gene

Aliases for PTX4 Gene

  • Pentraxin 4 2 3 5
  • Pentraxin 4, Long 2 3
  • Long Pentraxin 4 2 3
  • Pentraxin-4 3 4
  • C16orf38 3 4
  • Neuronal Pentraxin-Like Protein C16orf38 3
  • Chromosome 16 Open Reading Frame 38 2
  • PTX4 5

External Ids for PTX4 Gene

Previous HGNC Symbols for PTX4 Gene

  • C16orf38

Previous GeneCards Identifiers for PTX4 Gene

  • GC16M001535
  • GC16M001461

Summaries for PTX4 Gene

Entrez Gene Summary for PTX4 Gene

  • This gene belongs to the pentraxin superfamily, whose members encode highly conserved multifunctional proteins. The encoded protein, like other members of this family, contains a conserved pentraxin domain at the C-terminus. The highest levels of expression of the protein were observed in bone marrow, small intestine and testes. [provided by RefSeq, Jun 2016]

GeneCards Summary for PTX4 Gene

PTX4 (Pentraxin 4) is a Protein Coding gene. Diseases associated with PTX4 include Progressive Relapsing Multiple Sclerosis. An important paralog of this gene is NPTX2.

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PTX4 Gene

Genomics for PTX4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PTX4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J001492 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 -4.9 -4914 3.3 ZBTB33 HNRNPL PRDM10 TFE3 RFX5 CTCF FOXA1 LARP7 ZIC2 RBFOX2 TELO2 PTX4 piR-31173 lnc-PTX4-3 piR-43705 ENSG00000259840 TMEM204
GH16J001677 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 11 -190.6 -190604 4.4 SP1 CREB1 HNRNPL PRDM10 ZNF629 IKZF1 BACH1 FOS TARDBP FOXA1 JPT2 lnc-IFT140-2 piR-30118 TELO2 FAHD1 CLCN7 TSC2 CRAMP1 E4F1 WDR24
GH16J001530 Promoter/Enhancer 1.8 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 12.1 -46.2 -46242 10 HNRNPL CTCF LEF1 ZIC2 SP1 MNT NR2F2 POLR2A RAD21 MAX TMEM204 TELO2 FAHD1 PTX4 IFT140 CCDC154 NME3 TSR3 FBXL16 CLCN7
GH16J001528 Promoter/Enhancer 1 EPDnew dbSUPER 12.2 -39.7 -39678 0.1 ZSCAN4 MNT EGR1 KDM4B TRIM24 MIER1 ZFHX2 MYNN TAL1 PHF20 TMEM204 piR-56497-055 CCDC154 WDR24 TELO2 PTX4 RNF151 CHTF18 CRAMP1 WDR90
GH16J001540 Enhancer 1 ENCODE dbSUPER 12.1 -57.1 -57136 10.2 TFE3 IKZF1 RCOR2 PHF21A ZIC2 PATZ1 SP1 ZNF24 CEBPA SCRT2 TMEM204 IFT140 TELO2 JPT2 EME2 CRAMP1 ENSG00000226890 PTX4 CCDC154 ENSG00000261505
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PTX4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PTX4

Genomic Locations for PTX4 Gene

Genomic Locations for PTX4 Gene
chr16:1,485,886-1,488,981
(GRCh38/hg38)
Size:
3,096 bases
Orientation:
Minus strand
chr16:1,535,887-1,538,982
(GRCh37/hg19)
Size:
3,096 bases
Orientation:
Minus strand

Genomic View for PTX4 Gene

Genes around PTX4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTX4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTX4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PTX4 Gene

Proteins for PTX4 Gene

  • Protein details for PTX4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96A99-PTX4_HUMAN
    Recommended name:
    Pentraxin-4
    Protein Accession:
    Q96A99

    Protein attributes for PTX4 Gene

    Size:
    478 amino acids
    Molecular mass:
    52339 Da
    Cofactor:
    Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • [Isoform 1]: Not expressed in small intestine.

    Alternative splice isoforms for PTX4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PTX4 Gene

Post-translational modifications for PTX4 Gene

  • Glycosylation at Asn67 and Asn91

Other Protein References for PTX4 Gene

No data available for DME Specific Peptides for PTX4 Gene

Domains & Families for PTX4 Gene

Gene Families for PTX4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for PTX4 Gene

Suggested Antigen Peptide Sequences for PTX4 Gene

GenScript: Design optimal peptide antigens:
  • Pentraxin-4 (PTX4_HUMAN)
genes like me logo Genes that share domains with PTX4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PTX4 Gene

Function for PTX4 Gene

Molecular function for PTX4 Gene

UniProtKB/Swiss-Prot Induction:
Not induced by bacterial lipopolysaccharideS (LPS) or IL1/interleukin-1 in endothelium, monocytes or neutrophils. Not induced by PHA in lymphocytes.

Phenotypes From GWAS Catalog for PTX4 Gene

Gene Ontology (GO) - Molecular Function for PTX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PTX4: view

Phenotypes for PTX4 Gene

genes like me logo Genes that share phenotypes with PTX4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTX4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PTX4 Gene

Localization for PTX4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTX4 Gene

Secreted.

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 PTX4 gene
Compartment Confidence
extracellular 3
plasma membrane 1
cytoskeleton 1
nucleus 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for PTX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
genes like me logo Genes that share ontologies with PTX4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PTX4 Gene

Pathways & Interactions for PTX4 Gene

PathCards logo

SuperPathways for PTX4 Gene

No Data Available

Interacting Proteins for PTX4 Gene

STRING Interaction Network Preview (showing top 1 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: ENSP00000293922 Q96A99-PTX4_HUMAN for PTX4 Gene via STRING IID

Gene Ontology (GO) - Biological Process for PTX4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for PTX4 Gene

Drugs & Compounds for PTX4 Gene

(1) Drugs for PTX4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6556
genes like me logo Genes that share compounds with PTX4: view

Transcripts for PTX4 Gene

mRNA/cDNA for PTX4 Gene

2 REFSEQ mRNAs :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTX4

Alternative Splicing Database (ASD) splice patterns (SP) for PTX4 Gene

No ASD Table

Relevant External Links for PTX4 Gene

GeneLoc Exon Structure for
PTX4

Expression for PTX4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PTX4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PTX4 Gene

This gene is overexpressed in Testis (x6.8).

Protein differential expression in normal tissues from HIPED for PTX4 Gene

This gene is overexpressed in Cerebrospinal fluid (68.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PTX4 Gene



Protein tissue co-expression partners for PTX4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PTX4

SOURCE GeneReport for Unigene cluster for PTX4 Gene:

Hs.553770

mRNA Expression by UniProt/SwissProt for PTX4 Gene:

Q96A99-PTX4_HUMAN
Tissue specificity: Widely expressed at low levels with highest levels in small intestine, testis and brain. Very low expression in endothelial cells, monocytes, neutrophils and lymphocytes. Isoform 1 is not expressed in small intestine.
genes like me logo Genes that share expression patterns with PTX4: view

Primer Products

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for PTX4 Gene

Orthologs for PTX4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PTX4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PTX4 30 31
  • 98.66 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia -- 31
  • 81 (a)
OneToMany
PTX4 30
  • 78.07 (n)
-- 31
  • 47 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia PTX4 30 31
  • 77.29 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ptx4 30 17 31
  • 73.95 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ptx4 30
  • 73.48 (n)
Oppossum
(Monodelphis domestica)
Mammalia PTX4 31
  • 49 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PTX4 31
  • 43 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PTX4 31
  • 44 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ptx4 30
  • 56.56 (n)
Zebrafish
(Danio rerio)
Actinopterygii ptx4 30 31
  • 48.61 (n)
OneToOne
Species where no ortholog for PTX4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for PTX4 Gene

ENSEMBL:
Gene Tree for PTX4 (if available)
TreeFam:
Gene Tree for PTX4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PTX4: view image

Paralogs for PTX4 Gene

Paralogs for PTX4 Gene

genes like me logo Genes that share paralogs with PTX4: view

Variants for PTX4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PTX4 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs12445920 - p.Arg234Gln
rs13332460 - p.Ala317Ser
rs2667673 - p.Arg220Gly
rs2745098 - p.Arg281Lys
rs2745101 - p.Arg92Trp

Additional dbSNP identifiers (rs#s) for PTX4 Gene

Structural Variations from Database of Genomic Variants (DGV) for PTX4 Gene

Variant ID Type Subtype PubMed ID
dgv4854n54 CNV loss 21841781
esv2422427 CNV duplication 17116639
esv2762143 CNV gain 21179565
nsv457332 CNV loss 19166990
nsv571162 CNV loss 21841781
nsv819259 CNV gain 19587683
nsv952899 CNV deletion 24416366

Variation tolerance for PTX4 Gene

Residual Variation Intolerance Score: 99.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 22.23; 99.40% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTX4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PTX4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PTX4 Gene

Disorders for PTX4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PTX4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
progressive relapsing multiple sclerosis
  • prms
- elite association - COSMIC cancer census association via MalaCards
Search PTX4 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with PTX4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PTX4 Gene

Publications for PTX4 Gene

  1. Evolution of the pentraxin family: the new entry PTX4. (PMID: 20357257) Martinez de la Torre Y … Garlanda C (Journal of immunology (Baltimore, Md. : 1950) 2010) 3 4
  2. Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16. (PMID: 11157797) Daniels RJ … Higgs DR (Human molecular genetics 2001) 3 4
  3. Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. (PMID: 22504420) Estrada K … Rivadeneira F (Nature genetics 2012) 3
  4. The sequence and analysis of duplication-rich human chromosome 16. (PMID: 15616553) Martin J … Pennacchio LA (Nature 2004) 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 4

Products for PTX4 Gene

Sources for PTX4 Gene