Human Gene PTX3 (ENST00000295927.4_4) from GENCODE V47lift37
  Description: pentraxin 3 (from RefSeq NM_002852.4)
Gencode Transcript: ENST00000295927.4_4
Gencode Gene: ENSG00000163661.4_7
Transcript (Including UTRs)
   Position: hg19 chr3:157,154,639-157,161,422 Size: 6,784 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr3:157,154,723-157,160,768 Size: 6,046 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:157,154,639-157,161,422)mRNA (may differ from genome)Protein (381 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTX3_HUMAN
DESCRIPTION: RecName: Full=Pentraxin-related protein PTX3; AltName: Full=Pentaxin-related protein PTX3; AltName: Full=Tumor necrosis factor alpha-induced protein 5; Short=TNF alpha-induced protein 5; AltName: Full=Tumor necrosis factor-inducible gene 14 protein; Short=TSG-14; Flags: Precursor;
FUNCTION: Plays a role in the regulation of innate resistance to pathogens, inflammatory reactions, possibly clearance of self- components and female fertility (By similarity).
SUBUNIT: Homooctamer; disulfide-linked. Binds to C1q (By similarity).
SUBCELLULAR LOCATION: Secreted.
INDUCTION: By IL1B/interleukin-1 beta and TNF.
PTM: Glycosylated (Probable).
SIMILARITY: Contains 1 pentaxin domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PTX3
Diseases sorted by gene-association score: infectious myocarditis (8), hyper-igd syndrome (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1116.21 RPKM in Cells - Cultured fibroblasts
Total median expression: 1346.28 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -14.0084-0.167 Picture PostScript Text
3' UTR -135.70654-0.207 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp
IPR001759 - Pentaxin

Pfam Domains:
PF00354 - Pentaxin family
PF13385 - Concanavalin A-like lectin/glucanases superfamily

SCOP Domains:
49899 - Concanavalin A-like lectins/glucanases

ModBase Predicted Comparative 3D Structure on P26022
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001849 complement component C1q binding
GO:0001872 (1->3)-beta-D-glucan binding
GO:0005515 protein binding
GO:0042802 identical protein binding
GO:0046790 virion binding

Biological Process:
GO:0001878 response to yeast
GO:0006954 inflammatory response
GO:0008228 opsonization
GO:0043312 neutrophil degranulation
GO:0044869 negative regulation by host of viral exo-alpha-sialidase activity
GO:0044871 negative regulation by host of viral glycoprotein metabolic process
GO:0045087 innate immune response
GO:0045429 positive regulation of nitric oxide biosynthetic process
GO:0046597 negative regulation of viral entry into host cell
GO:0050766 positive regulation of phagocytosis
GO:1903016 negative regulation of exo-alpha-sialidase activity
GO:1903019 negative regulation of glycoprotein metabolic process

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0035580 specific granule lumen
GO:1904724 tertiary granule lumen


-  Descriptions from all associated GenBank mRNAs
  AK312705 - Homo sapiens cDNA, FLJ93104, highly similar to Homo sapiens pentaxin-related gene, rapidly induced by IL-1 beta (PTX3), mRNA.
BC039733 - Homo sapiens pentraxin-related gene, rapidly induced by IL-1 beta, mRNA (cDNA clone MGC:47747 IMAGE:5768379), complete cds.
X63613 - H.sapiens mRNA for pentaxin (PTX3).
BC027887 - Homo sapiens pentraxin-related gene, rapidly induced by IL-1 beta, mRNA (cDNA clone IMAGE:5222167), containing frame-shift errors.
M31166 - Human tumor necrosis factor-inducible (TSG-14) mRNA, complete cds.
X63053 - H.sapiens PTX3 mRNA.
AB590531 - Synthetic construct DNA, clone: pFN21AE1862, Homo sapiens PTX3 gene for pentraxin-related gene, rapidly induced by IL-1 beta, without stop codon, in Flexi system.
KJ897428 - Synthetic construct Homo sapiens clone ccsbBroadEn_06822 PTX3 gene, encodes complete protein.
JD524526 - Sequence 505550 from Patent EP1572962.
JD162571 - Sequence 143595 from Patent EP1572962.
JD550903 - Sequence 531927 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P26022 (Reactome details) participates in the following event(s):

R-HSA-6798749 Exocytosis of specific granule lumen proteins
R-HSA-6798745 Exocytosis of tertiary granule lumen proteins
R-HSA-6798695 Neutrophil degranulation
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B2R6T6, ENST00000295927.1, ENST00000295927.2, ENST00000295927.3, NM_002852, P26022, PTX3 , PTX3_HUMAN, Q38M82, TNFAIP5, TSG14, uc317lps.1, uc317lps.2
UCSC ID: ENST00000295927.4_4
RefSeq Accession: NM_002852.4
Protein: P26022 (aka PTX3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.