Human Gene PPBP (uc003hhj.3)
  Description: Homo sapiens pro-platelet basic protein (chemokine (C-X-C motif) ligand 7) (PPBP), mRNA.
RefSeq Summary (NM_002704): The protein encoded by this gene is a platelet-derived growth factor that belongs to the CXC chemokine family. This growth factor is a potent chemoattractant and activator of neutrophils. It has been shown to stimulate various cellular processes including DNA synthesis, mitosis, glycolysis, intracellular cAMP accumulation, prostaglandin E2 secretion, and synthesis of hyaluronic acid and sulfated glycosaminoglycan. It also stimulates the formation and secretion of plasminogen activator by synovial cells. The protein also is an antimicrobial protein with bactericidal and antifungal activity. [provided by RefSeq, Nov 2014]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Transcript (Including UTRs)
   Position: hg19 chr4:74,852,156-74,853,907 Size: 1,752 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr4:74,852,989-74,853,820 Size: 832 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:74,852,156-74,853,907)mRNA (may differ from genome)Protein (128 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CXCL7_HUMAN
DESCRIPTION: RecName: Full=Platelet basic protein; Short=PBP; AltName: Full=C-X-C motif chemokine 7; AltName: Full=Leukocyte-derived growth factor; Short=LDGF; AltName: Full=Macrophage-derived growth factor; Short=MDGF; AltName: Full=Small-inducible cytokine B7; Contains: RecName: Full=Connective tissue-activating peptide III; Short=CTAP-III; AltName: Full=LA-PF4; AltName: Full=Low-affinity platelet factor IV; Contains: RecName: Full=TC-2; Contains: RecName: Full=Connective tissue-activating peptide III(1-81); Short=CTAP-III(1-81); Contains: RecName: Full=Beta-thromboglobulin; Short=Beta-TG; Contains: RecName: Full=Neutrophil-activating peptide 2(74); Short=NAP-2(74); Contains: RecName: Full=Neutrophil-activating peptide 2(73); Short=NAP-2(73); Contains: RecName: Full=Neutrophil-activating peptide 2; Short=NAP-2; Contains: RecName: Full=TC-1; Contains: RecName: Full=Neutrophil-activating peptide 2(1-66); Short=NAP-2(1-66); Contains: RecName: Full=Neutrophil-activating peptide 2(1-63); Short=NAP-2(1-63); Flags: Precursor;
FUNCTION: LA-PF4 stimulates DNA synthesis, mitosis, glycolysis, intracellular cAMP accumulation, prostaglandin E2 secretion, and synthesis of hyaluronic acid and sulfated glycosaminoglycan. It also stimulates the formation and secretion of plasminogen activator by human synovial cells. NAP-2 is a ligand for CXCR1 and CXCR2, and NAP-2, NAP-2(73), NAP-2(74), NAP-2(1-66), and most potent NAP-2(1-63) are chemoattractants and activators for neutrophils. TC-1 and TC-2 are antibacterial proteins, in vitro released from activated platelet alpha-granules. CTAP-III(1-81) is more potent than CTAP-III desensitize chemokine-induced neutrophil activation.
SUBUNIT: Beta-thromboglobulin is a homotetramer.
SUBCELLULAR LOCATION: Secreted.
PTM: Proteolytic removal of residues 1-9 produces the active peptide connective tissue-activating peptide III (CTAP-III) (low- affinity platelet factor IV (LA-PF4)).
PTM: Proteolytic removal of residues 1-13 produces the active peptide beta-thromboglobulin, which is released from platelets along with platelet factor 4 and platelet-derived growth factor.
PTM: NAP-2(1-66) is produced by proteolytical processing, probably after secretion by leukocytes other than neutrophils.
PTM: NAP-2(73) and NAP-2(74) seem not be produced by proteolytical processing of secreted precursors but are released in an active form from platelets.
SIMILARITY: Belongs to the intercrine alpha (chemokine CxC) family.
WEB RESOURCE: Name=Wikipedia; Note=CXCL7 entry; URL="http://en.wikipedia.org/wiki/CXCL7";

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PPBP
CDC HuGE Published Literature: PPBP
Positive Disease Associations: Blood Vessels
Related Studies:
  1. Blood Vessels
    Ramachandran S Vasan et al. BMC medical genetics 2007, Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study., BMC medical genetics. [PubMed 17903301]
    In hypothesis-generating GWAS of echocardiography, ETT and BA vascular function in a moderate-sized community-based sample, we identified several SNPs that are candidates for replication attempts and we provide a web-based GWAS resource for the research community.
  2. Blood Vessels
    Ramachandran S Vasan et al. BMC medical genetics 2007, Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study., BMC medical genetics. [PubMed 17903301]
    In hypothesis-generating GWAS of echocardiography, ETT and BA vascular function in a moderate-sized community-based sample, we identified several SNPs that are candidates for replication attempts and we provide a web-based GWAS resource for the research community.

-  MalaCards Disease Associations
  MalaCards Gene Search: PPBP
Diseases sorted by gene-association score: erythromelalgia (8), essential thrombocythemia (5), colloid adenoma (4), peripheral vascular disease (4), atrial fibrillation (3), hemorrhagic disease (3), asthma (2), vascular disease (2), migraine with or without aura 1 (2), hypertension, essential (2), myocardial infarction (2), stroke, ischemic (2), listeria meningitis (1), thrombotic thrombocytopenic purpura, acquired (0)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 46.84 RPKM in Whole Blood
Total median expression: 85.75 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 -16.9087-0.194 Picture PostScript Text
3' UTR -156.14833-0.187 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
IPR001089 - Chemokine_CXC
IPR018048 - Chemokine_CXC_CS
IPR002473 - Chemokine_CXCL8/IL8
IPR001811 - Chemokine_IL8-like_dom

Pfam Domains:
PF00048 - Small cytokines (intecrine/chemokine), interleukin-8 like

SCOP Domains:
54117 - Interleukin 8-like chemokines

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1F9P - X-ray 1NAP - X-ray MuPIT 1TVX - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P02775
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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005125 cytokine activity
GO:0005355 glucose transmembrane transporter activity
GO:0008009 chemokine activity
GO:0008083 growth factor activity
GO:0045236 CXCR chemokine receptor binding

Biological Process:
GO:0002576 platelet degranulation
GO:0006935 chemotaxis
GO:0006952 defense response
GO:0006954 inflammatory response
GO:0006955 immune response
GO:0007186 G-protein coupled receptor signaling pathway
GO:0010469 regulation of receptor activity
GO:0031640 killing of cells of other organism
GO:0032496 response to lipopolysaccharide
GO:0042127 regulation of cell proliferation
GO:0042742 defense response to bacterium
GO:0043312 neutrophil degranulation
GO:0051781 positive regulation of cell division
GO:0060326 cell chemotaxis
GO:0070098 chemokine-mediated signaling pathway
GO:0090023 positive regulation of neutrophil chemotaxis
GO:1904659 glucose transmembrane transport

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0031091 platelet alpha granule
GO:0031093 platelet alpha granule lumen
GO:1904724 tertiary granule lumen


-  Descriptions from all associated GenBank mRNAs
  KJ891856 - Synthetic construct Homo sapiens clone ccsbBroadEn_01250 PPBP gene, encodes complete protein.
BC028217 - Homo sapiens pro-platelet basic protein (chemokine (C-X-C motif) ligand 7), mRNA (cDNA clone MGC:40008 IMAGE:5214257), complete cds.
M54995 - Human connective tissue activation peptide III mRNA, complete cds.
JD549288 - Sequence 530312 from Patent EP1572962.
CR456805 - Homo sapiens full open reading frame cDNA clone RZPDo834A1015D for gene PPBP, pro-platelet basic protein (chemokine (C-X-C motif) ligand 7); complete cds, incl. stopcodon.
AK312166 - Homo sapiens cDNA, FLJ92452, Homo sapiens pro-platelet basic protein (chemokine (C-X-C motif)ligand 7) (PPBP), mRNA.
DQ891020 - Synthetic construct clone IMAGE:100003650; FLH168582.01X; RZPDo839A1294D pro-platelet basic protein (chemokine (C-X-C motif) ligand 7) (PPBP) gene, encodes complete protein.
DQ894200 - Synthetic construct Homo sapiens clone IMAGE:100008660; FLH168578.01L; RZPDo839A1293D pro-platelet basic protein (chemokine (C-X-C motif) ligand 7) (PPBP) gene, encodes complete protein.
AB464075 - Synthetic construct DNA, clone: pF1KB6702, Homo sapiens PPBP gene for pro-platelet basic protein, without stop codon, in Flexi system.
JD422839 - Sequence 403863 from Patent EP1572962.
JD289976 - Sequence 271000 from Patent EP1572962.
JD106185 - Sequence 87209 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04060 - Cytokine-cytokine receptor interaction
hsa04062 - Chemokine signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein P02775 (Reactome details) participates in the following event(s):

R-HSA-481007 Exocytosis of platelet alpha granule contents
R-HSA-373813 Receptor CXCR2 binds ligands CXCL1 to 7
R-HSA-6798745 Exocytosis of tertiary granule lumen proteins
R-HSA-749454 The Ligand:GPCR:Gi complex dissociates
R-HSA-749456 Liganded Gi-activating GPCRs bind inactive heterotrimeric G-protein Gi
R-HSA-380073 Liganded Gi-activating GPCR acts as a GEF for Gi
R-HSA-114608 Platelet degranulation
R-HSA-380108 Chemokine receptors bind chemokines
R-HSA-6798695 Neutrophil degranulation
R-HSA-76005 Response to elevated platelet cytosolic Ca2+
R-HSA-418594 G alpha (i) signalling events
R-HSA-375276 Peptide ligand-binding receptors
R-HSA-168249 Innate Immune System
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-388396 GPCR downstream signalling
R-HSA-373076 Class A/1 (Rhodopsin-like receptors)
R-HSA-168256 Immune System
R-HSA-109582 Hemostasis
R-HSA-372790 Signaling by GPCR
R-HSA-500792 GPCR ligand binding
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B2R5F3, CTAP3, CXCL7, CXCL7_HUMAN, NM_002704, NP_002695, P02775, Q6IBJ8, SCYB7, TGB1, THBGB1
UCSC ID: uc003hhj.3
RefSeq Accession: NM_002704
Protein: P02775 (aka CXCL7_HUMAN)
CCDS: CCDS3563.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002704.3
exon count: 3CDS single in 3' UTR: no RNA size: 1307
ORF size: 387CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 974.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.