Human Gene PF4V1 (ENST00000226524.4_4) from GENCODE V47lift37
  Description: platelet factor 4 variant 1 (from RefSeq NM_002620.4)
Gencode Transcript: ENST00000226524.4_4
Gencode Gene: ENSG00000109272.4_7
Transcript (Including UTRs)
   Position: hg19 chr4:74,719,013-74,720,200 Size: 1,188 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr4:74,719,080-74,719,839 Size: 760 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:74,719,013-74,720,200)mRNA (may differ from genome)Protein (104 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PF4V_HUMAN
DESCRIPTION: RecName: Full=Platelet factor 4 variant; AltName: Full=C-X-C motif chemokine 4 variant; AltName: Full=CXCL4L1; AltName: Full=PF4alt; AltName: Full=PF4var1; Contains: RecName: Full=Platelet factor 4 variant(4-74); Contains: RecName: Full=Platelet factor 4 variant(5-74); Contains: RecName: Full=Platelet factor 4 variant(6-74); Flags: Precursor;
FUNCTION: Inhibitor of angiogenesis. Inhibitor of endothelial cell chemotaxis (in vitro).
SUBCELLULAR LOCATION: Secreted.
PTM: The N-terminal processed forms of platelet factor 4 variant seems to be produced by proteolytic cleavage. The most abundant form is Platelet factor 4 variant(5-74).
MASS SPECTROMETRY: Mass=8250.9; Method=Electrospray; Range=31-104; Note=Platelet factor 4 variant; Source=PubMed:15459074;
MASS SPECTROMETRY: Mass=7877.7; Method=Electrospray; Range=34-104; Note=Platelet factor 4 variant(4-74); Source=PubMed:15459074;
MASS SPECTROMETRY: Mass=7805.8; Method=Electrospray; Range=35-104; Note=Platelet factor 4 variant(5-74); Source=PubMed:15459074;
MASS SPECTROMETRY: Mass=7678.6; Method=Electrospray; Range=36-104; Note=Platelet factor 4 variant(6-74); Source=PubMed:15459074;
SIMILARITY: Belongs to the intercrine alpha (chemokine CxC) family.

-  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


-  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: 1.43 RPKM in Spleen
Total median expression: 5.30 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 -19.2067-0.287 Picture PostScript Text
3' UTR -60.80361-0.168 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

ModBase Predicted Comparative 3D Structure on P10720
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    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005125 cytokine activity
GO:0008009 chemokine activity
GO:0008201 heparin binding
GO:0045236 CXCR chemokine receptor binding

Biological Process:
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:0030168 platelet activation
GO:0030595 leukocyte chemotaxis
GO:0032496 response to lipopolysaccharide
GO:0042127 regulation of cell proliferation
GO:0070098 chemokine-mediated signaling pathway
GO:0090023 positive regulation of neutrophil chemotaxis

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space


-  Descriptions from all associated GenBank mRNAs
  LP896311 - Sequence 1175 from Patent EP3253886.
JD461107 - Sequence 442131 from Patent EP1572962.
BC130653 - Homo sapiens platelet factor 4 variant 1, mRNA (cDNA clone MGC:163525 IMAGE:40146684), complete cds.
BC130657 - Homo sapiens platelet factor 4 variant 1, mRNA (cDNA clone MGC:163529 IMAGE:40146688), complete cds.
HQ258042 - Synthetic construct Homo sapiens clone IMAGE:100072351 platelet factor 4 variant 1 (PF4V1) gene, encodes complete protein.
KJ891782 - Synthetic construct Homo sapiens clone ccsbBroadEn_01176 PF4V1 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: A1L4S0, CXCL4V1, ENST00000226524.1, ENST00000226524.2, ENST00000226524.3, NM_002620, P10720, PF4V_HUMAN, SCYB4V1, uc317dlw.1, uc317dlw.2
UCSC ID: ENST00000226524.4_4
RefSeq Accession: NM_002620.4
Protein: P10720 (aka PF4V_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.