Human Gene CXCL2 (uc003hhm.4)
  Description: Homo sapiens chemokine (C-X-C motif) ligand 2 (CXCL2), mRNA.
RefSeq Summary (NM_002089): This antimicrobial gene is part of a chemokine superfamily that encodes secreted proteins involved in immunoregulatory and inflammatory processes. The superfamily is divided into four subfamilies based on the arrangement of the N-terminal cysteine residues of the mature peptide. This chemokine, a member of the CXC subfamily, is expressed at sites of inflammation and may suppress hematopoietic progenitor cell proliferation. [provided by RefSeq, Sep 2014].
Transcript (Including UTRs)
   Position: hg19 chr4:74,962,754-74,964,997 Size: 2,244 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr4:74,963,473-74,964,837 Size: 1,365 Coding Exon Count: 4 

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 (chr4:74,962,754-74,964,997)mRNA (may differ from genome)Protein (107 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CXCL2_HUMAN
DESCRIPTION: RecName: Full=C-X-C motif chemokine 2; AltName: Full=Growth-regulated protein beta; Short=Gro-beta; AltName: Full=Macrophage inflammatory protein 2-alpha; Short=MIP2-alpha; Contains: RecName: Full=GRO-beta(5-73); AltName: Full=GRO-beta-T; AltName: Full=Hematopoietic synergistic factor; Short=HSF; AltName: Full=SB-251353; Flags: Precursor;
FUNCTION: Produced by activated monocytes and neutrophils and expressed at sites of inflammation. Hematoregulatory chemokine, which, in vitro, suppresses hematopoietic progenitor cell proliferation. GRO-beta(5-73) shows a highly enhanced hematopoietic activity.
SUBCELLULAR LOCATION: Secreted.
PTM: The N-terminal processed form GRO-beta(5-73) is produced by proteolytic cleavage after secretion from bone marrow stromal cells.
PHARMACEUTICAL: GRO-beta(5-73) is available under the name Garnocestim as immunomodulator. It is used prior to hematopoietic transplantation for peripheral blood stem cell mobilization and reduction of incidence, duration, and/or severity of chemotherapy induced cytopenias.
SIMILARITY: Belongs to the intercrine alpha (chemokine CxC) family.
WEB RESOURCE: Name=Wikipedia; Note=CXCL2 entry; URL="http://en.wikipedia.org/wiki/CXCL2";

-  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): CXCL2
CDC HuGE Published Literature: CXCL2
Positive Disease Associations: Leukocyte Count , sepsis , Sepsis|Systemic infection
Related Studies:
  1. Leukocyte Count
    Alexander P Reiner et al. PLoS genetics 2011, Genome-wide association study of white blood cell count in 16,388 African Americans: the continental origins and genetic epidemiology network (COGENT)., PLoS genetics. [PubMed 21738479]
  2. sepsis
    , A CXCL2 tandem repeat promoter polymorphism is associated with susceptibility to severe sepsis in the Spanish population, Genes Immun 2006. [PubMed 16421598]
  3. Sepsis|Systemic infection
    Jesns Villar et al. 2007, A CXCL2 polymorphism is associated with better outcomes in patients with severe sepsis., Critical care medicine 35(10) : 2292-7 2007. [PubMed 17944017]
    Association with mortality of severe sepsis
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CXCL2
Diseases sorted by gene-association score: pneumonia (5), keratitis (4), peritonitis (4), acanthamoeba keratitis (4), stachybotrys chartarum (2), retinitis pigmentosa 73 (2), demyelinating disease (2), nephrogenic systemic fibrosis (2)

-  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: 153.27 RPKM in Liver
Total median expression: 389.40 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 -70.04160-0.438 Picture PostScript Text
3' UTR -178.28719-0.248 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
1QNK - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P19875
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005125 cytokine activity
GO:0005515 protein binding
GO:0008009 chemokine activity
GO:0045236 CXCR chemokine receptor binding

Biological Process:
GO:0002237 response to molecule of bacterial origin
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:0019221 cytokine-mediated signaling pathway
GO:0031640 killing of cells of other organism
GO:0032496 response to lipopolysaccharide
GO:0042127 regulation of cell proliferation
GO:0060326 cell chemotaxis
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
  KJ891302 - Synthetic construct Homo sapiens clone ccsbBroadEn_00696 CXCL2 gene, encodes complete protein.
BC053653 - Homo sapiens chemokine (C-X-C motif) ligand 2, mRNA (cDNA clone IMAGE:5759939), with apparent retained intron.
LQ882874 - Sequence 23 from Patent WO2018160841.
M36820 - Human cytokine (GRO-beta) mRNA, complete cds.
LF206883 - JP 2014500723-A/14386: Polycomb-Associated Non-Coding RNAs.
BC015753 - Homo sapiens chemokine (C-X-C motif) ligand 2, mRNA (cDNA clone MGC:23071 IMAGE:4875789), complete cds.
X53799 - Human mRNA for macrophage inflammatory protein-2alpha (MIP2alpha).
LF213722 - JP 2014500723-A/21225: Polycomb-Associated Non-Coding RNAs.
M57731 - Human gro-beta mRNA, complete cds.
JD314449 - Sequence 295473 from Patent EP1572962.
JD199374 - Sequence 180398 from Patent EP1572962.
LF358960 - JP 2014500723-A/166463: Polycomb-Associated Non-Coding RNAs.
JD546693 - Sequence 527717 from Patent EP1572962.
JD263996 - Sequence 245020 from Patent EP1572962.
LF358959 - JP 2014500723-A/166462: Polycomb-Associated Non-Coding RNAs.
JD073547 - Sequence 54571 from Patent EP1572962.
JD247653 - Sequence 228677 from Patent EP1572962.
JD553627 - Sequence 534651 from Patent EP1572962.
AF043340 - Homo sapiens macrophage inflammatory protein 2 alpha (MIP2a) mRNA, partial cds.
CR542171 - Homo sapiens full open reading frame cDNA clone RZPDo834B0824D for gene CXCL2, chemokine (C-X-C motif) ligand 2; complete cds, incl. stopcodon.
AB590957 - Synthetic construct DNA, clone: pFN21AE1604, Homo sapiens CXCL2 gene for chemokine (C-X-C motif) ligand 2, without stop codon, in Flexi system.
AK311304 - Homo sapiens cDNA, FLJ18346.
BC005276 - Homo sapiens cDNA clone IMAGE:4071652, **** WARNING: chimeric clone ****.
AK308504 - Homo sapiens cDNA, FLJ98545.
CU677427 - Synthetic construct Homo sapiens gateway clone IMAGE:100018489 5' read CXCL2 mRNA.
JD190418 - Sequence 171442 from Patent EP1572962.
MA442460 - JP 2018138019-A/14386: Polycomb-Associated Non-Coding RNAs.
MA449299 - JP 2018138019-A/21225: Polycomb-Associated Non-Coding RNAs.
MA594537 - JP 2018138019-A/166463: Polycomb-Associated Non-Coding RNAs.
MA594536 - JP 2018138019-A/166462: Polycomb-Associated Non-Coding RNAs.
MP584524 - Sequence 23 from Patent WO2020081767.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04060 - Cytokine-cytokine receptor interaction
hsa04062 - Chemokine signaling pathway
hsa04621 - NOD-like receptor signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein P19875 (Reactome details) participates in the following event(s):

R-HSA-373813 Receptor CXCR2 binds ligands CXCL1 to 7
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-380108 Chemokine receptors bind chemokines
R-HSA-6783783 Interleukin-10 signaling
R-HSA-418594 G alpha (i) signalling events
R-HSA-375276 Peptide ligand-binding receptors
R-HSA-449147 Signaling by Interleukins
R-HSA-388396 GPCR downstream signalling
R-HSA-373076 Class A/1 (Rhodopsin-like receptors)
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-372790 Signaling by GPCR
R-HSA-500792 GPCR ligand binding
R-HSA-168256 Immune System
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: CXCL2_HUMAN, GRO2, GROB, MIP2A, NM_002089, NP_002080, P19875, Q6FGD6, Q9UPB8, SCYB2
UCSC ID: uc003hhm.4
RefSeq Accession: NM_002089
Protein: P19875 (aka CXCL2_HUMAN)
CCDS: CCDS34008.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002089.3
exon count: 4CDS single in 3' UTR: no RNA size: 1234
ORF size: 324CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 415.00frame shift in genome: no % Coverage: 97.49
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.