Human Gene XCL2 (ENST00000367819.3_7) from GENCODE V47lift37
  Description: X-C motif chemokine ligand 2 (from RefSeq NM_003175.4)
Gencode Transcript: ENST00000367819.3_7
Gencode Gene: ENSG00000143185.4_9
Transcript (Including UTRs)
   Position: hg19 chr1:168,510,006-168,513,235 Size: 3,230 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr1:168,510,190-168,513,202 Size: 3,013 Coding Exon Count: 3 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:168,510,006-168,513,235)mRNA (may differ from genome)Protein (114 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: XCL2_HUMAN
DESCRIPTION: RecName: Full=Cytokine SCM-1 beta; AltName: Full=C motif chemokine 2; AltName: Full=XC chemokine ligand 2; Flags: Precursor;
FUNCTION: Chemotactic activity for lymphocytes but not for monocytes or neutrophils (By similarity).
SUBCELLULAR LOCATION: Secreted.
SIMILARITY: Belongs to the intercrine gamma family.
WEB RESOURCE: Name=Wikipedia; Note=XCL2 entry; URL="http://en.wikipedia.org/wiki/XCL2";

-  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: 5.86 RPKM in Spleen
Total median expression: 15.96 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -7.7033-0.233 Picture PostScript Text
3' UTR -21.30184-0.116 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
IPR001811 - Chemokine_IL8-like_dom
IPR008105 - Chemokine_lymphotactin_XCL1

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

SCOP Domains:
54117 - Interleukin 8-like chemokines

ModBase Predicted Comparative 3D Structure on Q9UBD3
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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005125 cytokine activity
GO:0005515 protein binding
GO:0008009 chemokine activity
GO:0048020 CCR chemokine receptor binding

Biological Process:
GO:0002548 monocyte chemotaxis
GO:0006935 chemotaxis
GO:0006954 inflammatory response
GO:0006955 immune response
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0008015 blood circulation
GO:0010469 regulation of receptor activity
GO:0030593 neutrophil chemotaxis
GO:0043547 positive regulation of GTPase activity
GO:0048247 lymphocyte chemotaxis
GO:0070098 chemokine-mediated signaling pathway
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0071346 cellular response to interferon-gamma
GO:0071347 cellular response to interleukin-1
GO:0071356 cellular response to tumor necrosis factor

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


-  Descriptions from all associated GenBank mRNAs
  U23772 - Human lymphotactin precursor mRNA, complete cds.
BC070308 - Homo sapiens chemokine (C motif) ligand 2, mRNA (cDNA clone MGC:88310 IMAGE:30413788), complete cds.
BC069360 - Homo sapiens chemokine (C motif) ligand 2, mRNA (cDNA clone MGC:97475 IMAGE:7262751), complete cds.
CU686769 - Synthetic construct Homo sapiens gateway clone IMAGE:100022545 5' read XCL2 mRNA.
KJ892236 - Synthetic construct Homo sapiens clone ccsbBroadEn_01630 XCL2 gene, encodes complete protein.
AB590623 - Synthetic construct DNA, clone: pFN21AE1607, Homo sapiens XCL2 gene for chemokine (C motif) ligand 2, without stop codon, in Flexi system.

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

Protein Q9UBD3 (Reactome details) participates in the following event(s):

R-HSA-373339 Receptor CXC1 binds to the ligands lymphotactin and cytokine SCM-1 beta
R-HSA-749452 The Ligand:GPCR:Gq complex dissociates
R-HSA-749448 Liganded Gq-activating GPCRs bind inactive heterotrimeric Gq
R-HSA-379048 Liganded Gq/11-activating GPCRs act as GEFs for Gq/11
R-HSA-380108 Chemokine receptors bind chemokines
R-HSA-416476 G alpha (q) signalling events
R-HSA-375276 Peptide ligand-binding receptors
R-HSA-388396 GPCR downstream signalling
R-HSA-373076 Class A/1 (Rhodopsin-like receptors)
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: ENST00000367819.1, ENST00000367819.2, NM_003175, Q9UBD3, SCYC2, uc318gfo.1, uc318gfo.2, XCL2_HUMAN
UCSC ID: ENST00000367819.3_7
RefSeq Accession: NM_003175.4
Protein: Q9UBD3 (aka XCL2_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.