Atlas of Genetics and Cytogenetics in Oncology and Haematology


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XCL1 (X-C motif chemokine ligand 1)

Identity

Alias_namesLTN
SCYC1
small inducible cytokine subfamily C, member 1 (lymphotactin)
chemokine (C motif) ligand 1
Alias_symbol (synonym)LPTN
ATAC
SCM-1a
SCM-1
Other aliasSCM1
SCM1A
HGNC (Hugo) XCL1
LocusID (NCBI) 6375
Atlas_Id 52145
Location 1q24.2  [Link to chromosome band 1q24]
Location_base_pair Starts at 168576473 and ends at 168582077 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)XCL1   10645
Cards
Entrez_Gene (NCBI)XCL1  6375  X-C motif chemokine ligand 1
AliasesATAC; LPTN; LTN; SCM-1; 
SCM-1a; SCM1; SCM1A; SCYC1
GeneCards (Weizmann)XCL1
Ensembl hg19 (Hinxton)ENSG00000143184 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000143184 [Gene_View]  ENSG00000143184 [Sequence]  chr1:168576473-168582077 [Contig_View]  XCL1 [Vega]
ICGC DataPortalENSG00000143184
TCGA cBioPortalXCL1
AceView (NCBI)XCL1
Genatlas (Paris)XCL1
WikiGenes6375
SOURCE (Princeton)XCL1
Genetics Home Reference (NIH)XCL1
Genomic and cartography
GoldenPath hg38 (UCSC)XCL1  -     chr1:168576473-168582077 +  1q24.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)XCL1  -     1q24.2   [Description]    (hg19-Feb_2009)
EnsemblXCL1 - 1q24.2 [CytoView hg19]  XCL1 - 1q24.2 [CytoView hg38]
Mapping of homologs : NCBIXCL1 [Mapview hg19]  XCL1 [Mapview hg38]
OMIM600250   
Gene and transcription
Genbank (Entrez)BC069817 BC070309 BF433809 D43768 U23772
RefSeq transcript (Entrez)NM_002995
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)XCL1
Cluster EST : UnigeneHs.546295 [ NCBI ]
CGAP (NCI)Hs.546295
Alternative Splicing GalleryENSG00000143184
Gene ExpressionXCL1 [ NCBI-GEO ]   XCL1 [ EBI - ARRAY_EXPRESS ]   XCL1 [ SEEK ]   XCL1 [ MEM ]
Gene Expression Viewer (FireBrowse)XCL1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6375
GTEX Portal (Tissue expression)XCL1
Human Protein AtlasENSG00000143184-XCL1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP47992   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP47992  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP47992
Splice isoforms : SwissVarP47992
PhosPhoSitePlusP47992
Domains : Interpro (EBI)Chemokine_IL8-like_dom    Chemokine_XCL1/XCL2    Interleukin_8-like_sf   
Domain families : Pfam (Sanger)IL8 (PF00048)   
Domain families : Pfam (NCBI)pfam00048   
Domain families : Smart (EMBL)SCY (SM00199)  
Conserved Domain (NCBI)XCL1
DMDM Disease mutations6375
Blocks (Seattle)XCL1
PDB (SRS)1J8I    1J9O    2HDM    2JP1    2N54    2NYZ   
PDB (PDBSum)1J8I    1J9O    2HDM    2JP1    2N54    2NYZ   
PDB (IMB)1J8I    1J9O    2HDM    2JP1    2N54    2NYZ   
PDB (RSDB)1J8I    1J9O    2HDM    2JP1    2N54    2NYZ   
Structural Biology KnowledgeBase1J8I    1J9O    2HDM    2JP1    2N54    2NYZ   
SCOP (Structural Classification of Proteins)1J8I    1J9O    2HDM    2JP1    2N54    2NYZ   
CATH (Classification of proteins structures)1J8I    1J9O    2HDM    2JP1    2N54    2NYZ   
SuperfamilyP47992
Human Protein Atlas [tissue]ENSG00000143184-XCL1 [tissue]
Peptide AtlasP47992
HPRD02595
IPIIPI00026979   
Protein Interaction databases
DIP (DOE-UCLA)P47992
IntAct (EBI)P47992
FunCoupENSG00000143184
BioGRIDXCL1
STRING (EMBL)XCL1
ZODIACXCL1
Ontologies - Pathways
QuickGOP47992
Ontology : AmiGOpositive regulation of T cell mediated cytotoxicity  monocyte chemotaxis  positive regulation of leukocyte chemotaxis  negative regulation of T cell cytokine production  positive regulation of T cell cytokine production  negative regulation of T-helper 1 type immune response  extracellular region  extracellular space  extracellular space  cell  inflammatory response  signal transduction  G-protein coupled receptor signaling pathway  G-protein coupled receptor signaling pathway  cell-cell signaling  chemokine activity  chemokine activity  response to virus  regulation of signaling receptor activity  positive regulation of T cell chemotaxis  positive regulation of T cell chemotaxis  neutrophil chemotaxis  neutrophil chemotaxis  negative regulation of interferon-gamma production  negative regulation of interleukin-2 production  positive regulation of interleukin-10 production  mature natural killer cell chemotaxis  chemokine receptor binding  chemokine receptor binding  protein homodimerization activity  negative regulation of DNA-binding transcription factor activity  positive regulation of GTPase activity  negative regulation of transcription, DNA-templated  CCR chemokine receptor binding  lymphocyte chemotaxis  regulation of inflammatory response  release of sequestered calcium ion into cytosol  positive regulation of release of sequestered calcium ion into cytosol  chemokine-mediated signaling pathway  positive regulation of ERK1 and ERK2 cascade  cellular response to interferon-gamma  cellular response to interleukin-1  cellular response to interleukin-4  cellular response to tumor necrosis factor  cellular response to transforming growth factor beta stimulus  positive regulation of transforming growth factor beta production  positive regulation of granzyme B production  positive regulation of neutrophil chemotaxis  positive regulation of thymocyte migration  positive regulation of natural killer cell chemotaxis  positive regulation of granzyme A production  negative regulation of T-helper 1 cell activation  positive regulation of B cell chemotaxis  positive regulation of T-helper 2 cell cytokine production  positive regulation of T-helper 1 cell cytokine production  positive regulation of immunoglobulin production in mucosal tissue  negative regulation of CD4-positive, alpha-beta T cell proliferation  positive regulation of CD4-positive, alpha-beta T cell proliferation  positive regulation of CD8-positive, alpha-beta T cell proliferation  
Ontology : EGO-EBIpositive regulation of T cell mediated cytotoxicity  monocyte chemotaxis  positive regulation of leukocyte chemotaxis  negative regulation of T cell cytokine production  positive regulation of T cell cytokine production  negative regulation of T-helper 1 type immune response  extracellular region  extracellular space  extracellular space  cell  inflammatory response  signal transduction  G-protein coupled receptor signaling pathway  G-protein coupled receptor signaling pathway  cell-cell signaling  chemokine activity  chemokine activity  response to virus  regulation of signaling receptor activity  positive regulation of T cell chemotaxis  positive regulation of T cell chemotaxis  neutrophil chemotaxis  neutrophil chemotaxis  negative regulation of interferon-gamma production  negative regulation of interleukin-2 production  positive regulation of interleukin-10 production  mature natural killer cell chemotaxis  chemokine receptor binding  chemokine receptor binding  protein homodimerization activity  negative regulation of DNA-binding transcription factor activity  positive regulation of GTPase activity  negative regulation of transcription, DNA-templated  CCR chemokine receptor binding  lymphocyte chemotaxis  regulation of inflammatory response  release of sequestered calcium ion into cytosol  positive regulation of release of sequestered calcium ion into cytosol  chemokine-mediated signaling pathway  positive regulation of ERK1 and ERK2 cascade  cellular response to interferon-gamma  cellular response to interleukin-1  cellular response to interleukin-4  cellular response to tumor necrosis factor  cellular response to transforming growth factor beta stimulus  positive regulation of transforming growth factor beta production  positive regulation of granzyme B production  positive regulation of neutrophil chemotaxis  positive regulation of thymocyte migration  positive regulation of natural killer cell chemotaxis  positive regulation of granzyme A production  negative regulation of T-helper 1 cell activation  positive regulation of B cell chemotaxis  positive regulation of T-helper 2 cell cytokine production  positive regulation of T-helper 1 cell cytokine production  positive regulation of immunoglobulin production in mucosal tissue  negative regulation of CD4-positive, alpha-beta T cell proliferation  positive regulation of CD4-positive, alpha-beta T cell proliferation  positive regulation of CD8-positive, alpha-beta T cell proliferation  
Pathways : KEGGCytokine-cytokine receptor interaction    Chemokine signaling pathway   
NDEx NetworkXCL1
Atlas of Cancer Signalling NetworkXCL1
Wikipedia pathwaysXCL1
Orthology - Evolution
OrthoDB6375
GeneTree (enSembl)ENSG00000143184
Phylogenetic Trees/Animal Genes : TreeFamXCL1
HOVERGENP47992
HOGENOMP47992
Homologs : HomoloGeneXCL1
Homology/Alignments : Family Browser (UCSC)XCL1
Gene fusions - Rearrangements
Fusion : QuiverXCL1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerXCL1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)XCL1
dbVarXCL1
ClinVarXCL1
1000_GenomesXCL1 
Exome Variant ServerXCL1
ExAC (Exome Aggregation Consortium)ENSG00000143184
GNOMAD BrowserENSG00000143184
Varsome BrowserXCL1
Genetic variants : HAPMAP6375
Genomic Variants (DGV)XCL1 [DGVbeta]
DECIPHERXCL1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisXCL1 
Mutations
ICGC Data PortalXCL1 
TCGA Data PortalXCL1 
Broad Tumor PortalXCL1
OASIS PortalXCL1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICXCL1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDXCL1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch XCL1
DgiDB (Drug Gene Interaction Database)XCL1
DoCM (Curated mutations)XCL1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)XCL1 (select a term)
intoGenXCL1
Cancer3DXCL1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600250   
Orphanet
DisGeNETXCL1
MedgenXCL1
Genetic Testing Registry XCL1
NextProtP47992 [Medical]
TSGene6375
GENETestsXCL1
Target ValidationXCL1
Huge Navigator XCL1 [HugePedia]
snp3D : Map Gene to Disease6375
BioCentury BCIQXCL1
ClinGenXCL1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6375
Chemical/Pharm GKB GenePA35575
Clinical trialXCL1
Miscellaneous
canSAR (ICR)XCL1 (select the gene name)
Probes
Litterature
PubMed56 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineXCL1
EVEXXCL1
GoPubMedXCL1
iHOPXCL1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Mon Aug 27 12:02:04 CEST 2018

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