Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CXCL12 Gene

Aliases for CXCL12 Gene

  • C-X-C Motif Chemokine Ligand 12 2 3 5
  • Pre-B Cell Growth-Stimulating Factor 3 4
  • Chemokine (C-X-C Motif) Ligand 12 2 3
  • Intercrine Reduced In Hepatomas 3 4
  • Stromal Cell-Derived Factor 1 2 3
  • SDF1 3 4
  • PBSF 3 4
  • IRH 3 4
  • C-X-C Motif Chemokine 12 4
  • SCYB12 3
  • HSDF-1 4
  • TPAR1 3
  • SDF1A 4
  • SDF1B 4
  • SDF-1 4
  • TLSF 3
  • HIRH 4

External Ids for CXCL12 Gene

Previous HGNC Symbols for CXCL12 Gene

  • SDF1A
  • SDF1B
  • SDF1

Previous GeneCards Identifiers for CXCL12 Gene

  • GC10M044154
  • GC10M044640
  • GC10M044149
  • GC10M044185
  • GC10M044865
  • GC10M041391

Summaries for CXCL12 Gene

Entrez Gene Summary for CXCL12 Gene

  • This antimicrobial gene encodes a stromal cell-derived alpha chemokine member of the intercrine family. The encoded protein functions as the ligand for the G-protein coupled receptor, chemokine (C-X-C motif) receptor 4, and plays a role in many diverse cellular functions, including embryogenesis, immune surveillance, inflammation response, tissue homeostasis, and tumor growth and metastasis. Mutations in this gene are associated with resistance to human immunodeficiency virus type 1 infections. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]

GeneCards Summary for CXCL12 Gene

CXCL12 (C-X-C Motif Chemokine Ligand 12) is a Protein Coding gene. Diseases associated with CXCL12 include Hiv-1 and Aids Dementia Complex. Among its related pathways are Signaling by GPCR and Peptide ligand-binding receptors. GO annotations related to this gene include receptor binding and chemokine activity.

UniProtKB/Swiss-Prot for CXCL12 Gene

  • Chemoattractant active on T-lymphocytes, monocytes, but not neutrophils. Activates the C-X-C chemokine receptor CXCR4 to induce a rapid and transient rise in the level of intracellular calcium ions and chemotaxis. Also binds to atypical chemokine receptor ACKR3, which activates the beta-arrestin pathway and acts as a scavenger receptor for SDF-1. SDF-1-beta(3-72) and SDF-1-alpha(3-67) show a reduced chemotactic activity. Binding to cell surface proteoglycans seems to inhibit formation of SDF-1-alpha(3-67) and thus to preserve activity on local sites. Acts as a positive regulator of monocyte migration and a negative regulator of monocyte adhesion via the LYN kinase. Stimulates migration of monocytes and T-lymphocytes through its receptors, CXCR4 and ACKR3, and decreases monocyte adherence to surfaces coated with ICAM-1, a ligand for beta-2 integrins. SDF1A/CXCR4 signaling axis inhibits beta-2 integrin LFA-1 mediated adhesion of monocytes to ICAM-1 through LYN kinase. Inhibits CXCR4-mediated infection by T-cell line-adapted HIV-1. Plays a protective role after myocardial infarction. Induces down-regulation and internalization of ACKR3 expressed in various cells. Has several critical functions during embryonic development; required for B-cell lymphopoiesis, myelopoiesis in bone marrow and heart ventricular septum formation.

Gene Wiki entry for CXCL12 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CXCL12 Gene

Genomics for CXCL12 Gene

Regulatory Elements for CXCL12 Gene

Enhancers for CXCL12 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10F043689 1.5 FANTOM5 Ensembl ENCODE 10.8 +696.5 696470 2.0 ELF3 ATF1 PKNOX1 ZNF133 KLF17 ZNF2 RAD21 ZNF121 GLIS2 ZNF143 ZNF32 CXCL12 PIR60234 ENSG00000228426
GH10F044878 1.5 FANTOM5 Ensembl ENCODE 9.9 -492.6 -492640 1.7 SREBF2 ZNF335 ZNF121 GLIS2 ZNF366 ZNF143 KLF7 FOS KLF13 EGR2 TMEM72 ENSG00000234504 ENSG00000223462 AGAP10P CXCL12 AGAP4 EIF2AP4
GH10F044479 1.3 Ensembl ENCODE 10.5 -92.7 -92699 1.6 HDGF ATF1 SIN3A ZNF48 YY1 ELK1 GATA2 ZNF143 PAF1 SP5 CXCL12 ENSG00000270767 RPL9P21
GH10F044309 1.2 Ensembl ENCODE 10.6 +75.7 75693 2.4 HDGF ATF1 CREB3L1 GATA2 ZNF143 FOS KLF13 ZNF263 REST ZNF610 ZNF32-AS2 ZNF32-AS1 CXCL12 LOC101929465 PIR52448
GH10F044300 1.2 Ensembl ENCODE 10.4 +85.1 85096 2.4 PKNOX1 SIN3A FEZF1 ZNF207 FOS SP3 ZHX2 JUNB TSHZ1 TBX21 CXCL12 LOC101929465 PIR52448
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CXCL12 on UCSC Golden Path with GeneCards custom track

Genomic Location for CXCL12 Gene

Chromosome:
10
Start:
44,370,153 bp from pter
End:
44,386,493 bp from pter
Size:
16,341 bases
Orientation:
Minus strand

Genomic View for CXCL12 Gene

Genes around CXCL12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CXCL12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CXCL12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CXCL12 Gene

Proteins for CXCL12 Gene

  • Protein details for CXCL12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P48061-SDF1_HUMAN
    Recommended name:
    Stromal cell-derived factor 1
    Protein Accession:
    P48061
    Secondary Accessions:
    • B2R4G0
    • E7EVL0
    • H7BYN8
    • Q2L985
    • Q2L986
    • Q2L988
    • Q5IT36
    • Q6ICW0
    • Q9H554

    Protein attributes for CXCL12 Gene

    Size:
    93 amino acids
    Molecular mass:
    10666 Da
    Quaternary structure:
    • Monomer or homodimer; in equilibrium. Dimer formation is induced by non acidic pH and the presence of multivalent anions, and by binding to CXCR4 or heparin. Monomeric form is required for full chemotactic activity and resistance to ischemia/reperfusion injury, whereas the dimeric form acts as a partial agonist of CXCR4, stimulating Ca2+ mobilization but with no chemotactic activity and instead acts as a selective antagonist that blocks chemotaxis induced by the monomeric form. Interacts with the N-terminus of ACKR3.
    SequenceCaution:
    • Sequence=CAC10202.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CXCL12 Gene

    Alternative splice isoforms for CXCL12 Gene

neXtProt entry for CXCL12 Gene

Post-translational modifications for CXCL12 Gene

  • Processed forms SDF-1-beta(3-72) and SDF-1-alpha(3-67) are produced after secretion by proteolytic cleavage of isoforms Beta and Alpha, respectively. The N-terminal processing is probably achieved by DPP4. Isoform Alpha is first cleaved at the C-terminus to yield a SDF-1-alpha(1-67) intermediate before being processed at the N-terminus. The C-terminal processing of isoform Alpha is reduced by binding to heparin and, probably, cell surface proteoglycans.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • R&D Systems Antibodies for CXCL12 (CXCL12/SDF-1 beta)
  • R&D Systems Antibodies for CXCL12 (CXCL12/SDF-1)
  • Cell Signaling Technology (CST) Antibodies for CXCL12 (CXCL12)

Protein Products

No data available for DME Specific Peptides for CXCL12 Gene

Domains & Families for CXCL12 Gene

Gene Families for CXCL12 Gene

Protein Domains for CXCL12 Gene

Graphical View of Domain Structure for InterPro Entry

P48061

UniProtKB/Swiss-Prot:

SDF1_HUMAN :
  • Belongs to the intercrine alpha (chemokine CxC) family.
Family:
  • Belongs to the intercrine alpha (chemokine CxC) family.
genes like me logo Genes that share domains with CXCL12: view

Function for CXCL12 Gene

Molecular function for CXCL12 Gene

UniProtKB/Swiss-Prot Function:
Chemoattractant active on T-lymphocytes, monocytes, but not neutrophils. Activates the C-X-C chemokine receptor CXCR4 to induce a rapid and transient rise in the level of intracellular calcium ions and chemotaxis. Also binds to atypical chemokine receptor ACKR3, which activates the beta-arrestin pathway and acts as a scavenger receptor for SDF-1. SDF-1-beta(3-72) and SDF-1-alpha(3-67) show a reduced chemotactic activity. Binding to cell surface proteoglycans seems to inhibit formation of SDF-1-alpha(3-67) and thus to preserve activity on local sites. Acts as a positive regulator of monocyte migration and a negative regulator of monocyte adhesion via the LYN kinase. Stimulates migration of monocytes and T-lymphocytes through its receptors, CXCR4 and ACKR3, and decreases monocyte adherence to surfaces coated with ICAM-1, a ligand for beta-2 integrins. SDF1A/CXCR4 signaling axis inhibits beta-2 integrin LFA-1 mediated adhesion of monocytes to ICAM-1 through LYN kinase. Inhibits CXCR4-mediated infection by T-cell line-adapted HIV-1. Plays a protective role after myocardial infarction. Induces down-regulation and internalization of ACKR3 expressed in various cells. Has several critical functions during embryonic development; required for B-cell lymphopoiesis, myelopoiesis in bone marrow and heart ventricular septum formation.

Gene Ontology (GO) - Molecular Function for CXCL12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 receptor binding TAS 10358157
GO:0005125 cytokine activity IEA --
GO:0008009 chemokine activity IDA,TAS 12782716
GO:0008083 growth factor activity IEA --
GO:0042056 chemoattractant activity IBA --
genes like me logo Genes that share ontologies with CXCL12: view
genes like me logo Genes that share phenotypes with CXCL12: view

Animal Models for CXCL12 Gene

MGI Knock Outs for CXCL12:

Animal Model Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CXCL12 Gene

Localization for CXCL12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CXCL12 Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CXCL12 gene
Compartment Confidence
extracellular 5
plasma membrane 4
cytoskeleton 2
nucleus 2
cytosol 2
mitochondrion 1
endoplasmic reticulum 1
lysosome 1
endosome 1

Gene Ontology (GO) - Cellular Components for CXCL12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IEA --
GO:0005737 cytoplasm IEA --
GO:0005886 plasma membrane IEA --
GO:0009897 external side of plasma membrane IBA --
genes like me logo Genes that share ontologies with CXCL12: view

Pathways & Interactions for CXCL12 Gene

SuperPathways for CXCL12 Gene

SuperPathway Contained pathways
1 Apoptotic Pathways in Synovial Fibroblasts
2 PEDF Induced Signaling
3 GPCR Pathway
4 Chemokine Superfamily Pathway: Human/Mouse Ligand-Receptor Interactions
5 ERK Signaling
genes like me logo Genes that share pathways with CXCL12: view

SIGNOR curated interactions for CXCL12 Gene

Activates:

Gene Ontology (GO) - Biological Process for CXCL12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IEA --
GO:0001764 neuron migration IEA --
GO:0001938 positive regulation of endothelial cell proliferation IEA --
GO:0006874 cellular calcium ion homeostasis TAS 10772939
GO:0006935 chemotaxis TAS 12782716
genes like me logo Genes that share ontologies with CXCL12: view

Drugs & Compounds for CXCL12 Gene

(67) Drugs for CXCL12 Gene - From: DrugBank, PharmGKB, ClinicalTrials, DGIdb, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
rituximab Approved Pharma Therapeutic Antibodies 1654
Cyclophosphamide Approved, Investigational Pharma Nitrogen mustard alkylating agent and prodrug. 2829
Dexamethasone Approved, Investigational, Vet_approved Pharma Agonist 2084
Tinzaparin Approved Pharma Target, binder 37
alemtuzumab Approved, Investigational Pharma Therapeutic Antibodies 303

(48) Additional Compounds for CXCL12 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CXCL12: view

Transcripts for CXCL12 Gene

Unigene Clusters for CXCL12 Gene

Chemokine (C-X-C motif) ligand 12:
Representative Sequences:

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CXCL12 Gene

No ASD Table

Relevant External Links for CXCL12 Gene

GeneLoc Exon Structure for
CXCL12
ECgene alternative splicing isoforms for
CXCL12

Expression for CXCL12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CXCL12 Gene

Protein differential expression in normal tissues from HIPED for CXCL12 Gene

This gene is overexpressed in Urine (29.5) and Bone marrow mesenchymal stem cell (17.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CXCL12 Gene



Protein tissue co-expression partners for CXCL12 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CXCL12 Gene:

CXCL12

SOURCE GeneReport for Unigene cluster for CXCL12 Gene:

Hs.522891

mRNA Expression by UniProt/SwissProt for CXCL12 Gene:

P48061-SDF1_HUMAN
Tissue specificity: Isoform Alpha and isoform Beta are ubiquitously expressed, with highest levels detected in liver, pancreas and spleen. Isoform Gamma is mainly expressed in heart, with weak expression detected in several other tissues. Isoform Delta, isoform Epsilon and isoform Theta have highest expression levels in pancreas, with lower levels detected in heart, kidney, liver and spleen.
genes like me logo Genes that share expression patterns with CXCL12: view

No data available for mRNA differential expression in normal tissues for CXCL12 Gene

Orthologs for CXCL12 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CXCL12 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CXCL12 35
  • 100 (a)
OneToOne
LOC741624 34
  • 83.18 (n)
cow
(Bos Taurus)
Mammalia CXCL12 34 35
  • 88.64 (n)
dog
(Canis familiaris)
Mammalia CXCL12 34 35
  • 88.64 (n)
mouse
(Mus musculus)
Mammalia Cxcl12 34 16 35
  • 82.22 (n)
rat
(Rattus norvegicus)
Mammalia Cxcl12 34
  • 81.59 (n)
oppossum
(Monodelphis domestica)
Mammalia CXCL12 35
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CXCL12 35
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves CXCL12 34 35
  • 79.45 (n)
lizard
(Anolis carolinensis)
Reptilia CXCL12 35
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cxcl12 34
  • 70.72 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC68770 34
zebrafish
(Danio rerio)
Actinopterygii cxcl12a 35
  • 42 (a)
OneToMany
cxcl12b 35
  • 42 (a)
OneToMany
Species where no ortholog for CXCL12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CXCL12 Gene

ENSEMBL:
Gene Tree for CXCL12 (if available)
TreeFam:
Gene Tree for CXCL12 (if available)

Paralogs for CXCL12 Gene

(10) SIMAP similar genes for CXCL12 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with CXCL12: view

No data available for Paralogs for CXCL12 Gene

Variants for CXCL12 Gene

Sequence variations from dbSNP and Humsavar for CXCL12 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs387906400 other 44,378,102(-) CTGTG(A/G)CACTC intron-variant, utr-variant-3-prime
rs1023265 -- 44,379,440(-) GAGAT(C/T)CAGAG intron-variant
rs1029153 -- 44,371,698(-) AGTGA(C/T)GTAAT intron-variant, utr-variant-3-prime
rs10347 -- 44,370,304(-) AGGNC(A/G)ATTCC intron-variant, utr-variant-3-prime
rs10400003 -- 44,315,481(+) gagaa(C/T)tgctt intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CXCL12 Gene

Variant ID Type Subtype PubMed ID
nsv1038511 CNV loss 25217958
nsv1054649 CNV gain 25217958
nsv1068306 CNV deletion 25765185
nsv483001 CNV loss 15286789
nsv550699 CNV gain 21841781
nsv550700 CNV gain 21841781
nsv825357 CNV gain 20364138

Variation tolerance for CXCL12 Gene

Residual Variation Intolerance Score: 64.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.53; 11.56% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CXCL12 Gene

Human Gene Mutation Database (HGMD)
CXCL12
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CXCL12

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CXCL12 Gene

Disorders for CXCL12 Gene

MalaCards: The human disease database

(33) MalaCards diseases for CXCL12 Gene - From: OMIM, ClinVar, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
hiv-1
  • aids, slow progression to
aids dementia complex
  • adc
whim syndrome
  • warts, hypogammaglobulinemia, infections, and myelokathexis
ischemia
acute t cell leukemia
  • precursor t lymphoblastic leukemia
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for CXCL12

Genetic Association Database (GAD)
CXCL12
Human Genome Epidemiology (HuGE) Navigator
CXCL12
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CXCL12
genes like me logo Genes that share disorders with CXCL12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CXCL12 Gene

Publications for CXCL12 Gene

  1. Structure and chromosomal localization of the human stromal cell- derived factor 1 (SDF1) gene. (PMID: 7490086) Shirozu M. … Honjo T. (Genomics 1995) 2 3 4 22 64
  2. HIV infection and host genetic mutation among injecting drug-users of northeastern states of India. (PMID: 20411675) Sarkar K. … Chakraborti S. (J Health Popul Nutr 2010) 3 22 46 64
  3. CXCL12 rs1801157 polymorphism in patients with breast cancer, Hodgkin's lymphoma, and non-Hodgkin's lymphoma. (PMID: 19927352) de Oliveira K.B. … Watanabe M.A. (J. Clin. Lab. Anal. 2009) 3 22 46 64
  4. Analysis of CCR5, CCR2, SDF1 and RANTES gene polymorphisms in subjects with HIV-related PML and not determined leukoencephalopathy. (PMID: 17560067) Guerini F.R. … Ferrante P. (Biomed. Pharmacother. 2008) 3 22 46 64
  5. Plasma stromal cell-derived factor-1: host derived marker predictive of distant metastasis in breast cancer. (PMID: 18223219) Hassan S. … Basik M. (Clin. Cancer Res. 2008) 3 22 46 64

Products for CXCL12 Gene

Sources for CXCL12 Gene

Content
Loading form....