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Aliases for CXCL12 Gene

Aliases for CXCL12 Gene

  • Chemokine (C-X-C Motif) Ligand 12 2 3
  • SDF1 3 4 6
  • Pre-B Cell Growth-Stimulating Factor 3 4
  • Intercrine Reduced In Hepatomas 3 4
  • Stromal Cell-Derived Factor 1 2 3
  • 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 (Chemokine (C-X-C Motif) Ligand 12) is a Protein Coding gene. Diseases associated with CXCL12 include retinal hemangioblastoma and whim syndrome. Among its related pathways are PI-3K cascade and Signaling by GPCR. 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

Genomic Location for CXCL12 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Proteomics data for CXCL12 Gene at MOPED

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

Other Protein References for CXCL12 Gene

No data available for DME Specific Peptides for CXCL12 Gene

Domains for CXCL12 Gene

Gene Families for CXCL12 Gene

HGNC:

Protein Domains for CXCL12 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

P48061

UniProtKB/Swiss-Prot:

SDF1_HUMAN :
  • P48061
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:0008009 chemokine activity TAS 12782716
GO:0008083 growth factor activity IEA --
GO:0042379 chemokine receptor binding IMP 22457824
GO:0045236 CXCR chemokine receptor binding IDA 20388803
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:

miRNA for CXCL12 Gene

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for CXCL12 Gene

Localization for CXCL12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CXCL12 Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CXCL12 Gene COMPARTMENTS Subcellular localization image for CXCL12 gene
Compartment Confidence
extracellular 5
cytoskeleton 2
nucleus 2
plasma membrane 2
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:0005886 plasma membrane --
GO:0009897 external side of plasma membrane IEA --
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with CXCL12: view

Pathways for CXCL12 Gene

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

Gene Ontology (GO) - Biological Process for CXCL12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001569 patterning of blood vessels IEA --
GO:0001666 response to hypoxia IEA --
GO:0001667 ameboidal-type cell migration IEA --
GO:0001764 neuron migration IEA --
GO:0001938 positive regulation of endothelial cell proliferation IEA --
genes like me logo Genes that share ontologies with CXCL12: view

Compounds for CXCL12 Gene

(1) Drugbank Compounds for CXCL12 Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Tinzaparin
9041-08-1 target binder

(88) Novoseek inferred chemical compound relationships for CXCL12 Gene

Compound -log(P) Hits PubMed IDs
sdf 1 95 192
rantes 84.6 138
bicyclam 79.1 8
plerixafor 77.1 5
teck 74.5 6
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:

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 for CXCL12 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for CXCL12 Gene

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 expressions 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 36
  • 100 (a)
OneToOne
LOC741624 35
  • 83.18 (n)
  • 80.37 (a)
cow
(Bos Taurus)
Mammalia CXCL12 35
  • 88.64 (n)
  • 92.05 (a)
CXCL12 36
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CXCL12 35
  • 88.64 (n)
  • 93.18 (a)
CXCL12 36
  • 76 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Cxcl12 35
  • 82.22 (n)
  • 80.95 (a)
Cxcl12 16
Cxcl12 36
  • 71 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CXCL12 36
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CXCL12 36
  • 76 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Cxcl12 35
  • 81.59 (n)
  • 80 (a)
chicken
(Gallus gallus)
Aves CXCL12 35
  • 79.45 (n)
  • 83.56 (a)
CXCL12 36
  • 52 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CXCL12 36
  • 69 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia MGC68770 35
tropical clawed frog
(Silurana tropicalis)
Amphibia cxcl12 35
  • 70.72 (n)
  • 75.68 (a)
zebrafish
(Danio rerio)
Actinopterygii cxcl12a 36
  • 42 (a)
OneToMany
cxcl12b 36
  • 42 (a)
OneToMany
Species with no ortholog for CXCL12:
  • 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

Selected 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 MAF
rs2522 -- 44,371,856(+) AACCC(A/G)CAAGT utr-variant-3-prime
rs7777 -- 44,370,289(-) CGCAG(C/T)GTGCT utr-variant-3-prime
rs10347 -- 44,370,304(-) AGGNC(A/G)ATTCC utr-variant-3-prime
rs169097 -- 44,372,635(+) TTTGC(A/C/G/T)GGGCC utr-variant-3-prime
rs197452 -- 44,374,792(+) GGATC(C/T)GGGTG intron-variant

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

Variant ID Type Subtype PubMed ID
nsv825357 CNV Gain 20364138
nsv895089 CNV Gain 21882294
dgv645n71 CNV Gain 21882294
dgv646n71 CNV Loss 21882294
dgv647n71 CNV Loss 21882294
nsv895095 CNV Gain+Loss 21882294
nsv895098 CNV Loss 21882294
dgv648n71 CNV Loss 21882294

Relevant External Links for CXCL12 Gene

HapMap Linkage Disequilibrium report
CXCL12
Human Gene Mutation Database (HGMD)
CXCL12

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

Disorders for CXCL12 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (14) Diseases for CXCL12 Gene including...

Search for CXCL12 Gene in MalaCards »

(1) OMIM Diseases for CXCL12 Gene (600835)

(94) Novoseek inferred disease relationships for CXCL12 Gene

Disease -log(P) Hits PubMed IDs
whim syndrome 80.4 2
neovascularization 66.6 29
immunodeficiency 65.3 44
metastasis 62.8 161
tumors 51 159

Relevant External Links for CXCL12

Genetic Association Database (GAD)
CXCL12
Human Genome Epidemiology (HuGE) Navigator
CXCL12
genes like me logo Genes that share disorders with CXCL12: view

No data available for UniProtKB/Swiss-Prot 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 23
  2. The CXC chemokine SDF-1 is the ligand for LESTR/fusin and prevents infection by T-cell-line-adapted HIV-1. (PMID: 8752281) Oberlin E. … Moser B. (Nature 1996) 3 4 23
  3. Solution structure and basis for functional activity of stromal cell- derived factor-1; dissociation of CXCR4 activation from binding and inhibition of HIV-1. (PMID: 9384579) Crump M.P. … Clark-Lewis I. (EMBO J. 1997) 3 4 23
  4. Associations of CCR5, CCR2, and stromal cell-derived factor 1 genotypes with human immunodeficiency virus disease progression in patients receiving nucleoside therapy. (PMID: 11709782) Lathey J.L. … Katzenstein D.A. (J. Infect. Dis. 2001) 3 23 48
  5. Association between the SDF1-3'A allele and high levels of CD34(+) progenitor cells mobilized into peripheral blood in humans. (PMID: 11328308) Benboubker L. … Domenech J. (Br. J. Haematol. 2001) 3 23 48

Products for CXCL12 Gene

Sources for CXCL12 Gene

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