Human Gene CXCL12 (ENST00000343575.11_9) from GENCODE V47lift37
  Description: C-X-C motif chemokine ligand 12, transcript variant 1 (from RefSeq NM_199168.4)
Gencode Transcript: ENST00000343575.11_9
Gencode Gene: ENSG00000107562.18_13
Transcript (Including UTRs)
   Position: hg19 chr10:44,872,515-44,880,545 Size: 8,031 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr10:44,874,081-44,880,453 Size: 6,373 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:44,872,515-44,880,545)mRNA (may differ from genome)Protein (89 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SDF1_HUMAN
DESCRIPTION: RecName: Full=Stromal cell-derived factor 1; Short=SDF-1; Short=hSDF-1; AltName: Full=C-X-C motif chemokine 12; AltName: Full=Intercrine reduced in hepatomas; Short=IRH; Short=hIRH; AltName: Full=Pre-B cell growth-stimulating factor; Short=PBSF; Contains: RecName: Full=SDF-1-beta(3-72); Contains: RecName: Full=SDF-1-alpha(3-67); Flags: Precursor;
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 another C-X-C chemokine receptor CXCR7, 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 CXCR7, 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 CXCR7 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.
SUBUNIT: 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 CXCR7.
SUBCELLULAR LOCATION: Secreted.
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.
DEVELOPMENTAL STAGE: Isoform Alpha is ubiquitously expressed in fetal tissues. Isoform Beta and isoform Delta have more limited expression patterns, with highest levels detected in fetal spleen and fetal liver, respectively. Isoform Gamma and isoform Theta are weakly detected in fetal kidney.
PTM: 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.
MASS SPECTROMETRY: Mass=7959; Method=Electrospray; Range=22-89 (P48061-2); Source=PubMed:14525775;
MASS SPECTROMETRY: Mass=7606; Method=Electrospray; Range=24-88 (P48061-2); Source=PubMed:14525775;
MASS SPECTROMETRY: Mass=8522; Method=Electrospray; Range=22-93 (P48061-1); Source=PubMed:14525775;
MASS SPECTROMETRY: Mass=8297; Method=Electrospray; Range=24-93 (P48061-1); Source=PubMed:14525775;
SIMILARITY: Belongs to the intercrine alpha (chemokine CxC) family.
SEQUENCE CAUTION: Sequence=CAC10202.1; Type=Erroneous gene model prediction;
WEB RESOURCE: Name=Wikipedia; Note=SDF-1 entry; URL="http://en.wikipedia.org/wiki/SDF-1_%28biology%29";
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/cxcl12/";

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: CXCL12
Diseases sorted by gene-association score: hiv-1* (300), aids dementia complex (29), whim syndrome (26), ischemia (15), macular retinal edema (10), bursitis (9), type 1 diabetes mellitus 10 (9), lymphoplasmacytic lymphoma (8), acute t cell leukemia (8), agammaglobulinemia (8), myocardial infarction (7), retinal ischemia (7), central nervous system lymphoma (7), corneal neovascularization (7), clivus chordoma (7), limb ischemia (7), intraocular lymphoma (7), macroglobulinemia (7), primary central nervous system lymphoma (6), avoidant personality disorder (6), pelvic inflammatory disease (5), microvascular complications of diabetes 1 (5), cd45 deficiency (4), rheumatoid arthritis (4), retinal hemangioblastoma (4), chronic lymphocytic leukemia (3), breast cancer (3), primary immunodeficiency disease (3), kidney cancer (2), asthma (2), multiple myeloma (2), hematologic cancer (2), pulmonary fibrosis, idiopathic (1), colorectal cancer (1), human immunodeficiency virus infectious disease (1), lymphoma, non-hodgkin (1), leukemia, acute myeloid (0)
* = Manually curated disease association

-  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: 45.51 RPKM in Spleen
Total median expression: 489.20 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 -18.6092-0.202 Picture PostScript Text
3' UTR -489.601566-0.313 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
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
1A15 - X-ray 1QG7 - X-ray MuPIT 1SDF - NMR MuPIT 1VMC - NMR MuPIT 2J7Z - X-ray MuPIT 2K01 - NMR MuPIT 2K03 - NMR MuPIT 2K04 - NMR MuPIT 2K05 - NMR MuPIT 2KEC - NMR MuPIT 2KED - NMR MuPIT 2KEE - NMR MuPIT 2KOL - NMR MuPIT 2NWG - X-ray MuPIT 2SDF - NMR MuPIT 3GV3 - X-ray MuPIT 3HP3 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P48061
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-  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    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005125 cytokine activity
GO:0005178 integrin binding
GO:0008009 chemokine activity
GO:0008083 growth factor activity
GO:0042056 chemoattractant activity
GO:0042379 chemokine receptor binding
GO:0045236 CXCR chemokine receptor binding

Biological Process:
GO:0001666 response to hypoxia
GO:0001764 neuron migration
GO:0001938 positive regulation of endothelial cell proliferation
GO:0006874 cellular calcium ion homeostasis
GO:0006935 chemotaxis
GO:0006952 defense response
GO:0006955 immune response
GO:0007155 cell adhesion
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0007411 axon guidance
GO:0007420 brain development
GO:0008015 blood circulation
GO:0008064 regulation of actin polymerization or depolymerization
GO:0008284 positive regulation of cell proliferation
GO:0008344 adult locomotory behavior
GO:0009314 response to radiation
GO:0009408 response to heat
GO:0009612 response to mechanical stimulus
GO:0009615 response to virus
GO:0010469 regulation of receptor activity
GO:0010818 T cell chemotaxis
GO:0022029 telencephalon cell migration
GO:0030335 positive regulation of cell migration
GO:0031100 animal organ regeneration
GO:0031640 killing of cells of other organism
GO:0033603 positive regulation of dopamine secretion
GO:0033622 integrin activation
GO:0043434 response to peptide hormone
GO:0045666 positive regulation of neuron differentiation
GO:0045785 positive regulation of cell adhesion
GO:0048842 positive regulation of axon extension involved in axon guidance
GO:0050918 positive chemotaxis
GO:0050930 induction of positive chemotaxis
GO:0050965 detection of temperature stimulus involved in sensory perception of pain
GO:0050966 detection of mechanical stimulus involved in sensory perception of pain
GO:0051924 regulation of calcium ion transport
GO:0060326 cell chemotaxis
GO:0070098 chemokine-mediated signaling pathway
GO:0090026 positive regulation of monocyte chemotaxis
GO:0090280 positive regulation of calcium ion import
GO:1902230 negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage
GO:1903237 negative regulation of leukocyte tethering or rolling
GO:1990478 response to ultrasound
GO:2000406 positive regulation of T cell migration
GO:2000669 negative regulation of dendritic cell apoptotic process

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0009897 external side of plasma membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  DQ345519 - Homo sapiens stromal cell-derived factor 1 epsilon mRNA, complete cds.
DQ345520 - Homo sapiens stromal cell-derived factor 1 theta mRNA, complete cds.
LF207354 - JP 2014500723-A/14857: Polycomb-Associated Non-Coding RNAs.
U16752 - Human cytokine SDF-1-beta mRNA, complete cds.
E09669 - cDNA encoding human SDF-1 beta.
FB357022 - Sequence 907 from Patent WO2006128141.
L36033 - Human pre-B cell stimulating factor homologue (SDF1b) mRNA, complete cds.
LF213908 - JP 2014500723-A/21411: Polycomb-Associated Non-Coding RNAs.
AK311814 - Homo sapiens cDNA, FLJ92075, Homo sapiens chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1) (CXCL12), mRNA.
DQ345518 - Homo sapiens stromal cell-derived factor 1 gamma mRNA, complete cds.
AB385200 - Synthetic construct DNA, clone: pF1KB9267, Homo sapiens CXCL12 gene for stromal cell-derived factor 1 precursor, complete cds, without stop codon, in Flexi system.
AY644456 - Homo sapiens stromal cell-derived factor 1 gamma (CXCL12) mRNA, complete cds.
AB463489 - Synthetic construct DNA, clone: pF1KE0197, Homo sapiens CXCL12 gene for chemokine (C-X-C motif) ligand 12, without stop codon, in Flexi system.
AJ227905 - Homo sapiens partial mRNA; ID ED66-5A.
BC039893 - Homo sapiens chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1), mRNA (cDNA clone MGC:47612 IMAGE:5729604), complete cds.
E09668 - cDNA encoding human SDF-1 alpha.
L36034 - Human pre-B cell stimulating factor homologue (SDF1a) mRNA, complete cds.
U19495 - Human intercrine-alpha (hIRH) mRNA, complete cds.
BC031072 - Homo sapiens chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1), mRNA (cDNA clone IMAGE:5314832).
DQ345517 - Homo sapiens stromal cell-derived factor 1 delta mRNA, complete cds.
LF365329 - JP 2014500723-A/172832: Polycomb-Associated Non-Coding RNAs.
LF365328 - JP 2014500723-A/172831: Polycomb-Associated Non-Coding RNAs.
LF365327 - JP 2014500723-A/172830: Polycomb-Associated Non-Coding RNAs.
AY874118 - Homo sapiens stromal cell-derived factor 1a mRNA, complete cds.
AK292628 - Homo sapiens cDNA FLJ76575 complete cds, highly similar to Homo sapiens chemokine (C-X-C motif) ligand 12 (stromalcell-derived factor 1) (CXCL12), mRNA.
CR450283 - Homo sapiens full open reading frame cDNA clone RZPDo834A051D for gene CXCL12, chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1); complete cds; without stopcodon.
AK090482 - Homo sapiens mRNA for FLJ00404 protein.
LF212068 - JP 2014500723-A/19571: Polycomb-Associated Non-Coding RNAs.
LF213056 - JP 2014500723-A/20559: Polycomb-Associated Non-Coding RNAs.
JD487711 - Sequence 468735 from Patent EP1572962.
JD394920 - Sequence 375944 from Patent EP1572962.
MA449485 - JP 2018138019-A/21411: Polycomb-Associated Non-Coding RNAs.
MA600906 - JP 2018138019-A/172832: Polycomb-Associated Non-Coding RNAs.
MA600905 - JP 2018138019-A/172831: Polycomb-Associated Non-Coding RNAs.
MA600904 - JP 2018138019-A/172830: Polycomb-Associated Non-Coding RNAs.
MA442931 - JP 2018138019-A/14857: Polycomb-Associated Non-Coding RNAs.
MA447645 - JP 2018138019-A/19571: Polycomb-Associated Non-Coding RNAs.
MA448633 - JP 2018138019-A/20559: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_cxcr4Pathway - CXCR4 Signaling Pathway
h_Ccr5Pathway - Pertussis toxin-insensitive CCR5 Signaling in Macrophage

Reactome (by CSHL, EBI, and GO)

Protein P48061 (Reactome details) participates in the following event(s):

R-HSA-374214 Receptors CXCR4 and 7 bind CXCL12 ligand
R-HSA-8986258 SLIT2:ROBO1 binds CXCR4
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-1251985 Nuclear signaling by ERBB4
R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-376176 Signaling by ROBO receptors
R-HSA-418594 G alpha (i) signalling events
R-HSA-375276 Peptide ligand-binding receptors
R-HSA-1236394 Signaling by ERBB4
R-HSA-8939211 ESR-mediated signaling
R-HSA-422475 Axon guidance
R-HSA-388396 GPCR downstream signalling
R-HSA-373076 Class A/1 (Rhodopsin-like receptors)
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-1266738 Developmental Biology
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: B2R4G0, E7EVL0, ENST00000343575.1, ENST00000343575.10, ENST00000343575.2, ENST00000343575.3, ENST00000343575.4, ENST00000343575.5, ENST00000343575.6, ENST00000343575.7, ENST00000343575.8, ENST00000343575.9, H7BYN8, NM_199168, P48061, Q2L985, Q2L986, Q2L988, Q5IT36, Q6ICW0, Q9H554, SDF1, SDF1A, SDF1B, SDF1_HUMAN, uc317wro.1, uc317wro.2
UCSC ID: ENST00000343575.11_9
RefSeq Accession: NM_199168.4
Protein: P48061 (aka SDF1_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.