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Cxcl12 C-X-C motif chemokine ligand 12 [ Rattus norvegicus (Norway rat) ]

Gene ID: 24772, updated on 28-Nov-2021

Summary

Official Symbol
Cxcl12provided by RGD
Official Full Name
C-X-C motif chemokine ligand 12provided by RGD
Primary source
RGD:3651
See related
EnsemblRapid:ENSRNOG00000013589
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Sdf1
Summary
a chemoattractant molecule; involved in cell migration [RGD, Feb 2006]
Expression
Biased expression in Spleen (RPKM 358.2), Liver (RPKM 284.3) and 9 other tissues See more
Orthologs
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Genomic context

See Cxcl12 in Genome Data Viewer
Location:
4q42
Exon count:
4
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (150388326..150401173)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (149261044..149273891)

Chromosome 4 - NC_051339.1Genomic Context describing neighboring genes Neighboring gene uncharacterized protein C9orf85 homolog Neighboring gene uncharacterized LOC108350876 Neighboring gene uncharacterized LOC120102371 Neighboring gene uncharacterized LOC102548743 Neighboring gene small nucleolar RNA SNORA48

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables CXCR chemokine receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables CXCR chemokine receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables chemokine activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables chemokine activity ISO
Inferred from Sequence Orthology
more info
 
enables chemokine activity TAS
Traceable Author Statement
more info
PubMed 
enables chemokine receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables growth factor activity IEA
Inferred from Electronic Annotation
more info
 
enables integrin binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in T cell chemotaxis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within T cell proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in adult locomotory behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within ameboidal-type cell migration ISO
Inferred from Sequence Orthology
more info
 
involved_in animal organ regeneration IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide ISO
Inferred from Sequence Orthology
more info
 
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in brain development IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within brain development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within branching involved in blood vessel morphogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in cell chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell chemotaxis ISO
Inferred from Sequence Orthology
more info
 
involved_in cell migration TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within cell-cell adhesion ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to chemokine ISO
Inferred from Sequence Orthology
more info
 
involved_in chemokine (C-X-C motif) ligand 12 signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in chemokine-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in chemokine-mediated signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in defense response IEA
Inferred from Electronic Annotation
more info
 
involved_in detection of mechanical stimulus involved in sensory perception of pain IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in detection of temperature stimulus involved in sensory perception of pain IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in dopaminergic neuron differentiation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within germ cell development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within germ cell migration ISO
Inferred from Sequence Orthology
more info
 
involved_in immune response IEA
Inferred from Electronic Annotation
more info
 
involved_in induction of positive chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within induction of positive chemotaxis ISO
Inferred from Sequence Orthology
more info
 
involved_in integrin activation ISO
Inferred from Sequence Orthology
more info
 
involved_in killing of cells of other organism ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within motor neuron axon guidance ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of cell population proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of dendritic cell apoptotic process ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of leukocyte tethering or rolling ISO
Inferred from Sequence Orthology
more info
 
involved_in neuron migration IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within positive regulation of ERK1 and ERK2 cascade ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of T cell migration ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of axon extension involved in axon guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of calcium ion import ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of cell adhesion ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of cell migration ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of chemotaxis ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of dopamine secretion IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of endothelial cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of monocyte chemotaxis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of myoblast fusion ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of protein kinase B signaling ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of calcium ion transport IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within regulation of cell migration ISO
Inferred from Sequence Orthology
more info
 
involved_in response to heat IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to hypoxia IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to mechanical stimulus IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to peptide hormone IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to radiation IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to ultrasound IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in telencephalon cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in external side of plasma membrane ISO
Inferred from Sequence Orthology
more info
 
located_in extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
stromal cell-derived factor 1
Names
SDF-1 gamma
chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1)
stromal cell-derived factor-1 gamma

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001033882.1NP_001029054.1  stromal cell-derived factor 1 isoform beta precursor

    See identical proteins and their annotated locations for NP_001029054.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an internal exon and uses an alternate penultimate exon, compared to variant 1, resulting in a novel 3' coding region and 3' UTR. It encodes isoform beta which is longer and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    CK475409, CV081127, JACYVU010000149
    Conserved Domains (1) summary
    cd00273
    Location:2788
    Chemokine_CXC; 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; many members contain an RCxC motif ...
  2. NM_001033883.1NP_001029055.1  stromal cell-derived factor 1 isoform gamma precursor

    See identical proteins and their annotated locations for NP_001029055.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate 3' structure compared to variant 1, resulting in a novel 3' coding region and longer 3' UTR. It encodes isoform gamma which is longer and has a distinct C-terminus, compared to isoform alpha.
    Source sequence(s)
    AF217564, CK475409, JACYVU010000149
    UniProtKB/TrEMBL
    Q80YV8
    Related
    ENSRNOP00000059574.1, ENSRNOT00000066670.4
    Conserved Domains (1) summary
    cd00273
    Location:2788
    Chemokine_CXC; 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; many members contain an RCxC motif ...
  3. NM_022177.3NP_071513.1  stromal cell-derived factor 1 isoform alpha precursor

    See identical proteins and their annotated locations for NP_071513.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the isoform alpha.
    Source sequence(s)
    AF209976, BC078737, CK475409
    UniProtKB/TrEMBL
    Q9QZD1
    Conserved Domains (1) summary
    cd00273
    Location:2788
    Chemokine_CXC; 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; many members contain an RCxC motif ...

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051339.1 Reference mRatBN7.2 Primary Assembly

    Range
    150388326..150401173
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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