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

Gene ID: 24772, updated on 9-Oct-2018

Summary

Official Symbol
Cxcl12provided by RGD
Official Full Name
C-X-C motif chemokine ligand 12provided by RGD
Primary source
RGD:3651
See related
Ensembl: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

Genomic context

See Cxcl12 in Genome Data Viewer
Location:
4q42
Exon count:
4
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (149261044..149273891)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 4 NC_005103.3 (215195689..215208536)

Chromosome 4 - NC_005103.4Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108350751 Neighboring gene uncharacterized LOC108350876 Neighboring gene uncharacterized LOC102548743 Neighboring gene similar to ubiquitin-conjugating enzyme E2M

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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

General gene information

Markers

Homology

Gene Ontology Provided by RGD

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

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)
    AABR07061848, CK475409, CV081127
    Conserved Domains (1) summary
    cd00273
    Location:2788
    Chemokine_CXC; 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 ...
  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)
    AABR07061848, AF217564, CK475409
    UniProtKB/TrEMBL
    Q80YV8
    Related
    ENSRNOP00000059574.1, ENSRNOT00000066670.3
    Conserved Domains (1) summary
    cd00273
    Location:2788
    Chemokine_CXC; 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 ...
  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; 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 ...

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005103.4 Reference Rnor_6.0 Primary Assembly

    Range
    149261044..149273891
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate Rn_Celera

Genomic

  1. AC_000072.1 Alternate Rn_Celera

    Range
    139267343..139280188
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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