Xcl1 X-C motif chemokine ligand 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Xcl1provided by RGD
Official Full Name: X-C motif chemokine ligand 1provided by RGD
Primary source: RGD:620452
See related: EnsemblRapid:ENSRNOG00000002964 AllianceGenome:RGD:620452
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: Ltn; Scyc1
Summary: Predicted to enable CCR chemokine receptor binding activity; chemokine activity; and protein homodimerization activity. Predicted to be involved in several processes, including positive regulation of leukocyte migration; regulation of alpha-beta T cell activation; and regulation of gene expression. Predicted to act upstream of or within chemotaxis; establishment of localization in cell; and release of sequestered calcium ion into cytosol. Predicted to be active in extracellular space. Biomarker of anti-basement membrane glomerulonephritis. Orthologous to several human genes including XCL1 (X-C motif chemokine ligand 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Spleen (RPKM 62.9), Heart (RPKM 58.8) and 6 other tissues See more
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Genomic context

Location:: 13q23

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (79781784..79785440, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (77248687..77252343, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (83199402..83202845, complement)

Chromosome 13 - NC_086031.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Rat cytomegalovirus-encoded gamma-chemokine vXCL1 is a highly adapted, species-specific agonist for rat XCR1-positive dendritic cells.
Title: Rat cytomegalovirus-encoded γ-chemokine vXCL1 is a highly adapted, species-specific agonist for rat XCR1-positive dendritic cells.
XCR1 is upregulated at sites of trigeminal nerve injury with a time course that correlates with the development of spontaneous activity at these sites. Exposure of trigeminal brainstem tissue to XCL1 induces expression of c-Fos, pERK and pp38 immunolabeling in trigeminal subnucleus caudalis, and induces increased spontaneous low-threshold activity indicative of hyperexcitability within nociceptive circuitry.
Title: A Novel Role for Lymphotactin (XCL1) Signaling in the Nervous System: XCL1 Acts via its Receptor XCR1 to Increase Trigeminal Neuronal Excitability.
biology of vXCL1 offers an interesting opportunity to study the role of XCL1 and XCR1(+) DC in the cross-presentation of viral antigens
Title: Cytomegalovirus expresses the chemokine homologue vXCL1 capable of attracting XCR1+ CD4- dendritic cells.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables CCR chemokine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables chemokine activity	IBA Inferred from Biological aspect of Ancestor more info
enables chemokine activity	IEA Inferred from Electronic Annotation more info
enables chemokine activity	ISO Inferred from Sequence Orthology more info
enables chemokine receptor binding	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide	IBA Inferred from Biological aspect of Ancestor more info
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide	ISO Inferred from Sequence Orthology more info
involved_in cell chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell signaling	ISO Inferred from Sequence Orthology more info
involved_in cellular response to interleukin-4	IEA Inferred from Electronic Annotation more info
involved_in cellular response to interleukin-4	ISO Inferred from Sequence Orthology more info
involved_in cellular response to transforming growth factor beta stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to transforming growth factor beta stimulus	ISO Inferred from Sequence Orthology more info
involved_in chemokine-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within establishment of localization in cell	ISO Inferred from Sequence Orthology more info
involved_in immune response	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IBA Inferred from Biological aspect of Ancestor more info
involved_in mature natural killer cell chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in mature natural killer cell chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of CD4-positive, alpha-beta T cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of T cell cytokine production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of T-helper 1 cell activation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of interleukin-2 production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of type II interferon production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of B cell chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of B cell chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of CD4-positive, alpha-beta T cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of CD4-positive, alpha-beta T cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of CD8-positive, alpha-beta T cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of T cell chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell cytokine production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell mediated cytotoxicity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T-helper 1 cell cytokine production	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of T-helper 1 cell cytokine production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T-helper 2 cell cytokine production	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of T-helper 2 cell cytokine production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of granzyme A production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of granzyme B production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of immunoglobulin production in mucosal tissue	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of immunoglobulin production in mucosal tissue	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-10 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of leukocyte chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of natural killer cell chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of natural killer cell chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neutrophil chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of neutrophil chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of release of sequestered calcium ion into cytosol	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of thymocyte migration	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of thymocyte migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transforming growth factor beta production	ISO Inferred from Sequence Orthology more info
involved_in regulation of inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in release of sequestered calcium ion into cytosol	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within release of sequestered calcium ion into cytosol	ISO Inferred from Sequence Orthology more info
involved_in release of sequestered calcium ion into cytosol	ISO Inferred from Sequence Orthology more info
involved_in response to virus	ISO Inferred from Sequence Orthology more info
involved_in signal transduction	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IEA Inferred from Electronic Annotation more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: lymphotactin

Names: c motif chemokine 1; chemokine (C motif) ligand 1; cytokine SCM-1; small inducible cytokine subfamily C, member 1 (lymphotactin); small-inducible cytokine C1

NCBI Reference Sequences (RefSeq)

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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.