Cxcl13 C-X-C motif chemokine ligand 13 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cxcl13provided by RGD
Official Full Name: C-X-C motif chemokine ligand 13provided by RGD
Primary source: RGD:1564256
See related: Ensembl:ENSRNOG00000024899 AllianceGenome:RGD:1564256
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
Summary: Predicted to enable chemokine receptor binding activity; fibroblast growth factor binding activity; and heparin binding activity. Predicted to be involved in several processes, including cell chemotaxis; regulation of chemotaxis; and response to bacterium. Predicted to act upstream of or within lymph node development. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Orthologous to human CXCL13 (C-X-C motif chemokine ligand 13). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 277.5), Thymus (RPKM 100.5) and 6 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 14p22

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	14	NC_086032.1 (13912858..13917920, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	14	NC_051349.1 (13608894..13613965, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	14	NC_005113.4 (15253146..15258221, complement)

Chromosome 14 - NC_086032.1 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?

CXCL13/CXCR5 promote chronic postsurgical pain and astrocyte activation in rats by targeting NLRP3.
Title: CXCL13/CXCR5 promote chronic postsurgical pain and astrocyte activation in rats by targeting NLRP3.
LncRNA NONRATT009773.2 promotes bone cancer pain progression through the miR-708-5p/CXCL13 axis.
Title: LncRNA NONRATT009773.2 promotes bone cancer pain progression through the miR-708-5p/CXCL13 axis.
The roles of chemokine (C-X-C motif) ligand 13 in spinal cord ischemia-reperfusion injury in rats.
Title: The roles of chemokine (C-X-C motif) ligand 13 in spinal cord ischemia-reperfusion injury in rats.
Study highlighted the contribution of IL-17 pathway in the trafficking of CXCL13-induced GluN2B-containing N-methyl-d-aspartate receptor in the pathogenesis of remifentanil-induced hyperalgesia.
Title: CXCL13 regulates the trafficking of GluN2B-containing NMDA receptor via IL-17 in the development of remifentanil-induced hyperalgesia in rats.
Up-regulated CXCL13 has a negative role in morphine analgesia in relief of CIBP, which may provide a new target for the management of CIBP.
Title: Upregulation of (C-X-C motif) Ligand 13 (CXCL13) Attenuates Morphine Analgesia in Rats with Cancer-Induced Bone Pain.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables CCR10 chemokine receptor binding	ISO Inferred from Sequence Orthology more info
enables CXCR chemokine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables CXCR3 chemokine receptor binding	ISO Inferred from Sequence Orthology more info
enables CXCR5 chemokine receptor binding	ISO Inferred from Sequence Orthology more info
enables chemokine activity	IBA Inferred from Biological aspect of Ancestor more info
enables chemokine activity	ISO Inferred from Sequence Orthology more info
enables fibroblast growth factor binding	ISO Inferred from Sequence Orthology more info
enables heparin binding	ISO Inferred from Sequence Orthology more info
enables receptor ligand activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in B cell chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in B cell chemotaxis across high endothelial venule	ISO Inferred from Sequence Orthology more info
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 surface receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in cell-cell signaling	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lipopolysaccharide	IBA Inferred from Biological aspect of Ancestor more info
involved_in chemokine-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in defense response to bacterium	ISO Inferred from Sequence Orthology more info
involved_in endothelial cell chemotaxis to fibroblast growth factor	ISO Inferred from Sequence Orthology more info
involved_in inflammatory response	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within lymph node development	ISO Inferred from Sequence Orthology more info
involved_in lymph node development	ISO Inferred from Sequence Orthology more info
involved_in lymphocyte chemotaxis across high endothelial venule	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of endothelial cell chemotaxis to fibroblast growth factor	ISO Inferred from Sequence Orthology more info
involved_in neutrophil chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of T cell chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell-cell adhesion mediated by integrin	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cytosolic calcium ion concentration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of integrin activation	ISO Inferred from Sequence Orthology more info

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

General protein information

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Preferred Names: C-X-C motif chemokine 13

Names: chemokine (C-X-C motif) ligand 13

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.

mRNA and Protein(s)

NM_001017496.2 → NP_001017496.1 C-X-C motif chemokine 13 isoform 2 precursor

See identical proteins and their annotated locations for NP_001017496.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000014

UniProtKB/TrEMBL

Q5I0J6

Conserved Domains (1) summary

cd00273
Location:29 → 88

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 ...
NM_001419199.1 → NP_001406128.1 C-X-C motif chemokine 13 isoform 1 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000014

UniProtKB/TrEMBL

A6K673, F7F7W7

Related

ENSRNOP00000034304.4, ENSRNOT00000039383.5