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Xcr1 X-C motif chemokine receptor 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 301086, updated on 2-Nov-2024

Summary

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Official Symbol
Xcr1provided by RGD
Official Full Name
X-C motif chemokine receptor 1provided by RGD
Primary source
RGD:1311480
See related
EnsemblRapid:ENSRNOG00000006620 AllianceGenome:RGD:1311480
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable C-C chemokine binding activity and C-C chemokine receptor activity. Predicted to be involved in several processes, including calcium-mediated signaling; cell chemotaxis; and positive regulation of cytosolic calcium ion concentration. Predicted to act upstream of or within chemotaxis; release of sequestered calcium ion into cytosol; and response to cytokine. Predicted to be active in external side of plasma membrane. Orthologous to human XCR1 (X-C motif chemokine receptor 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Spleen (RPKM 27.1), Thymus (RPKM 22.0) and 6 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Xcr1 in Genome Data Viewer
Location:
8q32
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (132357020..132393596, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (123479454..123516168, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (132911474..132919110, complement)

Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene FYVE and coiled-coil domain autophagy adaptor 1 Neighboring gene basic leucine zipper and W2 domains 1, pseudogene 2 Neighboring gene C-X-C motif chemokine receptor 6 Neighboring gene CDK2-associated, cullin domain 1, pseudogene 1 Neighboring gene transcription initiation factor TFIID subunit 13-like Neighboring gene C-C motif chemokine receptor 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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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Related articles in PubMed

  1. Rat cytomegalovirus-encoded γ-chemokine vXCL1 is a highly adapted, species-specific agonist for rat XCR1-positive dendritic cells. Bauer A, et al. J Cell Sci, 2019 Nov 18. PMID 31649144
  2. Cytomegalovirus expresses the chemokine homologue vXCL1 capable of attracting XCR1+ CD4- dendritic cells. Geyer H, et al. J Virol, 2014 Jan. PMID 24155383, Free PMC Article
  3. Molecular cloning of mXCR1, the murine SCM-1/lymphotactin receptor. Yoshida T, et al. FEBS Lett, 1999 Sep 10. PMID 10518929
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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

Pathways from PubChem

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General gene information

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Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables C-C chemokine binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables C-C chemokine receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in calcium-mediated signaling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chemokine-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within chemotaxis ISO
Inferred from Sequence Orthology
more info
  
involved_in immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cytosolic calcium ion concentration IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within release of sequestered calcium ion into cytosol ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within response to cytokine ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
chemokine XC receptor 1
Names
chemokine (C motif) receptor 1

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)

  1. NM_001106871.1 → NP_001100341.1  chemokine XC receptor 1

    See identical proteins and their annotated locations for NP_001100341.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473954
    UniProtKB/TrEMBL
    A0A4D6YKT9, A0A4D6YN16, A0A4D6YRC8, A0A4D6YRD9, A0A4D6YTG8, A0A4D6YWI1, A0A4D6YWI5, A6I4C8, D3ZGG9
    Related
    ENSRNOP00000008747.5, ENSRNOT00000008747.8
    Conserved Domains (2) summary
    cd14964
    Location:44 → 68
    7tm_GPCRs; TM helix 1 [structural motif]
    cl28897
    Location:42 → 304
    7tm_GPCRs; seven-transmembrane G protein-coupled receptor superfamily

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086026.1 Reference GRCr8

    Range
    132357020..132393596 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039081319.2 → XP_038937247.1  chemokine XC receptor 1 isoform X2

    UniProtKB/TrEMBL
    A0A4D6YWI5
    Related
    ENSRNOP00000103086.1, ENSRNOT00000122011.1
    Conserved Domains (2) summary
    cd14964
    Location:26 → 53
    7tm_GPCRs; TM helix 1 [structural motif]
    cl28897
    Location:26 → 288
    7tm_GPCRs; seven-transmembrane G protein-coupled receptor superfamily

  2. XM_063265313.1 → XP_063121383.1  chemokine XC receptor 1 isoform X1

    Related
    ENSRNOP00000103296.1, ENSRNOT00000122533.1

  3. XM_039081320.2 → XP_038937248.1  chemokine XC receptor 1 isoform X3

    Conserved Domains (2) summary
    cd14964
    Location:23 → 53
    7tm_GPCRs; TM helix 3 [structural motif]
    cl28897
    Location:1 → 216
    7tm_GPCRs; seven-transmembrane G protein-coupled receptor superfamily
Nucleotide Protein Strain
Heading Accession and Version

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