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XCR1 X-C motif chemokine receptor 1 [ Homo sapiens (human) ]

Gene ID: 2829, updated on 18-Apr-2020

Summary

Official Symbol
XCR1provided by HGNC
Official Full Name
X-C motif chemokine receptor 1provided by HGNC
Primary source
HGNC:HGNC:1625
See related
Ensembl:ENSG00000173578 MIM:600552
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GPR5; CCXCR1
Summary
The protein encoded by this gene is a chemokine receptor belonging to the G protein-coupled receptor superfamily. The family members are characterized by the presence of 7 transmembrane domains and numerous conserved amino acids. This receptor is most closely related to RBS11 and the MIP1-alpha/RANTES receptor. It transduces a signal by increasing the intracellular calcium ions level. The viral macrophage inflammatory protein-II is an antagonist of this receptor and blocks signaling. Several alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Apr 2020]
Expression
Biased expression in lymph node (RPKM 2.0), spleen (RPKM 1.4) and 12 other tissues See more
Orthologs

Genomic context

See XCR1 in Genome Data Viewer
Location:
3p21.31
Exon count:
12
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (46016990..46086803, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (46062291..46068979, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene FYVE and coiled-coil domain autophagy adaptor 1 Neighboring gene C-X-C motif chemokine receptor 6 Neighboring gene uncharacterized LOC105377063 Neighboring gene nuclear receptor binding factor 2 pseudogene 2 Neighboring gene uncharacterized LOC105377067 Neighboring gene FLT1 pseudogene 1 Neighboring gene C-C motif chemokine receptor 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
C-C chemokine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
C-C chemokine receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemokine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemokine receptor activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
G protein-coupled receptor signaling pathway TAS
Traceable Author Statement
more info
 
G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger TAS
Traceable Author Statement
more info
PubMed 
calcium-mediated signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemokine-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
immune response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
inflammatory response TAS
Traceable Author Statement
more info
PubMed 
positive regulation of cytosolic calcium ion concentration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
release of sequestered calcium ion into cytosol IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell IEA
Inferred from Electronic Annotation
more info
 
external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
chemokine XC receptor 1
Names
G protein-coupled receptor 5
XC chemokine receptor 1
chemokine (C motif) XC receptor 1
chemokine (C motif) receptor 1
lymphotactin receptor

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_001024644.2NP_001019815.1  chemokine XC receptor 1

    See identical proteins and their annotated locations for NP_001019815.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 3. All three variants encode the same protein.
    Source sequence(s)
    AB189435, AC099782, BC069075, BC095533
    Consensus CDS
    CCDS2736.1
    UniProtKB/Swiss-Prot
    P46094
    UniProtKB/TrEMBL
    Q502V0, Q689E2
    Related
    ENSP00000310405.3, ENST00000309285.3
    Conserved Domains (1) summary
    cd15182
    Location:32298
    7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors
  2. NM_001381860.1NP_001368789.1  chemokine XC receptor 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript. All three variants encode the same protein.
    Source sequence(s)
    AC099782, AC104439, AC133140
  3. NM_005283.3NP_005274.1  chemokine XC receptor 1

    See identical proteins and their annotated locations for NP_005274.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 3. All three variants encode the same protein.
    Source sequence(s)
    AB189434, AC099782, BC069075, BC095533
    Consensus CDS
    CCDS2736.1
    UniProtKB/Swiss-Prot
    P46094
    UniProtKB/TrEMBL
    Q502V0, Q689E2
    Conserved Domains (1) summary
    cd15182
    Location:32298
    7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    46016990..46086803 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017006201.1XP_016861690.1  chemokine XC receptor 1 isoform X1

    UniProtKB/Swiss-Prot
    P46094
    Conserved Domains (1) summary
    cd15182
    Location:32298
    7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors
  2. XM_017006200.1XP_016861689.1  chemokine XC receptor 1 isoform X1

    UniProtKB/Swiss-Prot
    P46094
    Conserved Domains (1) summary
    cd15182
    Location:32298
    7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors
  3. XM_017006196.1XP_016861685.1  chemokine XC receptor 1 isoform X1

    UniProtKB/Swiss-Prot
    P46094
    Conserved Domains (1) summary
    cd15182
    Location:32298
    7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors
  4. XM_017006198.1XP_016861687.1  chemokine XC receptor 1 isoform X1

    UniProtKB/Swiss-Prot
    P46094
    Conserved Domains (1) summary
    cd15182
    Location:32298
    7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors
  5. XM_017006197.1XP_016861686.1  chemokine XC receptor 1 isoform X1

    UniProtKB/Swiss-Prot
    P46094
    Conserved Domains (1) summary
    cd15182
    Location:32298
    7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors
  6. XM_017006199.1XP_016861688.1  chemokine XC receptor 1 isoform X1

    UniProtKB/Swiss-Prot
    P46094
    Conserved Domains (1) summary
    cd15182
    Location:32298
    7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors

RNA

  1. XR_001740108.1 RNA Sequence

  2. XR_001740109.1 RNA Sequence

  3. XR_001740107.1 RNA Sequence

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