Human Gene XCR1 (ENST00000309285.4_7) from GENCODE V47lift37

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Description: X-C motif chemokine receptor 1, transcript variant 2 (from RefSeq NM_001024644.2)
Gencode Transcript: ENST00000309285.4_7
Gencode Gene: ENSG00000173578.9_10
Transcript (Including UTRs)
Position: hg19 chr3:46,058,499-46,068,975 Size: 10,477 Total Exon Count: 2 Strand: -
Coding Region
Position: hg19 chr3:46,062,438-46,063,439 Size: 1,002 Coding Exon Count: 1

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	RNA Structure	Protein Structure	Other Species	GO Annotations	mRNA Descriptions
Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr3:46,058,499-46,068,975)			mRNA (may differ from genome)		Protein (333 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	MGI	OMIM	PubMed	Reactome	UniProtKB
Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: XCR1_HUMAN DESCRIPTION: RecName: Full=Chemokine XC receptor 1; AltName: Full=G-protein coupled receptor 5; AltName: Full=Lymphotactin receptor; AltName: Full=XC chemokine receptor 1; FUNCTION: Receptor for chemokines SCYC1 and SCYC2. Subsequently transduces a signal by increasing the intracellular calcium ions level. SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein. SIMILARITY: Belongs to the G-protein coupled receptor 1 family.

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene C032668 1-nitropyrene D000082 Acetaminophen D002392 Catechin D005419 Flavonoids D010936 Plant Extracts D059808 Polyphenols D012822 Silicon Dioxide D053260 Soot D013241 Sterigmatocystin C402696 TMC 120A more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 1.39 RPKM in Skin - Sun Exposed (Lower leg) Total median expression: 5.48 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-16.20	98	-0.165	Picture	PostScript	Text
3' UTR	-1227.30	3939	-0.312	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR000276 - 7TM_GPCR_Rhodpsn
IPR005393 - Chemokine_lymphotactin_XCR1
IPR017452 - GPCR_Rhodpsn_supfam

Pfam Domains:
PF00001 - 7 transmembrane receptor (rhodopsin family)

SCOP Domains:
81321 - Family A G protein-coupled receptor-like

ModBase Predicted Comparative 3D Structure on P46094


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0004871 signal transducer activity GO:0004930 G-protein coupled receptor activity GO:0004950 chemokine receptor activity Biological Process: GO:0006935 chemotaxis GO:0006954 inflammatory response GO:0007165 signal transduction GO:0007186 G-protein coupled receptor signaling pathway GO:0007187 G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger GO:0007204 positive regulation of cytosolic calcium ion concentration GO:0070098 chemokine-mediated signaling pathway Cellular Component: GO:0005886 plasma membrane GO:0005887 integral component of plasma membrane GO:0016020 membrane GO:0016021 integral component of membrane

Descriptions from all associated GenBank mRNAs


	AK092973 - Homo sapiens cDNA FLJ35654 fis, clone SPLEN2013753. AX747832 - Sequence 1357 from Patent EP1308459. JD172792 - Sequence 153816 from Patent EP1572962. JD137568 - Sequence 118592 from Patent EP1572962. JD375077 - Sequence 356101 from Patent EP1572962. JD560473 - Sequence 541497 from Patent EP1572962. JD337777 - Sequence 318801 from Patent EP1572962. JD310709 - Sequence 291733 from Patent EP1572962. JD265756 - Sequence 246780 from Patent EP1572962. JD490357 - Sequence 471381 from Patent EP1572962. JD403402 - Sequence 384426 from Patent EP1572962. JD052031 - Sequence 33055 from Patent EP1572962. JD513127 - Sequence 494151 from Patent EP1572962. JD130440 - Sequence 111464 from Patent EP1572962. JD036637 - Sequence 17661 from Patent EP1572962. JD359884 - Sequence 340908 from Patent EP1572962. JD066089 - Sequence 47113 from Patent EP1572962. JD248317 - Sequence 229341 from Patent EP1572962. JD360402 - Sequence 341426 from Patent EP1572962. JD082987 - Sequence 64011 from Patent EP1572962. JD454352 - Sequence 435376 from Patent EP1572962. JD110212 - Sequence 91236 from Patent EP1572962. JD374890 - Sequence 355914 from Patent EP1572962. JD313252 - Sequence 294276 from Patent EP1572962. JD216968 - Sequence 197992 from Patent EP1572962. JD356131 - Sequence 337155 from Patent EP1572962. JD411316 - Sequence 392340 from Patent EP1572962. JD329597 - Sequence 310621 from Patent EP1572962. JD195410 - Sequence 176434 from Patent EP1572962. JD429715 - Sequence 410739 from Patent EP1572962. JD411190 - Sequence 392214 from Patent EP1572962. JD240246 - Sequence 221270 from Patent EP1572962. JD166384 - Sequence 147408 from Patent EP1572962. JD343619 - Sequence 324643 from Patent EP1572962. JD040584 - Sequence 21608 from Patent EP1572962. JD262687 - Sequence 243711 from Patent EP1572962. JD250913 - Sequence 231937 from Patent EP1572962. JD252942 - Sequence 233966 from Patent EP1572962. JD275407 - Sequence 256431 from Patent EP1572962. JD556108 - Sequence 537132 from Patent EP1572962. JD413930 - Sequence 394954 from Patent EP1572962. JD490198 - Sequence 471222 from Patent EP1572962. JD122811 - Sequence 103835 from Patent EP1572962. JD233852 - Sequence 214876 from Patent EP1572962. JD412496 - Sequence 393520 from Patent EP1572962. JD250785 - Sequence 231809 from Patent EP1572962. JD538607 - Sequence 519631 from Patent EP1572962. JD236535 - Sequence 217559 from Patent EP1572962. JD047199 - Sequence 28223 from Patent EP1572962. BC095533 - Homo sapiens chemokine (C motif) receptor 1, mRNA (cDNA clone MGC:111752 IMAGE:6971949), complete cds. BC069075 - Homo sapiens chemokine (C motif) receptor 1, mRNA (cDNA clone MGC:95350 IMAGE:7216889), complete cds. BC069589 - Homo sapiens chemokine (C motif) receptor 1, transcript variant 2, mRNA (cDNA clone MGC:97068 IMAGE:7262280), complete cds. AK314277 - Homo sapiens cDNA, FLJ95031, highly similar to Homo sapiens chemokine (C motif) receptor 1 (XCR1), mRNA. KJ891277 - Synthetic construct Homo sapiens clone ccsbBroadEn_00671 XCR1 gene, encodes complete protein. AB464479 - Synthetic construct DNA, clone: pF1KB8796, Homo sapiens XCR1 gene for chemokine (C motif) receptor 1, without stop codon, in Flexi system. AB189434 - Homo sapiens XCR1 mRNA for chemokine C motif receptor 1, partial cds. AB189435 - Homo sapiens XCR1 mRNA for chemokine C motif receptor 1, partial cds.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein P46094 (Reactome details) participates in the following event(s): R-HSA-373339 Receptor CXC1 binds to the ligands lymphotactin and cytokine SCM-1 beta R-HSA-749452 The Ligand:GPCR:Gq complex dissociates R-HSA-749448 Liganded Gq-activating GPCRs bind inactive heterotrimeric Gq R-HSA-379048 Liganded Gq/11-activating GPCRs act as GEFs for Gq/11 R-HSA-380108 Chemokine receptors bind chemokines R-HSA-416476 G alpha (q) signalling events R-HSA-375276 Peptide ligand-binding receptors R-HSA-388396 GPCR downstream signalling R-HSA-373076 Class A/1 (Rhodopsin-like receptors) R-HSA-372790 Signaling by GPCR R-HSA-500792 GPCR ligand binding R-HSA-162582 Signal Transduction

Other Names for This Gene


	Alternate Gene Symbols: CCXCR1, ENST00000309285.1, ENST00000309285.2, ENST00000309285.3, GPR5, NM_001024644, P46094, uc317omp.1, uc317omp.2, XCR1_HUMAN UCSC ID: ENST00000309285.4_7 RefSeq Accession: NM_001024644.2 Protein: P46094 (aka XCR1_HUMAN or CXC1_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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