Xcr1 (X-C motif chemokine receptor 1) - Rat Genome Database

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Gene: Xcr1 (X-C motif chemokine receptor 1) Rattus norvegicus
Analyze
Symbol: Xcr1
Name: X-C motif chemokine receptor 1
RGD ID: 1311480
Description: Predicted to be involved in immune response. Predicted to act upstream of or within chemotaxis; release of sequestered calcium ion into cytosol; and response to cytokine. Orthologous to human XCR1 (X-C motif chemokine receptor 1); PARTICIPATES IN chemokine mediated signaling pathway; cytokine mediated signaling pathway; INTERACTS WITH 3,3',4,4',5-pentachlorobiphenyl; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: chemokine (C motif) receptor 1; chemokine XC receptor 1; LOC301086
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28123,479,454 - 123,516,168 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,479,590 - 123,487,226 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8129,071,800 - 129,079,436 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.08127,270,777 - 127,278,413 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.08125,099,978 - 125,107,614 (-)NCBIRnor_WKY
Rnor_6.08132,911,474 - 132,919,110 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,911,486 - 132,919,110 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08132,062,477 - 132,091,285 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48128,612,753 - 128,620,389 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18128,635,635 - 128,636,605 (-)NCBI
Celera8122,587,775 - 122,595,411 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10518929   PMID:24155383   PMID:31649144  


Genomics

Comparative Map Data
Xcr1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28123,479,454 - 123,516,168 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,479,590 - 123,487,226 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8129,071,800 - 129,079,436 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.08127,270,777 - 127,278,413 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.08125,099,978 - 125,107,614 (-)NCBIRnor_WKY
Rnor_6.08132,911,474 - 132,919,110 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,911,486 - 132,919,110 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08132,062,477 - 132,091,285 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48128,612,753 - 128,620,389 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18128,635,635 - 128,636,605 (-)NCBI
Celera8122,587,775 - 122,595,411 (-)NCBICelera
Cytogenetic Map8q32NCBI
XCR1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38346,017,007 - 46,085,844 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl346,016,990 - 46,085,825 (-)EnsemblGRCh38hg38GRCh38
GRCh37346,058,499 - 46,127,336 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36346,037,295 - 46,043,983 (-)NCBINCBI36Build 36hg18NCBI36
Build 34346,037,441 - 46,038,443NCBI
Celera345,999,653 - 46,006,341 (-)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef346,106,108 - 46,112,796 (-)NCBIHuRef
CHM1_1346,011,957 - 46,018,641 (-)NCBICHM1_1
T2T-CHM13v2.0346,032,885 - 46,101,714 (-)NCBIT2T-CHM13v2.0
Xcr1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399123,681,380 - 123,691,094 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9123,681,380 - 123,691,094 (-)EnsemblGRCm39 Ensembl
GRCm389123,852,315 - 123,862,029 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,852,315 - 123,862,029 (-)EnsemblGRCm38mm10GRCm38
MGSCv379123,761,436 - 123,771,246 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369123,701,016 - 123,710,826 (-)NCBIMGSCv36mm8
Celera9124,300,685 - 124,310,371 (-)NCBICelera
Cytogenetic Map9F4NCBI
cM Map974.71NCBI
XCR1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1347,032,887 - 47,039,877 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl347,033,084 - 47,034,085 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0345,922,985 - 45,934,332 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
XCR1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12042,505,534 - 42,516,524 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2042,511,431 - 42,512,423 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2042,421,402 - 42,432,159 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02042,988,286 - 42,999,051 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2042,988,356 - 42,998,804 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12042,229,406 - 42,240,162 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02042,636,610 - 42,647,379 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02042,911,915 - 42,922,678 (+)NCBIUU_Cfam_GSD_1.0
Xcr1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118200,544,294 - 200,545,341 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493659693,433 - 94,434 (-)EnsemblSpeTri2.0
SpeTri2.0NW_00493659693,433 - 94,480 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XCR1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1329,150,379 - 29,159,637 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11329,150,376 - 29,233,802 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21332,246,790 - 32,330,226 (-)NCBISscrofa10.2Sscrofa10.2susScr3
XCR1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1227,495,008 - 7,503,202 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl227,496,260 - 7,497,261 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041159,658,784 - 159,667,802 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Xcr1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473074,915,383 - 74,919,308 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473074,913,815 - 74,921,198 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Xcr1
158 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:691
Count of miRNA genes:280
Interacting mature miRNAs:338
Transcripts:ENSRNOT00000008747
Prediction methods:Microtar, Miranda
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system renal system reproductive system respiratory system appendage
High
Medium 1
Low 3 1 12 4 18 4 5 11 11
Below cutoff 13 28 21 21 7 8 11 10 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008747   ⟹   ENSRNOP00000008747
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,479,590 - 123,487,226 (-)Ensembl
Rnor_6.0 Ensembl8132,911,486 - 132,919,110 (-)Ensembl
RefSeq Acc Id: NM_001106871   ⟹   NP_001100341
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28123,479,590 - 123,487,226 (-)NCBI
Rnor_6.08132,911,474 - 132,919,110 (-)NCBI
Rnor_5.08132,062,477 - 132,091,285 (-)NCBI
RGSC_v3.48128,612,753 - 128,620,389 (-)RGD
Celera8122,587,775 - 122,595,411 (-)RGD
Sequence:
RefSeq Acc Id: XM_039081319   ⟹   XP_038937247
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28123,479,454 - 123,516,168 (-)NCBI
RefSeq Acc Id: XM_039081320   ⟹   XP_038937248
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28123,479,454 - 123,483,723 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100341 (Get FASTA)   NCBI Sequence Viewer  
  XP_038937247 (Get FASTA)   NCBI Sequence Viewer  
  XP_038937248 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76749 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100341   ⟸   NM_001106871
- UniProtKB: D3ZGG9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008747   ⟸   ENSRNOT00000008747
RefSeq Acc Id: XP_038937247   ⟸   XM_039081319
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038937248   ⟸   XM_039081320
- Peptide Label: isoform X2
Protein Domains
G_PROTEIN_RECEP_F1_2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZGG9-F1-model_v2 AlphaFold D3ZGG9 1-338 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696414
Promoter ID:EPDNEW_R6939
Type:multiple initiation site
Name:Xcr1_1
Description:X-C motif chemokine receptor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08132,919,121 - 132,919,181EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311480 AgrOrtholog
BioCyc Gene G2FUF-28603 BioCyc
Ensembl Genes ENSRNOG00000006620 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008747 ENTREZGENE
  ENSRNOP00000008747.5 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008747 ENTREZGENE
  ENSRNOT00000008747.7 UniProtKB/TrEMBL
InterPro 7TM_GPCR_Rhodpsn UniProtKB/TrEMBL
  GPCR_Rhodpsn_supfam UniProtKB/TrEMBL
  XCR1_lymph_rcpt UniProtKB/TrEMBL
KEGG Report rno:301086 UniProtKB/TrEMBL
NCBI Gene 301086 ENTREZGENE
Pfam 7tm_1 UniProtKB/TrEMBL
PhenoGen Xcr1 PhenoGen
PRINTS GPCRRHODOPSN UniProtKB/TrEMBL
  LYMPHOTACTNR UniProtKB/TrEMBL
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/TrEMBL
  G_PROTEIN_RECEP_F1_2 UniProtKB/TrEMBL
UniProt A0A4D6YKT9_RAT UniProtKB/TrEMBL
  A0A4D6YKV7_RAT UniProtKB/TrEMBL
  A0A4D6YMZ8_RAT UniProtKB/TrEMBL
  A0A4D6YN16_RAT UniProtKB/TrEMBL
  A0A4D6YNW0_RAT UniProtKB/TrEMBL
  A0A4D6YNX2_RAT UniProtKB/TrEMBL
  A0A4D6YRB6_RAT UniProtKB/TrEMBL
  A0A4D6YRC8_RAT UniProtKB/TrEMBL
  A0A4D6YRD9_RAT UniProtKB/TrEMBL
  A0A4D6YTF9_RAT UniProtKB/TrEMBL
  A0A4D6YTG8_RAT UniProtKB/TrEMBL
  A0A4D6YVV8_RAT UniProtKB/TrEMBL
  A0A4D6YVW0_RAT UniProtKB/TrEMBL
  A0A4D6YVZ1_RAT UniProtKB/TrEMBL
  A0A4D6YWB6_RAT UniProtKB/TrEMBL
  A0A4D6YWC4_RAT UniProtKB/TrEMBL
  A0A4D6YWI1_RAT UniProtKB/TrEMBL
  A0A4D6YWI5_RAT UniProtKB/TrEMBL
  D3ZGG9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-22 Xcr1  X-C motif chemokine receptor 1  Xcr1  chemokine (C motif) receptor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Xcr1  chemokine (C motif) receptor 1   Xcr1_predicted  chemokine (C motif) receptor 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Xcr1_predicted  chemokine (C motif) receptor 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED