Xkr5 (XK related 5) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Xkr5 (XK related 5) Rattus norvegicus
Analyze
Symbol: Xkr5
Name: XK related 5
RGD ID: 1359335
Description: Predicted to be active in plasma membrane. Orthologous to human XKR5 (XK related 5); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC497083; X Kell blood group precursor-related family, member 5; X-linked Kx blood group related 5; XK, Kell blood group complex subunit-related family, member 5; XK-related protein 5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,577,387 - 77,595,377 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1677,577,481 - 77,595,376 (+)EnsemblGRCr8
mRatBN7.21670,874,983 - 70,892,972 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,875,093 - 70,892,967 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1676,151,932 - 76,169,828 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,598,425 - 79,616,419 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,847,843 - 74,865,833 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,744,786 - 75,762,694 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,744,786 - 75,762,693 (+)Ensemblrn6Rnor6.0
Rnor_5.01675,349,398 - 75,367,306 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41675,677,746 - 75,695,654 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1668,721,107 - 68,739,005 (+)NCBICelera
RGSC_v3.11675,678,010 - 75,695,918 (+)NCBI
Cytogenetic Map16q12.5NCBI
JBrowse:




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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Xkr5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,577,387 - 77,595,377 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1677,577,481 - 77,595,376 (+)EnsemblGRCr8
mRatBN7.21670,874,983 - 70,892,972 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,875,093 - 70,892,967 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1676,151,932 - 76,169,828 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,598,425 - 79,616,419 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,847,843 - 74,865,833 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,744,786 - 75,762,694 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,744,786 - 75,762,693 (+)Ensemblrn6Rnor6.0
Rnor_5.01675,349,398 - 75,367,306 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41675,677,746 - 75,695,654 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1668,721,107 - 68,739,005 (+)NCBICelera
RGSC_v3.11675,678,010 - 75,695,918 (+)NCBI
Cytogenetic Map16q12.5NCBI
XKR5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3886,808,517 - 6,835,524 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl86,805,013 - 6,835,526 (-)Ensemblhg38GRCh38
GRCh3786,666,038 - 6,693,046 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3686,653,448 - 6,680,447 (-)NCBIBuild 36Build 36hg18NCBI36
Celera86,643,512 - 6,670,635 (-)NCBICelera
Cytogenetic Map8p23.1NCBI
HuRef86,446,861 - 6,473,558 (-)NCBIHuRef
CHM1_186,755,323 - 6,782,440 (-)NCBICHM1_1
T2T-CHM13v2.086,563,754 - 6,590,758 (-)NCBIT2T-CHM13v2.0
Xkr5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39818,974,172 - 19,001,126 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl818,982,745 - 19,000,991 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38818,924,152 - 18,951,105 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl818,932,729 - 18,950,975 (-)Ensemblmm10GRCm38
MGSCv37818,932,729 - 18,950,973 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36818,932,707 - 18,950,936 (-)NCBIMGSCv36mm8
Celera819,065,916 - 19,084,206 (-)NCBICelera
Cytogenetic Map8A1.3NCBI
cM Map810.33NCBI
Xkr5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540353,964,723 - 53,984,006 (+)Ensembl
ChiLan1.0NW_00495540353,964,767 - 53,981,549 (+)NCBIChiLan1.0ChiLan1.0
XKR5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2721,610,994 - 21,640,008 (-)NCBINHGRI_mPanPan1-v2
Mhudiblu_PPA_v08445,644 - 472,659 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.186,812,602 - 6,839,844 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl86,812,607 - 6,839,844 (-)EnsemblpanPan2panpan1.1
XKR5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11658,836,581 - 58,861,698 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1658,841,135 - 58,852,668 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1654,364,926 - 54,386,992 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01657,186,836 - 57,208,918 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1657,186,689 - 57,208,421 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11659,000,817 - 59,022,898 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01655,195,070 - 55,217,143 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01655,568,846 - 55,592,179 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Xkr5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049434,733,305 - 4,753,216 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366154,734,805 - 4,753,194 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366154,734,805 - 4,753,194 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XKR5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1537,880,116 - 37,898,687 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11537,880,406 - 37,898,737 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21543,092,809 - 43,110,943 (-)NCBISscrofa10.2Sscrofa10.2susScr3
XKR5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.186,589,913 - 6,616,045 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl86,590,302 - 6,615,308 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605448,704,301 - 48,729,843 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Xkr5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248614,665,659 - 4,690,991 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Xkr5
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11365,235,928 - 65,253,753 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Xkr5
259 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:76
Count of miRNA genes:59
Interacting mature miRNAs:70
Transcripts:ENSRNOT00000032368
Prediction methods:Miranda, Rnahybrid, Targetscan
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164445512389455123Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165942871491442908Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)163439829479398294Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)163692878281928782Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)164199206486992064Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164445512389455123Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165942871491442908Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165942871491442908Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164909919691442908Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)167523528581732231Rat

Markers in Region
RH134696  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21670,892,574 - 70,892,762 (+)MAPPERmRatBN7.2
Rnor_6.01675,762,299 - 75,762,486NCBIRnor6.0
Rnor_5.01675,366,911 - 75,367,098UniSTSRnor5.0
RGSC_v3.41675,695,259 - 75,695,446UniSTSRGSC3.4
Celera1668,738,610 - 68,738,797UniSTS
RH 3.4 Map16703.5UniSTS
Cytogenetic Map16q12.5UniSTS
BF390395  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21670,890,063 - 70,890,215 (+)MAPPERmRatBN7.2
Rnor_6.01675,759,788 - 75,759,939NCBIRnor6.0
Rnor_5.01675,364,400 - 75,364,551UniSTSRnor5.0
RGSC_v3.41675,692,748 - 75,692,899UniSTSRGSC3.4
Celera1668,736,099 - 68,736,250UniSTS
RH 3.4 Map16702.3UniSTS
Cytogenetic Map16q12.5UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 159 91 90 59 83 59 6 345 182 11 138 80 91 31 16 16

Sequence


Ensembl Acc Id: ENSRNOT00000032368   ⟹   ENSRNOP00000032580
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1677,577,481 - 77,595,376 (+)Ensembl
mRatBN7.2 Ensembl1670,875,093 - 70,892,967 (+)Ensembl
Rnor_6.0 Ensembl1675,744,786 - 75,762,693 (+)Ensembl
RefSeq Acc Id: NM_001396398   ⟹   NP_001383327
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81677,577,479 - 77,595,377 (+)NCBI
mRatBN7.21670,875,066 - 70,892,970 (+)NCBI
RefSeq Acc Id: XM_039094745   ⟹   XP_038950673
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81677,577,423 - 77,595,377 (+)NCBI
mRatBN7.21670,875,020 - 70,892,970 (+)NCBI
RefSeq Acc Id: XM_039094747   ⟹   XP_038950675
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81677,577,426 - 77,595,377 (+)NCBI
mRatBN7.21670,875,014 - 70,892,970 (+)NCBI
RefSeq Acc Id: XM_063275627   ⟹   XP_063131697
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81677,577,387 - 77,593,793 (+)NCBI
Ensembl Acc Id: ENSRNOP00000032580   ⟸   ENSRNOT00000032368
RefSeq Acc Id: XP_038950675   ⟸   XM_039094747
- Peptide Label: isoform X1
- UniProtKB: Q5GH58 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038950673   ⟸   XM_039094745
- Peptide Label: isoform X1
- UniProtKB: Q5GH58 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001383327   ⟸   NM_001396398
- UniProtKB: F7F7I4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063131697   ⟸   XM_063275627
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5GH58-F1-model_v2 AlphaFold Q5GH58 1-509 view protein structure

Transcriptome

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

Promoters
RGD ID:13700214
Promoter ID:EPDNEW_R10738
Type:multiple initiation site
Name:Xkr5_1
Description:XK related 5
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_6.01675,744,800 - 75,744,860EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359335 AgrOrtholog
BioCyc Gene G2FUF-10808 BioCyc
Ensembl Genes ENSRNOG00000028636 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000032368 ENTREZGENE
  ENSRNOT00000032368.7 UniProtKB/TrEMBL
InterPro Membr_transp_prot_XK-like UniProtKB/TrEMBL
  XK-related_scramblase UniProtKB/TrEMBL
NCBI Gene 497083 ENTREZGENE
PANTHER XK-RELATED PROTEIN UniProtKB/TrEMBL
  XK-RELATED PROTEIN 5 UniProtKB/TrEMBL
Pfam XK-related UniProtKB/TrEMBL
PhenoGen Xkr5 PhenoGen
RatGTEx ENSRNOG00000028636 RatGTEx
UniProt F7F7I4 ENTREZGENE, UniProtKB/TrEMBL
  Q5GH58 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Xkr5  XK related 5  Xkr5  X-linked Kx blood group related 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-19 Xkr5  X-linked Kx blood group related 5  Xkr5  XK, Kell blood group complex subunit-related family, member 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-12-15 Xkr5  XK, Kell blood group complex subunit-related family, member 5  Xkr5  X Kell blood group precursor-related family, member 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Xkr5  X Kell blood group precursor-related family, member 5  LOC497083  XK-related protein 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 LOC497083  XK-related protein 5      Symbol and Name status set to provisional 70820 PROVISIONAL