Xkr4 (XK related 4) - Rat Genome Database

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Gene: Xkr4 (XK related 4) Rattus norvegicus
Analyze
Symbol: Xkr4
Name: XK related 4
RGD ID: 1549780
Description: Predicted to enable phospholipid scramblase activity and protein homodimerization activity. Predicted to be involved in apoptotic process involved in development; engulfment of apoptotic cell; and phosphatidylserine exposure on apoptotic cell surface. Predicted to be active in plasma membrane. Orthologous to human XKR4 (XK related 4); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: X Kell blood group precursor related family member 4; X-linked Kx blood group related 4; XK, Kell blood group complex subunit-related family, member 4; XK-related protein 4; XRG4
RGD Orthologs
Human
Mouse
Chinchilla
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
GRCr8520,694,433 - 21,095,350 (+)NCBIGRCr8
mRatBN7.2515,896,818 - 16,297,733 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl515,895,863 - 16,282,962 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx518,139,059 - 18,531,124 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0519,741,102 - 20,129,597 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0519,489,010 - 19,881,087 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0515,746,012 - 16,141,059 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl515,747,614 - 16,140,896 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0520,922,729 - 20,924,038 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0520,529,390 - 20,786,961 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4516,150,482 - 16,552,907 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera515,271,437 - 15,653,341 (+)NCBICelera
Cytogenetic Map5q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
plasma membrane  (IBA,IEA,ISO,ISS)

Molecular Function

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

Genomics

Comparative Map Data
Xkr4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8520,694,433 - 21,095,350 (+)NCBIGRCr8
mRatBN7.2515,896,818 - 16,297,733 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl515,895,863 - 16,282,962 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx518,139,059 - 18,531,124 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0519,741,102 - 20,129,597 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0519,489,010 - 19,881,087 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0515,746,012 - 16,141,059 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl515,747,614 - 16,140,896 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0520,922,729 - 20,924,038 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0520,529,390 - 20,786,961 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4516,150,482 - 16,552,907 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera515,271,437 - 15,653,341 (+)NCBICelera
Cytogenetic Map5q12NCBI
XKR4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38855,102,028 - 55,542,054 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl855,102,028 - 55,542,054 (+)EnsemblGRCh38hg38GRCh38
GRCh37856,014,588 - 56,454,613 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36856,177,571 - 56,601,268 (+)NCBINCBI36Build 36hg18NCBI36
Celera852,005,765 - 52,428,770 (+)NCBICelera
Cytogenetic Map8q12.1NCBI
HuRef851,483,309 - 51,906,398 (+)NCBIHuRef
CHM1_1856,066,642 - 56,490,559 (+)NCBICHM1_1
T2T-CHM13v2.0855,479,588 - 55,919,328 (+)NCBIT2T-CHM13v2.0
Xkr4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3913,269,956 - 3,741,733 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl13,276,124 - 3,741,721 (-)EnsemblGRCm39 Ensembl
GRCm3813,199,733 - 3,671,948 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl13,205,901 - 3,671,498 (-)EnsemblGRCm38mm10GRCm38
MGSCv3713,204,563 - 3,661,579 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3613,204,563 - 3,661,579 (-)NCBIMGSCv36mm8
Celera13,222,752 - 3,677,461 (-)NCBICelera
Cytogenetic Map1A1NCBI
cM Map11.6NCBI
Xkr4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545414,313,308 - 14,687,687 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545414,311,466 - 14,704,334 (+)NCBIChiLan1.0ChiLan1.0
XKR4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2770,752,499 - 71,193,752 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1846,477,114 - 46,918,128 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0851,541,410 - 51,982,587 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1848,883,194 - 49,338,840 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl848,914,778 - 49,336,906 (+)Ensemblpanpan1.1panPan2
XKR4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1296,640,108 - 7,081,182 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl296,640,108 - 7,064,029 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha296,955,719 - 7,396,555 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0296,718,168 - 7,155,918 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl296,718,237 - 7,140,881 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1296,694,846 - 7,136,803 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0296,860,019 - 7,304,621 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0297,138,740 - 7,581,032 (+)NCBIUU_Cfam_GSD_1.0
Xkr4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530372,487,107 - 72,897,540 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364961,888,068 - 2,287,963 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364961,887,943 - 2,289,928 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XKR4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl476,062,430 - 76,382,818 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1476,056,895 - 76,382,976 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
XKR4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1851,169,122 - 51,427,310 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603990,220,104 - 90,652,025 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Xkr4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473577,042 - 543,924 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Xkr4
3091 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:153
Count of miRNA genes:122
Interacting mature miRNAs:134
Transcripts:ENSRNOT00000029503
Prediction methods:Miranda, Rnahybrid
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
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5818750118616199Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat

Markers in Region
D5Got208  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2516,029,447 - 16,029,591 (+)MAPPERmRatBN7.2
Rnor_6.0515,860,105 - 15,860,248NCBIRnor6.0
Rnor_5.0520,643,289 - 20,643,432UniSTSRnor5.0
RGSC_v3.4516,286,509 - 16,286,652UniSTSRGSC3.4
Celera515,400,209 - 15,400,352UniSTS
Cytogenetic Map5q12UniSTS
AI196452  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2380,378,265 - 80,378,358 (+)MAPPERmRatBN7.2
mRatBN7.2516,046,131 - 16,046,224 (+)MAPPERmRatBN7.2
Rnor_6.0383,311,048 - 83,311,140NCBIRnor6.0
Rnor_6.0515,876,789 - 15,876,881NCBIRnor6.0
Rnor_5.0520,659,973 - 20,660,065UniSTSRnor5.0
Rnor_5.0390,010,665 - 90,010,757UniSTSRnor5.0
RGSC_v3.4516,303,193 - 16,303,285UniSTSRGSC3.4
RGSC_v3.4378,819,798 - 78,819,890UniSTSRGSC3.4
Celera515,416,892 - 15,416,984UniSTS
Celera379,572,623 - 79,572,715UniSTS
Cytogenetic Map3q31UniSTS
Cytogenetic Map5q12UniSTS
RH131924  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2516,068,350 - 16,068,538 (-)MAPPERmRatBN7.2
mRatBN7.2X140,681,929 - 140,682,117 (+)MAPPERmRatBN7.2
Rnor_6.0X145,423,206 - 145,423,393NCBIRnor6.0
Rnor_6.0516,079,717 - 16,079,904NCBIRnor6.0
Rnor_5.0520,862,886 - 20,863,073UniSTSRnor5.0
Rnor_5.0X145,445,518 - 145,445,705UniSTSRnor5.0
RGSC_v3.4X147,969,780 - 147,969,967UniSTSRGSC3.4
RGSC_v3.4516,326,660 - 16,326,847UniSTSRGSC3.4
Celera515,438,743 - 15,438,930UniSTS
CeleraX136,680,775 - 136,680,962UniSTS
Cytogenetic Map5q12UniSTS
AU048033  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2516,050,328 - 16,050,619 (+)MAPPERmRatBN7.2
Rnor_6.0515,881,217 - 15,881,507NCBIRnor6.0
Rnor_5.0520,664,401 - 20,664,691UniSTSRnor5.0
RGSC_v3.4516,308,025 - 16,308,315UniSTSRGSC3.4
Celera515,421,019 - 15,421,309UniSTS
Cytogenetic Map5q12UniSTS


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 nervous system renal system reproductive system respiratory system appendage
High
Medium 45 1 2
Low 8 21 8 15 8 8 8 29 10 19 9 8
Below cutoff 2 33 28 25 4 25 3 25 17

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000029503   ⟹   ENSRNOP00000029598
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl515,895,863 - 16,282,962 (+)Ensembl
Rnor_6.0 Ensembl515,747,614 - 16,140,896 (-)Ensembl
RefSeq Acc Id: NM_001011971   ⟹   NP_001011971
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8520,694,433 - 21,080,579 (+)NCBI
mRatBN7.2515,896,818 - 16,282,962 (+)NCBI
Rnor_6.0515,746,012 - 16,141,059 (-)NCBI
Rnor_5.0520,529,390 - 20,786,961 (-)NCBI
Rnor_5.0520,922,729 - 20,924,038 (-)NCBI
RGSC_v3.4516,150,482 - 16,552,907 (+)RGD
Celera515,271,437 - 15,653,341 (+)RGD
Sequence:
RefSeq Acc Id: XR_010066347
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8520,694,875 - 21,095,350 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001011971 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT07107 (Get FASTA)   NCBI Sequence Viewer  
  EDM11599 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000029598
  ENSRNOP00000029598.7
GenBank Protein Q5GH59 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001011971   ⟸   NM_001011971
- UniProtKB: Q5GH59 (UniProtKB/Swiss-Prot),   A0A8L2QFT8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000029598   ⟸   ENSRNOT00000029503

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5GH59-F1-model_v2 AlphaFold Q5GH59 1-647 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1549780 AgrOrtholog
BioCyc Gene G2FUF-42140 BioCyc
Ensembl Genes ENSRNOG00000027276 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029503 ENTREZGENE
  ENSRNOT00000029503.7 UniProtKB/TrEMBL
InterPro XK-rel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:297801 UniProtKB/Swiss-Prot
NCBI Gene 297801 ENTREZGENE
PANTHER XK-RELATED PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  XK-RELATED PROTEIN 4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam XK-related UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Xkr4 PhenoGen
RatGTEx ENSRNOG00000027276 RatGTEx
UniProt A0A8L2QFT8 ENTREZGENE, UniProtKB/TrEMBL
  Q5GH59 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Xkr4  XK related 4  Xkr4  X-linked Kx blood group related 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-11 Xkr4  X-linked Kx blood group related 4  Xkr4  XK, Kell blood group complex subunit-related family, member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-12-15 Xkr4  XK, Kell blood group complex subunit-related family, member 4  Xkr4  X Kell blood group precursor related family member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Xkr4  X Kell blood group precursor related family member 4  XRG4  XK-related protein 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-09-15 XRG4  XK-related protein 4      Symbol and Name status set to provisional 70820 PROVISIONAL