Xkr9 (XK related 9) - 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: Xkr9 (XK related 9) Rattus norvegicus
Analyze
Symbol: Xkr9
Name: XK related 9
RGD ID: 1359260
Description: Predicted to enable phospholipid scramblase activity. Predicted to be involved in phosphatidylserine exposure on apoptotic cell surface. Predicted to be located in plasma membrane. Predicted to be active in membrane. Orthologous to human XKR9 (XK related 9); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: X Kell blood group precursor related family member 9 homolog; X-linked Kx blood group related 9; XK, Kell blood group complex subunit-related family, member 9; XK-related protein 9; XRG9
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8510,316,510 - 10,345,253 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl510,316,513 - 10,345,253 (-)EnsemblGRCr8
mRatBN7.255,530,384 - 5,562,168 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl55,533,416 - 5,562,168 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx57,670,939 - 7,699,700 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.059,309,847 - 9,338,590 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.059,001,013 - 9,029,756 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.054,946,332 - 4,975,436 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl54,946,006 - 4,975,436 (-)Ensemblrn6Rnor6.0
Rnor_5.054,914,209 - 4,948,129 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.454,733,198 - 4,763,409 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera55,118,209 - 5,146,740 (-)NCBICelera
RGSC_v3.154,733,198 - 4,763,409 (-)NCBI
Cytogenetic Map5q11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

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

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
Additional References at PubMed
PMID:34263724  


Genomics

Comparative Map Data
Xkr9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8510,316,510 - 10,345,253 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl510,316,513 - 10,345,253 (-)EnsemblGRCr8
mRatBN7.255,530,384 - 5,562,168 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl55,533,416 - 5,562,168 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx57,670,939 - 7,699,700 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.059,309,847 - 9,338,590 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.059,001,013 - 9,029,756 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.054,946,332 - 4,975,436 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl54,946,006 - 4,975,436 (-)Ensemblrn6Rnor6.0
Rnor_5.054,914,209 - 4,948,129 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.454,733,198 - 4,763,409 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera55,118,209 - 5,146,740 (-)NCBICelera
RGSC_v3.154,733,198 - 4,763,409 (-)NCBI
Cytogenetic Map5q11NCBI
XKR9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38870,669,339 - 71,065,805 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl870,669,332 - 70,790,371 (+)Ensemblhg38GRCh38
GRCh37871,581,574 - 71,648,177 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36871,744,154 - 71,810,731 (+)NCBIBuild 36Build 36hg18NCBI36
Celera867,579,235 - 67,644,725 (+)NCBICelera
Cytogenetic Map8q13.3NCBI
HuRef867,074,347 - 67,141,404 (+)NCBIHuRef
CHM1_1871,637,118 - 71,702,619 (+)NCBICHM1_1
T2T-CHM13v2.0871,099,221 - 71,495,619 (+)NCBIT2T-CHM13v2.0
Xkr9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39113,738,962 - 13,772,454 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl113,738,995 - 13,771,947 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38113,668,738 - 13,702,230 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl113,668,771 - 13,701,723 (+)Ensemblmm10GRCm38
MGSCv37113,658,852 - 13,691,804 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36113,653,985 - 13,686,937 (+)NCBIMGSCv36mm8
Celera113,624,640 - 13,659,712 (+)NCBICelera
Cytogenetic Map1A3NCBI
cM Map14.31NCBI
Xkr9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554449,025,635 - 9,053,775 (-)Ensembl
ChiLan1.0NW_0049554449,027,662 - 9,059,911 (-)NCBIChiLan1.0ChiLan1.0
XKR9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2786,402,957 - 86,954,506 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1862,032,406 - 62,583,893 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0867,194,689 - 67,259,983 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1868,855,081 - 68,920,235 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl868,855,081 - 68,920,235 (+)EnsemblpanPan2panpan1.1
XKR9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12919,709,517 - 19,794,811 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2919,753,291 - 19,794,747 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2919,969,019 - 20,054,217 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02919,806,810 - 19,892,306 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2919,851,731 - 19,893,054 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12919,844,319 - 19,929,436 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02919,910,946 - 19,996,054 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02920,191,844 - 20,277,096 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Xkr9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530359,442,277 - 59,459,975 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366481,573 - 5,784 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366481,607 - 5,784 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XKR9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl464,679,170 - 64,707,710 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1464,678,734 - 64,727,495 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2470,309,649 - 70,341,116 (-)NCBISscrofa10.2Sscrofa10.2susScr3
XKR9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1866,406,484 - 66,463,500 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl866,441,550 - 66,463,496 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603974,954,790 - 75,022,625 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Xkr9
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11148,294,260 - 148,317,319 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Xkr9
126 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:249
Count of miRNA genes:167
Interacting mature miRNAs:193
Transcripts:ENSRNOT00000062006
Prediction methods:Microtar, 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
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5692228237468560Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5692228281330203Rat
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)5706553574335773Rat
631551Vetf1Vascular elastic tissue fragility QTL 150.0001aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)5706553510687501Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5862723052665523Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906487027358Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5862723053627230Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906491770353Rat


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
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 2 7 62 85 79 55 15 55 6 169 41 44 55 50 24 7 7

Sequence


Ensembl Acc Id: ENSRNOT00000062006   ⟹   ENSRNOP00000058714
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl510,316,513 - 10,345,253 (-)Ensembl
mRatBN7.2 Ensembl55,533,416 - 5,562,168 (-)Ensembl
Rnor_6.0 Ensembl54,946,694 - 4,975,436 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000081661   ⟹   ENSRNOP00000074619
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl54,946,006 - 4,972,124 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000166527   ⟹   ENSRNOP00000109576
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl510,316,513 - 10,345,153 (-)Ensembl
RefSeq Acc Id: NM_001012229   ⟹   NP_001012229
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8510,316,510 - 10,345,253 (-)NCBI
mRatBN7.255,533,413 - 5,562,168 (-)NCBI
Rnor_6.054,946,693 - 4,975,436 (-)NCBI
Rnor_5.054,914,209 - 4,948,129 (-)NCBI
RGSC_v3.454,733,198 - 4,763,409 (-)RGD
Celera55,118,209 - 5,146,740 (-)RGD
Sequence:
RefSeq Acc Id: XM_006237733   ⟹   XP_006237795
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8510,316,510 - 10,345,141 (-)NCBI
mRatBN7.255,530,384 - 5,562,059 (-)NCBI
Rnor_6.054,946,332 - 4,975,326 (-)NCBI
Rnor_5.054,914,209 - 4,948,129 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001012229 (Get FASTA)   NCBI Sequence Viewer  
  XP_006237795 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT07112 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000058714
  ENSRNOP00000058714.2
  ENSRNOP00000109576.1
RefSeq Acc Id: NP_001012229   ⟸   NM_001012229
- UniProtKB: Q5GH54 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237795   ⟸   XM_006237733
- Peptide Label: isoform X1
- UniProtKB: Q5GH54 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000074619   ⟸   ENSRNOT00000081661
Ensembl Acc Id: ENSRNOP00000058714   ⟸   ENSRNOT00000062006
Ensembl Acc Id: ENSRNOP00000109576   ⟸   ENSRNOT00000166527

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5GH54-F1-model_v2 AlphaFold Q5GH54 1-373 view protein structure

Transcriptome

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

Promoters
RGD ID:13693530
Promoter ID:EPDNEW_R4053
Type:multiple initiation site
Name:Xkr9_1
Description:XK related 9
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_6.054,975,400 - 4,975,460EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359260 AgrOrtholog
BioCyc Gene G2FUF-42263 BioCyc
Ensembl Genes ENSRNOG00000040289 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000062006 ENTREZGENE
  ENSRNOT00000062006.5 UniProtKB/TrEMBL
  ENSRNOT00000166527.1 UniProtKB/TrEMBL
InterPro Membr_transp_prot_XK-like UniProtKB/TrEMBL
  XK-related_scramblase UniProtKB/TrEMBL
KEGG Report rno:497099 UniProtKB/TrEMBL
NCBI Gene 497099 ENTREZGENE
PANTHER XK-RELATED PROTEIN UniProtKB/TrEMBL
  XK-RELATED PROTEIN 9 UniProtKB/TrEMBL
Pfam XK-related UniProtKB/TrEMBL
PhenoGen Xkr9 PhenoGen
RatGTEx ENSRNOG00000040289 RatGTEx
UniProt A0ABK0LFK8_RAT UniProtKB/TrEMBL
  Q5GH54 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Xkr9  XK related 9  Xkr9  X-linked Kx blood group related 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-25 Xkr9  X-linked Kx blood group related 9  Xkr9  XK, Kell blood group complex subunit-related family, member 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-12-15 Xkr9  XK, Kell blood group complex subunit-related family, member 9  Xkr9  X Kell blood group precursor related family member 9 homolog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Xkr9  X Kell blood group precursor related family member 9 homolog  XRG9  XK-related protein 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 XRG9  XK-related protein 9      Symbol and Name status set to provisional 70820 PROVISIONAL