Vhl (von Hippel-Lindau tumor suppressor) - Rat Genome Database

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Gene: Vhl (von Hippel-Lindau tumor suppressor) Rattus norvegicus
Analyze
Symbol: Vhl
Name: von Hippel-Lindau tumor suppressor
RGD ID: 3960
Description: Is predicted to contribute to ubiquitin-protein transferase activity. Involved in several processes, including negative regulation of transcription by RNA polymerase II; regulation of catecholamine metabolic process; and response to ethanol. Localizes to several cellular components, including VCB complex; cytosol; and mitochondrion. Biomarker of nephroblastoma and urinary bladder cancer. Human ortholog(s) of this gene implicated in several diseases, including pancreatic cancer (multiple); pheochromocytoma; polycythemia (multiple); renal cell carcinoma; and von Hippel-Lindau disease. Orthologous to several human genes including VHL (von Hippel-Lindau tumor suppressor); PARTICIPATES IN hypoxia inducible factor pathway; altered hypoxia inducible factor pathway; proteasome degradation pathway involving cullin-dependent ubiquitin ligases; INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: pVHL; Vhlh; von Hippel-Lindau disease tumor suppressor; von Hippel-Lindau syndrome; von Hippel-Lindau syndrome homolog; von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24146,772,483 - 146,779,376 (+)NCBI
Rnor_6.0 Ensembl4145,580,799 - 145,587,845 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04145,580,869 - 145,587,835 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04208,877,266 - 208,884,234 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44149,529,396 - 149,536,289 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14149,774,236 - 149,781,130 (+)NCBI
Celera4135,326,806 - 135,333,699 (+)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
angiogenesis  (ISO)
blood vessel endothelial cell migration  (ISO)
camera-type eye morphogenesis  (ISO)
ciliary body morphogenesis  (ISO)
extracellular matrix organization  (ISO)
eye pigmentation  (ISO)
homeostasis of number of retina cells  (ISO)
iris morphogenesis  (ISO)
melanin metabolic process  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of endothelial cell differentiation  (ISO)
negative regulation of gene expression  (ISO)
negative regulation of hypoxia-inducible factor-1alpha signaling pathway  (ISO)
negative regulation of receptor signaling pathway via JAK-STAT  (ISO)
negative regulation of thymocyte apoptotic process  (ISO)
negative regulation of transcription by RNA polymerase II  (IMP)
negative regulation of transcription from RNA polymerase II promoter in response to hypoxia  (ISO)
neuron differentiation  (IDA)
pancreatic A cell differentiation  (ISO)
positive regulation of epithelial cell proliferation  (ISO)
positive regulation of transcription, DNA-templated  (ISO)
proteasomal protein catabolic process  (ISO)
protein catabolic process  (ISO)
protein transport  (ISO)
protein ubiquitination  (IBA,IEA,ISO)
regulation of apoptotic signaling pathway  (ISO)
regulation of catecholamine metabolic process  (IMP)
regulation of cellular protein localization  (ISO)
regulation of gene expression  (ISO)
regulation of postsynapse organization  (ISO)
regulation of protein catabolic process at postsynapse, modulating synaptic transmission  (ISO)
regulation of thymocyte apoptotic process  (ISO)
regulation of transcription, DNA-templated  (IDA,ISO)
response to ethanol  (IEP)
response to hypoxia  (IMP)
type B pancreatic cell differentiation  (ISO)

Cellular Component

Molecular Function

References

References - curated
1. Assadi F and Brackbill EL, Am J Kidney Dis. 2003 Jan;41(1):E3.
2. Audenet F, etal., BJU Int. 2012 Jun;109(12):1864-70. doi: 10.1111/j.1464-410X.2011.10661.x. Epub 2011 Oct 28.
3. Bauer AL, etal., Cancer Res 2002 Mar 15;62(6):1682-7.
4. Chen G, etal., J Huazhong Univ Sci Technolog Med Sci. 2009 Apr;29(2):220-6. Epub 2009 Apr 28.
5. Choy MK, etal., J Cell Physiol. 2010 Mar;222(3):635-9.
6. Curley SA, etal., Ann Surg. 1998 Feb;227(2):229-35.
7. Duan DR, etal., Proc Natl Acad Sci U S A 1995 Jul 3;92(14):6459-63.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. Higashida T, etal., J Neurosurg. 2010 Mar 19.
10. Kamura T, etal., Genes Dev. 2004 Dec 15;18(24):3055-65.
11. Kamura T, etal., Science. 1999 Apr 23;284(5414):657-61.
12. Kikuchi Y, etal., Jpn J Cancer Res. 1995 Oct;86(10):905-9.
13. Kim WY and Kaelin WG, J Clin Oncol 2004 Dec 15;22(24):4991-5004.
14. Li J, etal., Exp Mol Pathol. 2004 Dec;77(3):184-92.
15. Melnikov AA, etal., J Surg Oncol. 2009 Feb 1;99(2):119-22.
16. MGD data from the GO Consortium
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. OMIM Disease Annotation Pipeline
19. Pause A, etal., Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2156-61.
20. Perrotta S, etal., Blood. 2006 Jan 15;107(2):514-9. Epub 2005 Oct 6.
21. Pipeline to import KEGG annotations from KEGG into RGD
22. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
23. Rafty LA and Khachigian LM, J Cell Biochem 2002;85(3):490-5.
24. RGD automated data pipeline
25. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
26. RGD automated import pipeline for gene-chemical interactions
27. Schmitt AM, etal., Endocr Relat Cancer. 2009 Dec;16(4):1219-27. Epub 2009 Aug 18.
28. Schnell PO, etal., J Neurochem 2003 Apr;85(2):483-91.
29. Seeburg PH, etal., Cold Spring Harb Symp Quant Biol 1990;55(48):29-40.
30. Semenza GL Physiology (Bethesda). 2009 Apr;24:97-106.
31. Shiao YH, etal., Cancer Lett 2002 May 8;179(1):33-8.
32. Shiao YH, etal., Cancer Res. 2000 Jun 1;60(11):2816-9.
33. Wang YQ, etal., Biochem Biophys Res Commun. 2004 Apr 30;317(2):358-62.
34. Yamazaki Y, etal., Neuroreport. 2010 Mar 10;21(4):287-92.
Additional References at PubMed
PMID:7660122   PMID:8599582   PMID:11641274   PMID:12169691   PMID:12604794   PMID:12832481   PMID:15010533   PMID:15094462   PMID:15181450   PMID:15456877   PMID:15824735   PMID:16129783  
PMID:16537898   PMID:17519558   PMID:17825299   PMID:17942596   PMID:17973242   PMID:17981124   PMID:22506063   PMID:22627278   PMID:23338840   PMID:24899725   PMID:25186293   PMID:25779090  
PMID:26972007   PMID:27324785   PMID:29401731   PMID:33309718  


Genomics

Comparative Map Data
Vhl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24146,772,483 - 146,779,376 (+)NCBI
Rnor_6.0 Ensembl4145,580,799 - 145,587,845 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04145,580,869 - 145,587,835 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04208,877,266 - 208,884,234 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44149,529,396 - 149,536,289 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14149,774,236 - 149,781,130 (+)NCBI
Celera4135,326,806 - 135,333,699 (+)NCBICelera
Cytogenetic Map4q42NCBI
VHL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl310,141,778 - 10,153,667 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl310,141,008 - 10,152,220 (+)EnsemblGRCh38hg38GRCh38
GRCh38310,141,778 - 10,153,667 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37310,183,462 - 10,195,351 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36310,158,319 - 10,168,762 (+)NCBINCBI36hg18NCBI36
Build 34310,158,318 - 10,168,744NCBI
Celera310,118,983 - 10,129,426 (+)NCBI
Cytogenetic Map3p25.3NCBI
HuRef310,119,232 - 10,131,274 (+)NCBIHuRef
CHM1_1310,133,330 - 10,145,363 (+)NCBICHM1_1
Vhl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396113,600,955 - 113,608,595 (+)NCBIGRCm39mm39
GRCm39 Ensembl6113,600,920 - 113,608,594 (+)Ensembl
GRCm386113,623,994 - 113,631,634 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6113,623,959 - 113,631,633 (+)EnsemblGRCm38mm10GRCm38
MGSCv376113,574,015 - 113,581,627 (+)NCBIGRCm37mm9NCBIm37
MGSCv366113,589,798 - 113,597,410 (+)NCBImm8
Celera6115,450,882 - 115,458,459 (+)NCBICelera
Cytogenetic Map6E3NCBI
cM Map652.81NCBI
Vhl
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555611,573,525 - 1,580,511 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555611,573,525 - 1,578,295 (+)NCBIChiLan1.0ChiLan1.0
VHL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1310,430,143 - 10,440,234 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl310,430,143 - 10,440,234 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0310,077,630 - 10,089,499 (+)NCBIMhudiblu_PPA_v0panPan3
VHL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1208,206,616 - 8,211,347 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl208,206,616 - 8,211,323 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha208,240,602 - 8,245,270 (-)NCBI
ROS_Cfam_1.0208,235,897 - 8,240,567 (-)NCBI
UMICH_Zoey_3.1207,958,176 - 7,962,844 (-)NCBI
UNSW_CanFamBas_1.0208,303,525 - 8,308,231 (-)NCBI
UU_Cfam_GSD_1.0208,277,313 - 8,281,981 (-)NCBI
Vhl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494215,769,090 - 15,776,167 (+)NCBI
SpeTri2.0NW_0049366023,135,790 - 3,140,622 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VHL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1366,334,591 - 66,342,654 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11366,334,535 - 66,342,401 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21373,406,841 - 73,414,691 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VHL
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12246,184,621 - 46,203,065 (+)NCBI
ChlSab1.1 Ensembl2246,184,756 - 46,204,428 (+)Ensembl
Vhl
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247315,350,912 - 5,359,286 (-)NCBI

Position Markers
RH128791  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24146,779,079 - 146,779,291 (+)MAPPER
Rnor_6.04145,587,539 - 145,587,750NCBIRnor6.0
Rnor_5.04208,883,938 - 208,884,149UniSTSRnor5.0
RGSC_v3.44149,535,993 - 149,536,204UniSTSRGSC3.4
Celera4135,333,403 - 135,333,614UniSTS
RH 3.4 Map4947.8UniSTS
Cytogenetic Map4q41.3-q42.1UniSTS
UniSTS:235523  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24146,778,951 - 146,779,160 (+)MAPPER
Rnor_6.04145,587,411 - 145,587,619NCBIRnor6.0
Rnor_5.04208,883,810 - 208,884,018UniSTSRnor5.0
RGSC_v3.44149,535,865 - 149,536,073UniSTSRGSC3.4
Celera4135,333,275 - 135,333,483UniSTS
Cytogenetic Map4q41.3-q42.1UniSTS
PMC23053P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24146,772,705 - 146,772,815 (+)MAPPER
Rnor_6.04145,581,092 - 145,581,201NCBIRnor6.0
Rnor_5.04208,877,489 - 208,877,598UniSTSRnor5.0
RGSC_v3.44149,529,619 - 149,529,728UniSTSRGSC3.4
Celera4135,327,029 - 135,327,138UniSTS
Cytogenetic Map4q41.3-q42.1UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)423850384169318094Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)436615599145611886Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)443414605155469929Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)443414792146942075Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)443414792146942075Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)446898276145611886Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)449906054145611886Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)455324953148360954Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)458640017154427984Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)463537179157286626Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)481959983152055009Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)484475257178931073Rat
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)486312589146942261Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)486312589147702403Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)486438317168047091Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)494893247168046938Rat
2302049Pia32Pristane induced arthritis QTL 325.10.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)4105277348150277348Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4105682594150682594Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4105971071168047091Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106347236151347236Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4108876717169215811Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109636356154636356Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109636356154636356Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110702761155702761Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110702761155702761Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4112807675157807675Rat
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4115372758150038284Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4116726724157291438Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4117926139162926139Rat
70201Gcr1Gastric cancer resistance QTL 12.7stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)4119705414146087100Rat
12798527Anxrr58Anxiety related response QTL 584.110.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4120318422146087100Rat
2293840Kiddil9Kidney dilation QTL 92.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)4120400597146942261Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4123111827168111827Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123478354168478354Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4123587009168587009Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4124442168169442168Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4125884464168047091Rat
1358364Sradr4Stress Responsive Adrenal Weight QTL 44.92adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)4128602727173602727Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4131834282176834282Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4131864442176864442Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132455408168047091Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)4134917642179917642Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4136351734180689124Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4136908430182878540Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4137171018182171018Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4145373934176509907Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4145547014184226339Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4145547014184226339Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:303
Count of miRNA genes:184
Interacting mature miRNAs:233
Transcripts:ENSRNOT00000013727
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.


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 3 34 26 10 19 10 1 1 74 35 41 11 1
Low 9 31 31 31 7 10 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013727   ⟹   ENSRNOP00000013727
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4145,580,799 - 145,587,845 (+)Ensembl
RefSeq Acc Id: NM_052801   ⟹   NP_434688
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24146,772,483 - 146,779,376 (+)NCBI
Rnor_6.04145,580,869 - 145,587,835 (+)NCBI
Rnor_5.04208,877,266 - 208,884,234 (+)NCBI
RGSC_v3.44149,529,396 - 149,536,289 (+)RGD
Celera4135,326,806 - 135,333,699 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_434688   ⟸   NM_052801
- UniProtKB: Q64259 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000013727   ⟸   ENSRNOT00000013727

Transcriptome

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

Promoters
RGD ID:13693310
Promoter ID:EPDNEW_R3834
Type:multiple initiation site
Name:Vhl_1
Description:von Hippel-Lindau tumor suppressor
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_6.04145,580,848 - 145,580,908EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3960 AgrOrtholog
Ensembl Genes ENSRNOG00000010258 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000013727 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000013727 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.750.10 UniProtKB/Swiss-Prot
  2.60.40.780 UniProtKB/Swiss-Prot
InterPro VHL UniProtKB/Swiss-Prot
  VHL_alpha_dom UniProtKB/Swiss-Prot
  VHL_alpha_dom_sf UniProtKB/Swiss-Prot
  VHL_beta_dom UniProtKB/Swiss-Prot
  VHL_beta_dom_sf UniProtKB/Swiss-Prot
  VHL_sf UniProtKB/Swiss-Prot
  VHL_tumour_suppress_b/a_dom UniProtKB/Swiss-Prot
KEGG Report rno:24874 UniProtKB/Swiss-Prot
NCBI Gene 24874 ENTREZGENE
PANTHER PTHR15160:SF10 UniProtKB/Swiss-Prot
Pfam VHL UniProtKB/Swiss-Prot
  VHL_C UniProtKB/Swiss-Prot
PharmGKB VHL RGD
PhenoGen Vhl PhenoGen
Superfamily-SCOP SSF49468 UniProtKB/Swiss-Prot
UniProt Q64259 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q64197 UniProtKB/Swiss-Prot
  Q80WY8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-08 Vhl  von Hippel-Lindau tumor suppressor  Vhl  von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-26 Vhl  von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase  Vhl  von Hippel-Lindau tumor suppressor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Vhl  von Hippel-Lindau tumor suppressor  Vhlh  von Hippel-Lindau syndrome homolog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-15 Vhlh  von Hippel-Lindau syndrome homolog  Vhl  von Hippel-Lindau tumor suppressor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-18 Vhl  von Hippel-Lindau tumor suppressor  Vhl  von Hippel-Lindau syndrome homolog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Vhl  von Hippel-Lindau syndrome homolog    von Hippel-Lindau syndrome  Name updated 629478 APPROVED
2002-06-10 Vhl  von Hippel-Lindau syndrome      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization may translocate between the nucleus and cytosol 730251
gene_disease human homolog often observed to be mutated in renal clear cell type carcinoma 625549
gene_disease downregulated in nitrosoamine-induced eosinophilic epithelial tumors and nitrosoethyl urea induced nephroblastomas 625549
gene_disease mutation of the human homolog is associated with von Hippel-Lindau disease and with sporadic renal carcinoma 730251
gene_expression expressed in adult kidney and 16-day fetal kidney 625549
gene_product 20 and 22kDa protein 625549