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

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Gene: Vhl (von Hippel-Lindau tumor suppressor) Rattus norvegicus
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Symbol: Vhl
Name: von Hippel-Lindau tumor suppressor
RGD ID: 3960
Description: Predicted to enable several functions, including protein serine/threonine kinase binding activity; transcription elongation factor activity; and ubiquitin-like ligase-substrate adaptor activity. Predicted to contribute to ubiquitin-protein transferase activity. Involved in several processes, including regulation of primary metabolic process; response to ethanol; and response to hypoxia. Part of VCB complex. Used to study Parkinsonism. 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 human 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
Previously 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
Black Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Vhll  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84148,328,099 - 148,334,992 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl4148,328,079 - 148,334,991 (+)EnsemblGRCr8
mRatBN7.24146,772,483 - 146,779,376 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4146,772,468 - 146,779,377 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx4152,156,905 - 152,163,822 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04147,937,768 - 147,944,685 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04146,566,004 - 146,572,922 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.04145,580,869 - 145,587,835 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4145,580,799 - 145,587,845 (+)Ensemblrn6Rnor6.0
Rnor_5.04208,877,266 - 208,884,234 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.44149,529,396 - 149,536,289 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera4135,326,806 - 135,333,699 (+)NCBICelera
RGSC_v3.14149,774,236 - 149,781,130 (+)NCBI
Cytogenetic Map4q42NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
aflatoxin B1  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
beta-lapachone  (ISO)
bisphenol A  (EXP,ISO)
Butylbenzyl phthalate  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
cobalt atom  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
desferrioxamine B  (ISO)
diazinon  (EXP,ISO)
Dibutyl phosphate  (ISO)
dichlorine  (EXP)
dieldrin  (EXP)
dioxygen  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
glycidol  (EXP)
graphite  (EXP)
hydrogen peroxide  (ISO)
iron dichloride  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
malathion  (ISO)
manganese(II) chloride  (ISO)
menadione  (ISO)
methotrexate  (ISO)
minocycline  (ISO)
motexafin gadolinium  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nickel dichloride  (EXP,ISO)
Nor-9-carboxy-delta9-THC  (ISO)
ozone  (EXP)
paracetamol  (EXP,ISO)
perfluorooctanoic acid  (EXP)
quercetin  (ISO)
resveratrol  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium chloride  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc acetate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
amyloid fibril formation  (ISO)
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 autophagy  (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 signal transduction  (ISO)
negative regulation of thymocyte apoptotic process  (ISO)
negative regulation of TORC1 signaling  (ISO,ISS)
negative regulation of transcription by RNA polymerase II  (IMP,ISO)
negative regulation of transcription elongation by RNA polymerase II  (ISO)
neuron differentiation  (IDA)
pancreatic A cell differentiation  (ISO)
positive regulation of DNA-templated transcription  (ISO)
positive regulation of epithelial cell proliferation  (ISO)
proteasomal protein catabolic process  (ISO)
proteasome-mediated ubiquitin-dependent protein catabolic process  (ISO,ISS)
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 response to hypoxia  (ISO)
regulation of DNA-templated transcription  (IDA,ISO)
regulation of gene expression  (IEA,ISO)
regulation of postsynapse organization  (IEA,ISO)
regulation of protein localization  (ISO)
regulation of thymocyte apoptotic process  (ISO)
regulation protein catabolic process at postsynapse  (IEA,ISO)
response to ethanol  (IEP)
response to hypoxia  (IEA,IMP)
type B pancreatic cell differentiation  (ISO)

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Bilateral pheochromocytomas and congenital anomalies associated with a de novo germline mutation in the von Hippel-Lindau gene. Assadi F and Brackbill EL, Am J Kidney Dis. 2003 Jan;41(1):E3.
2. Genetic pathways involved in carcinogenesis of clear cell renal cell carcinoma: genomics towards personalized medicine. 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. Endogenous von Hippel-Lindau tumor suppressor protein regulates catecholaminergic phenotype in PC12 cells. Bauer AL, etal., Cancer Res 2002 Mar 15;62(6):1682-7.
4. Identification of differently expressed genes in chemical carcinogen-induced rat bladder cancers. Chen G, etal., J Huazhong Univ Sci Technolog Med Sci. 2009 Apr;29(2):220-6. Epub 2009 Apr 28.
5. PKB/Akt activation inhibits p53-mediated HIF1A degradation that is independent of MDM2. Choy MK, etal., J Cell Physiol. 2010 Mar;222(3):635-9.
6. Surgical decision-making affected by clinical and genetic screening of a novel kindred with von Hippel-Lindau disease and pancreatic islet cell tumors. Curley SA, etal., Ann Surg. 1998 Feb;227(2):229-35.
7. Characterization of the VHL tumor suppressor gene product: localization, complex formation, and the effect of natural inactivating mutations. Duan DR, etal., Proc Natl Acad Sci U S A 1995 Jul 3;92(14):6459-63.
8. 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.
9. Skin-derived precursors differentiating into dopaminergic neuronal cells in the brains of Parkinson disease model rats. Higashida T, etal., J Neurosurg. 2010 Mar 19.
10. VHL-box and SOCS-box domains determine binding specificity for Cul2-Rbx1 and Cul5-Rbx2 modules of ubiquitin ligases. Kamura T, etal., Genes Dev. 2004 Dec 15;18(24):3055-65.
11. Rbx1, a component of the VHL tumor suppressor complex and SCF ubiquitin ligase. Kamura T, etal., Science. 1999 Apr 23;284(5414):657-61.
12. Cloning of the rat homologue of the von Hippel-Lindau tumor suppressor gene and its non-somatic mutation in rat renal cell carcinomas. Kikuchi Y, etal., Jpn J Cancer Res. 1995 Oct;86(10):905-9.
13. Role of VHL gene mutation in human cancer. Kim WY and Kaelin WG, J Clin Oncol 2004 Dec 15;22(24):4991-5004.
14. High Frequency of Ovarian Cyst Development in Vhl2B/+;Snf5+/- Mice. Kuwahara Y, etal., Am J Pathol. 2018 Jul;188(7):1510-1516. doi: 10.1016/j.ajpath.2018.03.010. Epub 2018 Apr 22.
15. Liver hypoxia and lack of recovery after reperfusion at high blood alcohol levels in the intragastric feeding model of alcohol liver disease. Li J, etal., Exp Mol Pathol. 2004 Dec;77(3):184-92.
16. Adipose-derived exosomes deliver miR-23a/b to regulate tumor growth in hepatocellular cancer by targeting the VHL/HIF axis. Liu Y, etal., J Physiol Biochem. 2019 Aug;75(3):391-401. doi: 10.1007/s13105-019-00692-6. Epub 2019 Jul 18.
17. Methylation profile of circulating plasma DNA in patients with pancreatic cancer. Melnikov AA, etal., J Surg Oncol. 2009 Feb 1;99(2):119-22.
18. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
19. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
20. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
21. The von Hippel-Lindau tumor-suppressor gene product forms a stable complex with human CUL-2, a member of the Cdc53 family of proteins. Pause A, etal., Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2156-61.
22. Von Hippel-Lindau-dependent polycythemia is endemic on the island of Ischia: identification of a novel cluster. Perrotta S, etal., Blood. 2006 Jan 15;107(2):514-9. Epub 2005 Oct 6.
23. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
24. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
25. von Hippel-Lindau tumor suppressor protein represses platelet-derived growth factor B-chain gene expression via the Sp1 binding element in the proximal PDGF-B promoter. Rafty LA and Khachigian LM, J Cell Biochem 2002;85(3):490-5.
26. GOA pipeline RGD automated data pipeline
27. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
29. VHL inactivation is an important pathway for the development of malignant sporadic pancreatic endocrine tumors. Schmitt AM, etal., Endocr Relat Cancer. 2009 Dec;16(4):1219-27. Epub 2009 Aug 18.
30. Regulation of tyrosine hydroxylase promoter activity by the von Hippel-Lindau tumor suppressor protein and hypoxia-inducible transcription factors. Schnell PO, etal., J Neurochem 2003 Apr;85(2):483-91.
31. The GABAA receptor family: molecular and functional diversity. Seeburg PH, etal., Cold Spring Harb Symp Quant Biol 1990;55(48):29-40.
32. Regulation of oxygen homeostasis by hypoxia-inducible factor 1. Semenza GL Physiology (Bethesda). 2009 Apr;24:97-106.
33. Down-regulation of von Hippel-Lindau protein in N-nitroso compound-induced rat non-clear cell renal tumors. Shiao YH, etal., Cancer Lett 2002 May 8;179(1):33-8.
34. The von Hippel-Lindau tumor suppressor targets to mitochondria. Shiao YH, etal., Cancer Res. 2000 Jun 1;60(11):2816-9.
35. Regulatory role of vHL/HIF-1alpha in hypoxia-induced VEGF production in hepatic stellate cells. Wang YQ, etal., Biochem Biophys Res Commun. 2004 Apr 30;317(2):358-62.
36. Engrafted VHL peptide-delivered bone marrow stromal cells promote spinal cord repair in rats. 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
GRCr84148,328,099 - 148,334,992 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl4148,328,079 - 148,334,991 (+)EnsemblGRCr8
mRatBN7.24146,772,483 - 146,779,376 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4146,772,468 - 146,779,377 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx4152,156,905 - 152,163,822 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04147,937,768 - 147,944,685 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04146,566,004 - 146,572,922 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.04145,580,869 - 145,587,835 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4145,580,799 - 145,587,845 (+)Ensemblrn6Rnor6.0
Rnor_5.04208,877,266 - 208,884,234 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.44149,529,396 - 149,536,289 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera4135,326,806 - 135,333,699 (+)NCBICelera
RGSC_v3.14149,774,236 - 149,781,130 (+)NCBI
Cytogenetic Map4q42NCBI
VHL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38310,141,778 - 10,153,667 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl310,141,778 - 10,153,676 (+)Ensemblhg38GRCh38
GRCh37310,183,462 - 10,195,351 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36310,158,319 - 10,168,762 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34310,158,318 - 10,168,744NCBI
Celera310,118,983 - 10,129,426 (+)NCBICelera
Cytogenetic Map3p25.3NCBI
HuRef310,119,232 - 10,131,274 (+)NCBIHuRef
CHM1_1310,133,330 - 10,145,363 (+)NCBICHM1_1
T2T-CHM13v2.0310,134,670 - 10,146,564 (+)NCBIT2T-CHM13v2.0
Vhl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396113,600,955 - 113,608,595 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6113,600,920 - 113,608,594 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm386113,623,994 - 113,631,634 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6113,623,959 - 113,631,633 (+)Ensemblmm10GRCm38
MGSCv376113,574,015 - 113,581,627 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv366113,589,798 - 113,597,410 (+)NCBIMGSCv36mm8
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 (+)Ensembl
ChiLan1.0NW_0049555611,573,525 - 1,578,295 (+)NCBIChiLan1.0ChiLan1.0
VHL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2210,136,301 - 10,148,703 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1310,141,061 - 10,153,463 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0310,077,630 - 10,089,499 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1310,430,143 - 10,440,234 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl310,430,143 - 10,440,234 (+)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha208,240,602 - 8,245,270 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0208,235,897 - 8,240,567 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl208,234,824 - 8,240,587 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1207,958,176 - 7,962,844 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0208,303,525 - 8,308,231 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0208,277,313 - 8,281,981 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Vhl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494215,769,090 - 15,776,167 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366023,135,821 - 3,140,447 (-)EnsemblSpeTri2.0 Ensembl
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 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11366,334,535 - 66,342,401 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21373,406,841 - 73,414,691 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VHL
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12246,184,621 - 46,203,065 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2246,184,756 - 46,204,428 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666041120,354,296 - 120,362,332 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vhl
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247315,350,912 - 5,359,286 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Vhl
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1632,905,242 - 32,913,452 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Vhl
18 total Variants
miRNA Target Status (No longer updated)

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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)486583980149763391Rat
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4117737142152833657Rat
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)4146370897184426481Rat
1358364Sradr4Stress Responsive Adrenal Weight QTL 44.92adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)4131384565176384565Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)427730518170099664Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4123870974168870974Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4140059299181024663Rat
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)4146370897184426481Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4108206096153206096Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4106848959168870974Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4127263297172263297Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4147299608184426481Rat
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)4146370897184426481Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4111383604156383604Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)482944895154403548Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4137430611182430611Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)445429897149763204Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4123870974168870974Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4140059299184426481Rat
70201Gcr1Gastric cancer resistance QTL 12.7stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)4103834277148834277Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)457613339151163960Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)412212457182430611Rat
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)4146370897184426481Rat
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)4107346299152346299Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4134095016179095016Rat
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)4112427331157427331Rat
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)4112427331157427331Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4117559384162559384Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4140059299184426481Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)460916264184426481Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4111383604156383604Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)494638356168870820Rat
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)4126334185171334185Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4123870974168870974Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)445429897149763204Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4124700988169700988Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)460916264174095838Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)4100752691179366077Rat
1581566Eae21Experimental allergic encephalomyelitis QTL 216.2body mass (VT:0001259)maximum body weight loss to initial body weight ratio (CMO:0001400)4137447185182447185Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)445429709157555683Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)460916264184426481Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)486709649168870974Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4134199006168870974Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4148121375176967367Rat
2293840Kiddil9Kidney dilation QTL 92.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)4113634167149763391Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)465495851159259805Rat
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)4116184844161184844Rat
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)4121020385148834277Rat
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)4146370897184426481Rat

Markers in Region
RH128791  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24146,779,079 - 146,779,291 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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


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 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000013727   ⟹   ENSRNOP00000013727
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4148,328,079 - 148,334,991 (+)Ensembl
mRatBN7.2 Ensembl4146,772,468 - 146,779,377 (+)Ensembl
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
GRCr84148,328,099 - 148,334,992 (+)NCBI
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:
Protein Sequences
Protein RefSeqs NP_434688 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA86874 (Get FASTA)   NCBI Sequence Viewer  
  AAB35675 (Get FASTA)   NCBI Sequence Viewer  
  AAD37344 (Get FASTA)   NCBI Sequence Viewer  
  EDL91551 (Get FASTA)   NCBI Sequence Viewer  
  EDL91552 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000013727
  ENSRNOP00000013727.1
GenBank Protein Q64259 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_434688   ⟸   NM_052801
- UniProtKB: Q64197 (UniProtKB/Swiss-Prot),   Q80WY8 (UniProtKB/Swiss-Prot),   Q64259 (UniProtKB/Swiss-Prot),   A6IBT3 (UniProtKB/TrEMBL),   A6IBT4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000013727   ⟸   ENSRNOT00000013727
Protein Domains
von Hippel-Lindau disease tumour suppressor alpha   von Hippel-Lindau disease tumour suppressor beta

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q64259-F1-model_v2 AlphaFold Q64259 1-185 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3960 AgrOrtholog
BioCyc Gene G2FUF-43370 BioCyc
Ensembl Genes ENSRNOG00000010258 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000013727 ENTREZGENE
  ENSRNOT00000013727.4 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.750.10 UniProtKB/Swiss-Prot
  2.60.40.780 UniProtKB/Swiss-Prot
InterPro 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
Pfam VHL UniProtKB/Swiss-Prot
  VHL_C UniProtKB/Swiss-Prot
PharmGKB VHL RGD
PhenoGen Vhl PhenoGen
RatGTEx ENSRNOG00000010258 RatGTEx
Superfamily-SCOP SSF49468 UniProtKB/Swiss-Prot
UniProt A6IBT3 ENTREZGENE, UniProtKB/TrEMBL
  A6IBT4 ENTREZGENE, UniProtKB/TrEMBL
  Q64197 ENTREZGENE
  Q64259 ENTREZGENE
  Q80WY8 ENTREZGENE
  VHL_RAT 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