Vps8 (VPS8 subunit of CORVET complex) - Rat Genome Database
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Gene: Vps8 (VPS8 subunit of CORVET complex) Rattus norvegicus
Analyze
Symbol: Vps8
Name: VPS8 subunit of CORVET complex
RGD ID: 1309443
Description: Predicted to have metal ion binding activity. Predicted to be involved in endosomal vesicle fusion. Predicted to localize to CORVET complex and early endosome. Orthologous to human VPS8 (VPS8 subunit of CORVET complex); INTERACTS WITH bisphenol A; decabromodiphenyl ether; (-)-epigallocatechin 3-gallate (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC287990; RGD1309443; similar to mKIAA0804 protein; vacuolar protein sorting 8 homolog; vacuolar protein sorting 8 homolog (S. cerevisiae); vacuolar protein sorting-associated protein 8 homolog; VPS8 CORVET complex subunit
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
mRatBN7.21179,402,236 - 79,634,234 (-)NCBI
Rnor_6.0 Ensembl1183,105,064 - 83,300,409 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01183,104,912 - 83,323,606 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01186,184,133 - 86,400,369 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41181,635,546 - 81,866,781 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11181,693,489 - 81,956,899 (-)NCBI
Celera1178,253,172 - 78,478,852 (-)NCBICelera
Cytogenetic Map11q23NCBI
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
CORVET complex  (IBA,ISO)
early endosome  (IBA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:25266290  


Genomics

Comparative Map Data
Vps8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21179,402,236 - 79,634,234 (-)NCBI
Rnor_6.0 Ensembl1183,105,064 - 83,300,409 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01183,104,912 - 83,323,606 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01186,184,133 - 86,400,369 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41181,635,546 - 81,866,781 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11181,693,489 - 81,956,899 (-)NCBI
Celera1178,253,172 - 78,478,852 (-)NCBICelera
Cytogenetic Map11q23NCBI
VPS8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3184,812,143 - 185,052,614 (+)EnsemblGRCh38hg38GRCh38
GRCh383184,812,143 - 185,052,614 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373184,529,925 - 184,770,402 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh373184,529,954 - 184,770,402 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363186,012,625 - 186,253,096 (+)NCBINCBI36hg18NCBI36
Celera3182,976,573 - 183,217,415 (+)NCBI
Cytogenetic Map3q27.2NCBI
HuRef3181,939,950 - 182,180,425 (+)NCBIHuRef
CHM1_13184,492,807 - 184,733,266 (+)NCBICHM1_1
Vps8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391621,241,859 - 21,463,431 (+)NCBIGRCm39mm39
GRCm381621,423,118 - 21,644,681 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1621,423,118 - 21,644,680 (+)EnsemblGRCm38mm10GRCm38
MGSCv371621,423,191 - 21,644,753 (+)NCBIGRCm37mm9NCBIm37
MGSCv361621,337,101 - 21,558,663 (+)NCBImm8
Celera1621,989,997 - 22,212,312 (+)NCBICelera
Cytogenetic Map16B1NCBI
Vps8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542022,504,440 - 22,715,094 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542022,504,076 - 22,715,094 (-)NCBIChiLan1.0ChiLan1.0
VPS8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13190,329,884 - 190,567,701 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3190,329,567 - 190,567,700 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03181,850,827 - 182,089,846 (+)NCBIMhudiblu_PPA_v0panPan3
VPS8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3417,632,208 - 17,889,036 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13417,632,749 - 17,889,607 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Vps8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365784,842,899 - 5,091,439 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13122,693,746 - 122,951,688 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113122,693,681 - 122,953,625 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213132,225,073 - 132,278,113 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS8
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1154,368,144 - 4,607,691 (-)NCBI
ChlSab1.1 Ensembl154,367,706 - 4,607,656 (-)Ensembl
Vps8
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473071,544,572 - 71,782,622 (-)NCBI

Position Markers
D11Rat55  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01183,172,413 - 83,172,639NCBIRnor6.0
Rnor_5.01186,251,638 - 86,251,864UniSTSRnor5.0
RGSC_v3.41181,703,066 - 81,703,293RGDRGSC3.4
RGSC_v3.41181,703,067 - 81,703,293UniSTSRGSC3.4
RGSC_v3.11181,760,656 - 81,760,882RGD
Celera1178,320,662 - 78,320,888UniSTS
RH 3.4 Map11654.4RGD
RH 3.4 Map11654.4UniSTS
SHRSP x BN Map1136.5499UniSTS
SHRSP x BN Map1136.5499RGD
Cytogenetic Map11q23UniSTS
RH132254  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01183,104,928 - 83,105,113NCBIRnor6.0
Rnor_5.01186,184,153 - 86,184,338UniSTSRnor5.0
RGSC_v3.41181,635,566 - 81,635,751UniSTSRGSC3.4
Celera1178,253,188 - 78,253,373UniSTS
RH 3.4 Map11654.4UniSTS
Cytogenetic Map11q23UniSTS
BF387449  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01183,133,505 - 83,133,660NCBIRnor6.0
Rnor_5.01186,212,730 - 86,212,885UniSTSRnor5.0
RGSC_v3.41181,664,144 - 81,664,299UniSTSRGSC3.4
Celera1178,281,759 - 78,281,914UniSTS
RH 3.4 Map11654.1UniSTS
Cytogenetic Map11q23UniSTS
BF399377  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01183,133,817 - 83,133,981NCBIRnor6.0
Rnor_5.01186,213,042 - 86,213,206UniSTSRnor5.0
RGSC_v3.41181,664,456 - 81,664,620UniSTSRGSC3.4
Celera1178,282,071 - 78,282,235UniSTS
RH 3.4 Map11654.1UniSTS
Cytogenetic Map11q23UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114309033886714631Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114658320986714631Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115785881090463843Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115994302390463843Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)116010984287141948Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)116265336586714475Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116265336586714483Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116449467190463843Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116934231986312439Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116964970890463843Rat
1354656Bvd3Brain ventricular dilatation QTL 33.640.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)117272002986994795Rat
10450831Scl80Serum cholesterol level QTL 804.70.01blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)118035840887200449Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:322
Count of miRNA genes:113
Interacting mature miRNAs:122
Transcripts:ENSRNOT00000029255, ENSRNOT00000058274, ENSRNOT00000058276
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.


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 2 22 20 4 19 4 1 1 74 35 38 11 1
Low 1 21 37 37 37 7 10 3 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000029255   ⟹   ENSRNOP00000030100
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1183,105,064 - 83,300,409 (-)Ensembl
RefSeq Acc Id: XM_006221186   ⟹   XP_006221248
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1178,253,172 - 78,478,852 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006221188   ⟹   XP_006221250
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1178,253,523 - 78,478,615 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006221189   ⟹   XP_006221251
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1178,253,523 - 78,478,722 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006221190   ⟹   XP_006221252
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1178,253,523 - 78,478,852 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248575   ⟹   XP_006248637
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21179,402,587 - 79,634,234 (-)NCBI
Rnor_6.01183,104,912 - 83,323,606 (-)NCBI
Rnor_5.01186,184,133 - 86,400,369 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248577   ⟹   XP_006248639
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21179,402,587 - 79,633,998 (-)NCBI
Rnor_6.01183,105,263 - 83,323,369 (-)NCBI
Rnor_5.01186,184,133 - 86,400,369 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248578   ⟹   XP_006248640
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21179,402,587 - 79,634,053 (-)NCBI
Rnor_6.01183,105,263 - 83,323,476 (-)NCBI
Rnor_5.01186,184,133 - 86,400,369 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248579   ⟹   XP_006248641
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21179,402,587 - 79,634,234 (-)NCBI
Rnor_6.01183,105,263 - 83,323,606 (-)NCBI
Rnor_5.01186,184,133 - 86,400,369 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008758163   ⟹   XP_008756385
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1178,302,518 - 78,478,852 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008768831   ⟹   XP_008767053
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01183,154,269 - 83,323,606 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598225   ⟹   XP_017453714
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21179,402,587 - 79,634,134 (-)NCBI
Rnor_6.01183,105,263 - 83,323,584 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598226   ⟹   XP_017453715
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01183,105,263 - 83,312,308 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017604364   ⟹   XP_017459853
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1178,253,523 - 78,478,829 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088953   ⟹   XP_038944881
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21179,402,587 - 79,627,405 (-)NCBI
RefSeq Acc Id: XM_039088954   ⟹   XP_038944882
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21179,402,236 - 79,624,060 (-)NCBI
RefSeq Acc Id: XM_039088955   ⟹   XP_038944883
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21179,402,587 - 79,634,234 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_006221252   ⟸   XM_006221190
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006221248   ⟸   XM_006221186
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006221251   ⟸   XM_006221189
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006221250   ⟸   XM_006221188
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006248641   ⟸   XM_006248579
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006248637   ⟸   XM_006248575
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006248640   ⟸   XM_006248578
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006248639   ⟸   XM_006248577
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008756385   ⟸   XM_008758163
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008767053   ⟸   XM_008768831
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017459853   ⟸   XM_017604364
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017453714   ⟸   XM_017598225
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453715   ⟸   XM_017598226
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000030100   ⟸   ENSRNOT00000029255
RefSeq Acc Id: XP_038944882   ⟸   XM_039088954
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944883   ⟸   XM_039088955
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944881   ⟸   XM_039088953
- Peptide Label: isoform X1
Protein Domains
RING-type   WD_REPEATS_REGION

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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:1309443 AgrOrtholog
Ensembl Genes ENSRNOG00000001764 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000030100 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029255 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
InterPro Vps8_central_dom UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_dom UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
NCBI Gene 287990 ENTREZGENE
Pfam Vps8 UniProtKB/TrEMBL
PhenoGen Vps8 PhenoGen
PROSITE WD_REPEATS_2 UniProtKB/TrEMBL
  WD_REPEATS_REGION UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/TrEMBL
SMART RING UniProtKB/TrEMBL
Superfamily-SCOP WD40_like UniProtKB/TrEMBL
UniProt D4A5F7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-02 Vps8  VPS8 subunit of CORVET complex  Vps8  VPS8 CORVET complex subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-25 Vps8  VPS8 CORVET complex subunit  Vps8  vacuolar protein sorting 8 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-26 Vps8  vacuolar protein sorting 8 homolog (S. cerevisiae)  RGD1309443_predicted  similar to mKIAA0804 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1309443_predicted  similar to mKIAA0804 protein (predicted)  LOC287990_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC287990_predicted  similar to mKIAA0804 protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL