Vps54 (VPS54 subunit of GARP complex) - Rat Genome Database

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Gene: Vps54 (VPS54 subunit of GARP complex) Rattus norvegicus
Analyze
Symbol: Vps54
Name: VPS54 subunit of GARP complex
RGD ID: 628718
Description: Predicted to enable syntaxin binding activity. Predicted to be involved in several processes, including Golgi to vacuole transport; negative regulation of motor neuron apoptotic process; and retrograde transport, endosome to Golgi. Predicted to act upstream of or within several processes, including homeostasis of number of cells within a tissue; musculoskeletal movement; and neurofilament cytoskeleton organization. Located in membrane and trans-Golgi network. Orthologous to human VPS54 (VPS54 subunit of GARP complex); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: vacuolar protein sorting 54 (yeast); vacuolar protein sorting 54 homolog; vacuolar protein sorting 54 homolog (S. cerevisiae); vacuolar protein sorting-associated protein 54; VPS54 GARP complex subunit; Vps54-like; Vsp54
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Vps54-ps1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21495,378,821 - 95,455,871 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1495,378,012 - 95,455,857 (+)Ensembl
Rnor_6.014106,153,407 - 106,207,715 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14106,153,575 - 106,207,658 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014106,220,200 - 106,274,489 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414102,018,126 - 102,072,258 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.114102,037,336 - 102,091,469 (+)NCBI
Celera1494,414,915 - 94,468,850 (+)NCBICelera
Cytogenetic Map14q22NCBI
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

Cellular Component
cytosol  (IEA)
GARP complex  (IBA,IEA,ISO,ISS)
Golgi apparatus  (ISO)
membrane  (IDA)
nucleoplasm  (IEA,ISO)
perinuclear region of cytoplasm  (IEA,ISO)
trans-Golgi network  (IDA,IEA,ISO,ISS)

Molecular Function

References

Additional References at PubMed
PMID:8815872   PMID:11493023   PMID:15878329   PMID:19620288   PMID:25795912  


Genomics

Comparative Map Data
Vps54
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21495,378,821 - 95,455,871 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1495,378,012 - 95,455,857 (+)Ensembl
Rnor_6.014106,153,407 - 106,207,715 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14106,153,575 - 106,207,658 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014106,220,200 - 106,274,489 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414102,018,126 - 102,072,258 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.114102,037,336 - 102,091,469 (+)NCBI
Celera1494,414,915 - 94,468,850 (+)NCBICelera
Cytogenetic Map14q22NCBI
VPS54
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38263,892,150 - 64,019,428 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl263,892,146 - 64,019,428 (-)EnsemblGRCh38hg38GRCh38
GRCh37264,119,284 - 64,246,562 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36263,973,171 - 64,099,718 (-)NCBINCBI36hg18NCBI36
Build 34264,031,317 - 64,157,865NCBI
Celera263,964,934 - 64,091,495 (-)NCBI
Cytogenetic Map2p15-p14NCBI
HuRef263,859,380 - 63,986,062 (-)NCBIHuRef
CHM1_1264,049,942 - 64,176,502 (-)NCBICHM1_1
T2T-CHM13v2.0263,899,706 - 64,027,065 (-)NCBI
Vps54
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391121,189,032 - 21,271,133 (+)NCBIGRCm39mm39
GRCm39 Ensembl1121,189,281 - 21,271,136 (+)Ensembl
GRCm381121,239,032 - 21,321,133 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1121,239,281 - 21,321,136 (+)EnsemblGRCm38mm10GRCm38
MGSCv371121,138,892 - 21,221,136 (+)NCBIGRCm37mm9NCBIm37
MGSCv361121,139,284 - 21,221,136 (+)NCBImm8
Celera1123,411,563 - 23,469,500 (+)NCBICelera
Cytogenetic Map11A3.1NCBI
cM Map1113.89NCBI
Vps54
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542420,327,754 - 20,445,980 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542420,329,009 - 20,443,652 (+)NCBIChiLan1.0ChiLan1.0
VPS54
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A65,085,093 - 65,176,657 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A65,086,374 - 65,176,634 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A63,959,930 - 64,087,102 (-)NCBIMhudiblu_PPA_v0panPan3
VPS54
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11063,598,373 - 63,676,753 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1063,599,229 - 63,676,747 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1063,487,248 - 63,565,630 (-)NCBI
ROS_Cfam_1.01064,607,383 - 64,685,416 (-)NCBI
ROS_Cfam_1.0 Ensembl1064,608,155 - 64,683,345 (-)Ensembl
UMICH_Zoey_3.11064,289,180 - 64,367,317 (-)NCBI
UNSW_CanFamBas_1.01064,598,125 - 64,676,956 (-)NCBI
UU_Cfam_GSD_1.01064,890,757 - 64,968,754 (-)NCBI
Vps54
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629219,648,881 - 19,735,890 (+)NCBI
SpeTri2.0NW_0049364918,835,397 - 8,922,403 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS54
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl377,856,138 - 77,975,439 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1377,856,093 - 77,978,194 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2381,716,210 - 81,780,374 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS54
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11443,000,960 - 43,127,129 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1443,008,915 - 43,125,850 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604568,734,694 - 68,867,307 (-)NCBIVero_WHO_p1.0
Vps54
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247629,457,705 - 9,563,779 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046247629,457,283 - 9,570,311 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH138139  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21495,416,471 - 95,416,659 (+)MAPPERmRatBN7.2
Rnor_6.014106,168,316 - 106,168,503NCBIRnor6.0
Rnor_5.014106,235,090 - 106,235,277UniSTSRnor5.0
RGSC_v3.414102,032,865 - 102,033,052UniSTSRGSC3.4
Celera1494,429,625 - 94,429,812UniSTS
RH 3.4 Map14755.0UniSTS
Cytogenetic Map14q22UniSTS
AI454148  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2757,833,480 - 57,833,661 (+)MAPPERmRatBN7.2
mRatBN7.21495,454,753 - 95,454,933 (+)MAPPERmRatBN7.2
Rnor_6.014106,206,598 - 106,206,777NCBIRnor6.0
Rnor_6.0764,392,620 - 64,392,800NCBIRnor6.0
Rnor_5.014106,273,372 - 106,273,551UniSTSRnor5.0
Rnor_5.0764,613,297 - 64,613,477UniSTSRnor5.0
RGSC_v3.4761,940,887 - 61,941,067UniSTSRGSC3.4
RGSC_v3.414102,071,146 - 102,071,325UniSTSRGSC3.4
Celera1494,467,738 - 94,467,917UniSTS
Celera755,015,447 - 55,015,627UniSTS
RH 3.4 Map14753.7UniSTS
Cytogenetic Map14q22UniSTS
Cytogenetic Map7q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)147995092195876975Rat
4889951Bss92Bone structure and strength QTL 923.9tibia area (VT:1000281)tibia-fibula cortical bone total cross-sectional area (CMO:0001721)148205747195876975Rat
1582201Sffal2Serum free fatty acids level QTL 240.0002blood free fatty acid amount (VT:0001553)serum free fatty acids level (CMO:0000547)149255388695876975Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:142
Count of miRNA genes:100
Interacting mature miRNAs:125
Transcripts:ENSRNOT00000010264
Prediction methods:Miranda, 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 57 41 19 41 4 4 74 35 37 11 4
Low 9 4 7 4 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010264   ⟹   ENSRNOP00000010264
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1495,378,012 - 95,455,857 (+)Ensembl
Rnor_6.0 Ensembl14106,153,575 - 106,207,658 (+)Ensembl
RefSeq Acc Id: NM_173147   ⟹   NP_775170
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21495,401,728 - 95,455,871 (+)NCBI
Rnor_6.014106,153,577 - 106,207,710 (+)NCBI
Rnor_5.014106,220,200 - 106,274,489 (+)NCBI
RGSC_v3.414102,018,126 - 102,072,258 (+)RGD
Celera1494,414,915 - 94,468,850 (+)RGD
Sequence:
RefSeq Acc Id: XM_039091646   ⟹   XP_038947574
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21495,378,821 - 95,455,871 (+)NCBI
RefSeq Acc Id: XM_039091647   ⟹   XP_038947575
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21495,378,825 - 95,455,133 (+)NCBI
RefSeq Acc Id: XM_039091648   ⟹   XP_038947576
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21495,378,821 - 95,455,133 (+)NCBI
RefSeq Acc Id: XM_039091649   ⟹   XP_038947577
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21495,378,821 - 95,455,133 (+)NCBI
RefSeq Acc Id: XM_039091650   ⟹   XP_038947578
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21495,378,821 - 95,455,294 (+)NCBI
RefSeq Acc Id: XR_005492900
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21495,378,821 - 95,455,871 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_775170   ⟸   NM_173147
- Sequence:
RefSeq Acc Id: ENSRNOP00000010264   ⟸   ENSRNOT00000010264
RefSeq Acc Id: XP_038947574   ⟸   XM_039091646
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947578   ⟸   XM_039091650
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038947577   ⟸   XM_039091649
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038947576   ⟸   XM_039091648
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038947575   ⟸   XM_039091647
- Peptide Label: isoform X1
Protein Domains
Vps54   Vps54_N

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9JMK8-F1-model_v2 AlphaFold Q9JMK8 1-965 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628718 AgrOrtholog
BioCyc Gene G2FUF-14834 BioCyc
Ensembl Genes ENSRNOG00000007125 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000010264 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010264 ENTREZGENE, UniProtKB/TrEMBL
InterPro Vps54 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vps54_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VPS54_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:286932 UniProtKB/Swiss-Prot
NCBI Gene 286932 ENTREZGENE
PANTHER PTHR12965 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Vps54 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vps54_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vps54 PhenoGen
UniProt G3V6Z1_RAT UniProtKB/TrEMBL
  Q9JMK8 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-02 Vps54  VPS54 subunit of GARP complex  Vps54  VPS54 GARP complex subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-25 Vps54  VPS54 GARP complex subunit  Vps54  vacuolar protein sorting 54 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Vps54  vacuolar protein sorting 54 homolog (S. cerevisiae)  Vps54  vacuolar protein sorting 54 (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 Vps54  vacuolar protein sorting 54 (yeast)      Name updated 1299863 APPROVED
2004-09-10 Vps54  Vps54-like  Vsp54    Symbol and Name updated 1299863 APPROVED
2003-02-27 Vsp54  Vps54-like      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_homology homolog of yeast Vps54 619586