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 chemical synaptic transmission; cytosolic transport; and neurogenesis. 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
Black Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Vps54-ps1  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81499,580,120 - 99,657,178 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1499,580,148 - 99,657,164 (+)EnsemblGRCr8
mRatBN7.21495,378,821 - 95,455,871 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1495,378,012 - 95,455,857 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1499,748,500 - 99,803,139 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014100,988,838 - 101,043,480 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01497,462,359 - 97,517,004 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.014106,153,407 - 106,207,715 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14106,153,575 - 106,207,658 (+)Ensemblrn6Rnor6.0
Rnor_5.014106,220,200 - 106,274,489 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.414102,018,126 - 102,072,258 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1494,414,915 - 94,468,850 (+)NCBICelera
RGSC_v3.114102,037,336 - 102,091,469 (+)NCBI
Cytogenetic Map14q22NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
apoptotic DNA fragmentation  (IEA,ISO)
astrocyte differentiation  (IEA,ISO)
cellular response to progesterone stimulus  (IEA,ISO)
gene expression  (IEA,ISO)
Golgi to vacuole transport  (IBA)
homeostasis of number of cells  (IEA,ISO)
homeostasis of number of cells within a tissue  (ISO)
in utero embryonic development  (IEA,ISO)
intracellular calcium ion homeostasis  (IEA,ISO)
intracellular protein localization  (IEA,ISO)
L-glutamate import  (IEA,ISO)
limb development  (IEA,ISO)
limb morphogenesis  (IEA,ISO)
lysosomal transport  (ISO)
microglia differentiation  (IEA,ISO)
mitochondrion organization  (IEA,ISO)
motor behavior  (IEA,ISO)
motor neuron apoptotic process  (IEA,ISO)
musculoskeletal movement  (ISO)
negative regulation of motor neuron apoptotic process  (IEA,ISO)
neural tissue regeneration  (IEA,ISO)
neurofilament cytoskeleton organization  (ISO)
neuroinflammatory response  (IEA,ISO)
neuromuscular synaptic transmission  (IEA,ISO)
neuron apoptotic process  (IEA,ISO)
neuron projection morphogenesis  (IEA,ISO)
post-embryonic forelimb morphogenesis  (IEA,ISO)
protein localization to cell surface  (IEA,ISO)
protein targeting to ER  (IEA,ISO)
protein targeting to lysosome  (IEA,ISO)
protein targeting to vacuole  (IEA,ISO)
protein transport  (IEA)
regulation of growth  (ISO)
respiratory electron transport chain  (IEA,ISO)
response to antibiotic  (IEA,ISO)
response to calcium ion  (IEA,ISO)
retrograde transport, endosome to Golgi  (IBA,IEA,ISO)
skeletal muscle tissue development  (IEA,ISO)
skeletal muscle tissue growth  (IEA,ISO)
spermatid differentiation  (IEA,ISO)
sphingolipid catabolic process  (IEA,ISO)
striated muscle contraction  (IEA,ISO)
synaptic transmission, GABAergic  (IEA,ISO)
synaptic transmission, glutamatergic  (IEA,ISO)
thrombin-activated receptor signaling pathway  (IEA,ISO)
ubiquitin recycling  (IEA,ISO)
vacuole organization  (IEA,ISO)
vesicle-mediated cholesterol transport  (IEA,ISO)

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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. A proposed clinical application of a model of CO2 laser radiation induced damage craters. Canestri F, J Med Eng Technol. 1988 May-Jun;12(3):112-7. doi: 10.3109/03091908809030166.
2. 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.
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. EARP is a multisubunit tethering complex involved in endocytic recycling. Schindler C, etal., Nat Cell Biol. 2015 May;17(5):639-50. doi: 10.1038/ncb3129. Epub 2015 Mar 23.
7. The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles. Topalidou I, etal., PLoS Genet. 2016 May 18;12(5):e1006074. doi: 10.1371/journal.pgen.1006074. eCollection 2016 May.
8. Identification, characterization and cytogenetic mapping of a yeast Vps54 homolog in rat and mouse. Walter L, etal., Gene 2002 Feb 20;285(1-2):213-20.
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
GRCr81499,580,120 - 99,657,178 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1499,580,148 - 99,657,164 (+)EnsemblGRCr8
mRatBN7.21495,378,821 - 95,455,871 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1495,378,012 - 95,455,857 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1499,748,500 - 99,803,139 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014100,988,838 - 101,043,480 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01497,462,359 - 97,517,004 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.014106,153,407 - 106,207,715 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14106,153,575 - 106,207,658 (+)Ensemblrn6Rnor6.0
Rnor_5.014106,220,200 - 106,274,489 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.414102,018,126 - 102,072,258 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1494,414,915 - 94,468,850 (+)NCBICelera
RGSC_v3.114102,037,336 - 102,091,469 (+)NCBI
Cytogenetic Map14q22NCBI
VPS54
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38263,892,150 - 64,019,428 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl263,892,146 - 64,019,476 (-)Ensemblhg38GRCh38
GRCh37264,119,284 - 64,246,562 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36263,973,171 - 64,099,718 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34264,031,317 - 64,157,865NCBI
Celera263,964,934 - 64,091,495 (-)NCBICelera
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 (-)NCBIT2T-CHM13v2.0
Vps54
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391121,189,032 - 21,271,133 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1121,189,281 - 21,271,136 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381121,239,032 - 21,321,133 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1121,239,281 - 21,321,136 (+)Ensemblmm10GRCm38
MGSCv371121,138,892 - 21,221,136 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361121,139,284 - 21,221,136 (+)NCBIMGSCv36mm8
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 (+)Ensembl
ChiLan1.0NW_00495542420,329,009 - 20,443,652 (+)NCBIChiLan1.0ChiLan1.0
VPS54
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21262,380,379 - 62,507,197 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A62,384,330 - 62,510,395 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A63,959,930 - 64,087,102 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A65,085,093 - 65,176,657 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A65,086,374 - 65,176,634 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1063,487,248 - 63,565,630 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01064,607,383 - 64,685,416 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1064,608,155 - 64,683,345 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11064,289,180 - 64,367,317 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01064,598,125 - 64,676,956 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01064,890,757 - 64,968,754 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Vps54
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629219,648,881 - 19,735,890 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364918,833,285 - 8,922,711 (-)EnsemblSpeTri2.0 Ensembl
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 - 77,975,429 (+)EnsemblsusScr11Sscrofa11.1
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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1443,008,915 - 43,125,850 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604568,734,694 - 68,867,307 (-)NCBIVero_WHO_p1.0Vero_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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247629,457,283 - 9,570,311 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Vps54
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11189,428,683 - 89,504,206 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Vps54
373 total Variants
miRNA Target Status (No longer updated)

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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1582201Sffal2Serum free fatty acids level QTL 240.0002blood free fatty acid amount (VT:0001553)serum free fatty acids level (CMO:0000547)1496755448100078267Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)1484164970100078267Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1459848686104848686Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1477914838104348525Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1433424686102238540Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1474255551109089856Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1462398852107398852Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1477640071100078267Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1460854936105854936Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1474255551109089856Rat
4889951Bss92Bone structure and strength QTL 923.9tibia area (VT:1000281)tibia-fibula cortical bone total cross-sectional area (CMO:0001721)1486271332100078267Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1459848686104848686Rat

Markers in Region
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


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
23 13 83 215 91 90 59 159 59 6 491 285 22 193 116 124 31 34 34

Sequence


Ensembl Acc Id: ENSRNOT00000010264   ⟹   ENSRNOP00000010264
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1499,580,148 - 99,657,164 (+)Ensembl
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
GRCr81499,603,036 - 99,657,178 (+)NCBI
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_039091649   ⟹   XP_038947577
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81499,580,120 - 99,657,173 (+)NCBI
mRatBN7.21495,378,821 - 95,455,133 (+)NCBI
RefSeq Acc Id: XM_039091650   ⟹   XP_038947578
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81499,580,120 - 99,657,173 (+)NCBI
mRatBN7.21495,378,821 - 95,455,294 (+)NCBI
RefSeq Acc Id: XM_063272889   ⟹   XP_063128959
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81499,580,124 - 99,657,173 (+)NCBI
RefSeq Acc Id: XR_010057346
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81499,580,120 - 99,652,911 (+)NCBI
Protein Sequences
Protein RefSeqs NP_775170 (Get FASTA)   NCBI Sequence Viewer  
  XP_038947577 (Get FASTA)   NCBI Sequence Viewer  
  XP_038947578 (Get FASTA)   NCBI Sequence Viewer  
  XP_063128959 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAB96885 (Get FASTA)   NCBI Sequence Viewer  
  EDL97954 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000010264
GenBank Protein Q9JMK8 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_775170   ⟸   NM_173147
- UniProtKB: Q9JMK8 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000010264   ⟸   ENSRNOT00000010264
RefSeq Acc Id: XP_038947578   ⟸   XM_039091650
- Peptide Label: isoform X2
- UniProtKB: Q9JMK8 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_038947577   ⟸   XM_039091649
- Peptide Label: isoform X1
- UniProtKB: Q9JMK8 (UniProtKB/Swiss-Prot),   G3V6Z1 (UniProtKB/TrEMBL),   A6JQ37 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063128959   ⟸   XM_063272889
- Peptide Label: isoform X1
- UniProtKB: Q9JMK8 (UniProtKB/Swiss-Prot),   A6JQ37 (UniProtKB/TrEMBL),   G3V6Z1 (UniProtKB/TrEMBL)
Protein Domains
Vacuolar protein sorting-associated protein 54 C-   Vacuolar protein sorting-associated protein 54 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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628718 AgrOrtholog
BioCyc Gene G2FUF-14834 BioCyc
Ensembl Genes ENSRNOG00000007125 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000010264 ENTREZGENE
Gene3D-CATH 1.20.1280.130 UniProtKB/Swiss-Prot
  6.10.250.860 UniProtKB/Swiss-Prot
InterPro Vps54 UniProtKB/Swiss-Prot
  Vps54_C UniProtKB/Swiss-Prot
  VPS54_N UniProtKB/Swiss-Prot
KEGG Report rno:286932 UniProtKB/Swiss-Prot
NCBI Gene 286932 ENTREZGENE
PANTHER PTHR12965 UniProtKB/Swiss-Prot
  VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 54 UniProtKB/Swiss-Prot
Pfam Vps54 UniProtKB/Swiss-Prot
  Vps54_N UniProtKB/Swiss-Prot
PhenoGen Vps54 PhenoGen
RatGTEx ENSRNOG00000007125 RatGTEx
UniProt A6JQ37 ENTREZGENE, UniProtKB/TrEMBL
  G3V6Z1 ENTREZGENE, 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