VPS53 (VPS53 subunit of GARP complex) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: VPS53 (VPS53 subunit of GARP complex) Canis lupus familiaris
Analyze
Symbol: VPS53
Name: VPS53 subunit of GARP complex
RGD ID: 12397394
Description: INVOLVED IN lysosomal transport (ortholog); ASSOCIATED WITH genetic disease (ortholog); microcephaly (ortholog); Neurodevelopmental Disorders (ortholog); FOUND IN trans-Golgi network (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: vacuolar protein sorting-associated protein 53 homolog; VPS53, GARP complex subunit
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1945,074,066 - 45,239,569 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl945,074,100 - 45,214,066 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha944,224,566 - 44,391,993 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0945,892,548 - 46,060,240 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl945,892,566 - 46,035,516 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1944,670,971 - 44,838,890 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0944,964,695 - 45,132,085 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0945,043,233 - 45,211,135 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
VPS53
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1945,074,066 - 45,239,569 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl945,074,100 - 45,214,066 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha944,224,566 - 44,391,993 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0945,892,548 - 46,060,240 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl945,892,566 - 46,035,516 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1944,670,971 - 44,838,890 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0944,964,695 - 45,132,085 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0945,043,233 - 45,211,135 (+)NCBIUU_Cfam_GSD_1.0
VPS53
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3817508,668 - 714,839 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl17508,503 - 721,717 (-)EnsemblGRCh38hg38GRCh38
GRCh3717411,908 - 618,079 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3617382,698 - 564,758 (-)NCBINCBI36Build 36hg18NCBI36
Celera17423,924 - 629,862 (-)NCBICelera
Cytogenetic Map17p13.3NCBI
HuRef17325,008 - 528,642 (-)NCBIHuRef
CHM1_117418,907 - 623,396 (-)NCBICHM1_1
T2T-CHM13v2.017391,960 - 599,311 (-)NCBIT2T-CHM13v2.0
Vps53
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391175,937,052 - 76,070,464 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1175,937,052 - 76,070,473 (-)EnsemblGRCm39 Ensembl
GRCm381176,046,226 - 76,179,638 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1176,046,226 - 76,179,647 (-)EnsemblGRCm38mm10GRCm38
MGSCv371175,859,728 - 75,993,132 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361175,862,421 - 75,995,825 (-)NCBIMGSCv36mm8
Celera1183,555,285 - 83,692,488 (-)NCBICelera
Cytogenetic Map11B5NCBI
cM Map1145.92NCBI
Vps53
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81061,418,076 - 61,536,912 (-)NCBIGRCr8
mRatBN7.21060,919,820 - 61,038,674 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1060,919,820 - 61,038,676 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1065,561,939 - 65,680,825 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01065,067,390 - 65,186,273 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01060,537,918 - 60,656,979 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01064,218,596 - 64,341,064 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1064,222,276 - 64,341,109 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01063,672,733 - 63,793,858 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41063,410,886 - 63,535,682 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11063,424,683 - 63,543,200 (-)NCBI
Celera1059,935,404 - 60,054,107 (-)NCBICelera
Cytogenetic Map10q24NCBI
Vps53
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554812,130,888 - 2,264,924 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554812,130,669 - 2,265,065 (-)NCBIChiLan1.0ChiLan1.0
VPS53
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2198,042,929 - 8,261,718 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1179,602,776 - 9,812,194 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v017400,048 - 576,119 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.117416,136 - 604,705 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl17414,782 - 604,705 (-)Ensemblpanpan1.1panPan2
Vps53
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560244,189,381 - 44,329,957 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365387,067,327 - 7,205,768 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365387,067,332 - 7,207,852 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS53
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1247,143,098 - 47,291,161 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11247,141,749 - 47,291,169 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21249,308,850 - 49,456,068 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS53
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.116302,771 - 464,572 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl16303,414 - 464,574 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605921,622,848 - 21,752,483 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps53
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247863,614,811 - 3,778,069 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247863,614,775 - 3,779,644 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in VPS53
1293 total Variants

Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
6 5 5 23 22 16 6 6 6 6 33 22 12 14 10

Sequence


Ensembl Acc Id: ENSCAFT00000030338   ⟹   ENSCAFP00000028186
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl945,074,100 - 45,214,066 (+)Ensembl
Ensembl Acc Id: ENSCAFT00845024625   ⟹   ENSCAFP00845019370
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl945,892,566 - 46,035,273 (+)Ensembl
Ensembl Acc Id: ENSCAFT00845024672   ⟹   ENSCAFP00845019416
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl945,892,573 - 46,035,516 (+)Ensembl
Ensembl Acc Id: ENSCAFT00845024736   ⟹   ENSCAFP00845019463
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl945,892,573 - 46,035,516 (+)Ensembl
Ensembl Acc Id: ENSCAFT00845024786   ⟹   ENSCAFP00845019495
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl945,892,573 - 46,035,516 (+)Ensembl
RefSeq Acc Id: XM_038486583   ⟹   XP_038342511
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1944,670,971 - 44,815,082 (+)NCBI
RefSeq Acc Id: XM_038548440   ⟹   XP_038404368
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0945,043,233 - 45,186,390 (+)NCBI
RefSeq Acc Id: XM_038612378   ⟹   XP_038468306
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0944,964,695 - 45,108,262 (+)NCBI
RefSeq Acc Id: XM_038677654   ⟹   XP_038533582
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0945,892,548 - 46,035,513 (+)NCBI
RefSeq Acc Id: XM_548308   ⟹   XP_548308
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1945,074,066 - 45,217,009 (+)NCBI
Dog10K_Boxer_Tasha944,224,566 - 44,367,284 (+)NCBI
Sequence:
RefSeq Acc Id: XR_002630160
Type: NON-CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1945,074,066 - 45,239,569 (+)NCBI
Dog10K_Boxer_Tasha944,224,566 - 44,391,993 (+)NCBI
Sequence:
RefSeq Acc Id: XR_005331052
Type: NON-CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1944,670,971 - 44,838,890 (+)NCBI
RefSeq Acc Id: XR_005364750
Type: NON-CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0945,043,233 - 45,211,135 (+)NCBI
RefSeq Acc Id: XR_005399189
Type: NON-CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0944,964,695 - 45,132,085 (+)NCBI
RefSeq Acc Id: XR_005432520
Type: NON-CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0945,892,548 - 46,060,240 (+)NCBI
RefSeq Acc Id: XP_548308   ⟸   XM_548308
- UniProtKB: A0A8C0NJH5 (UniProtKB/TrEMBL),   A0A8I3NLI3 (UniProtKB/TrEMBL),   A0A8C0KCV4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCAFP00000028186   ⟸   ENSCAFT00000030338
RefSeq Acc Id: XP_038342511   ⟸   XM_038486583
RefSeq Acc Id: XP_038468306   ⟸   XM_038612378
RefSeq Acc Id: XP_038533582   ⟸   XM_038677654
- UniProtKB: A0A8C0NJH5 (UniProtKB/TrEMBL),   A0A8I3NLI3 (UniProtKB/TrEMBL),   A0A8C0KCV4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038404368   ⟸   XM_038548440
- UniProtKB: A0A8C0KCV4 (UniProtKB/TrEMBL),   A0A8C0NJH5 (UniProtKB/TrEMBL),   A0A8I3NLI3 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSCAFP00845019416   ⟸   ENSCAFT00845024672
Ensembl Acc Id: ENSCAFP00845019370   ⟸   ENSCAFT00845024625
Ensembl Acc Id: ENSCAFP00845019495   ⟸   ENSCAFT00845024786
Ensembl Acc Id: ENSCAFP00845019463   ⟸   ENSCAFT00845024736
Protein Domains
Vps53 C-terminal   Vps53 N-terminal


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000019101 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030016194 UniProtKB/TrEMBL
  ENSCAFG00040002216 UniProtKB/TrEMBL
  ENSCAFG00845013795 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000030338.4 UniProtKB/TrEMBL
  ENSCAFT00000100774.1 UniProtKB/TrEMBL
  ENSCAFT00030029850.1 UniProtKB/TrEMBL
  ENSCAFT00030029936.1 UniProtKB/TrEMBL
  ENSCAFT00030029973.1 UniProtKB/TrEMBL
  ENSCAFT00030030027.1 UniProtKB/TrEMBL
  ENSCAFT00040004223.1 UniProtKB/TrEMBL
  ENSCAFT00845024625.1 UniProtKB/TrEMBL
  ENSCAFT00845024672 ENTREZGENE
  ENSCAFT00845024672.1 UniProtKB/TrEMBL
  ENSCAFT00845024736.1 UniProtKB/TrEMBL
  ENSCAFT00845024786.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.357.110 UniProtKB/TrEMBL
  Methyl-accepting chemotaxis protein UniProtKB/TrEMBL
InterPro Vps53 UniProtKB/TrEMBL
  Vps53_C UniProtKB/TrEMBL
  Vps53_C_sf UniProtKB/TrEMBL
  Vps53_N UniProtKB/TrEMBL
KEGG Report cfa:491188 UniProtKB/TrEMBL
NCBI Gene VPS53 ENTREZGENE
PANTHER PTHR12820 UniProtKB/TrEMBL
  VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 53 HOMOLOG UniProtKB/TrEMBL
Pfam VPS53_C UniProtKB/TrEMBL
  Vps53_N UniProtKB/TrEMBL
UniProt A0A8C0KCV4 ENTREZGENE
  A0A8C0NJH5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0NKX1_CANLF UniProtKB/TrEMBL
  A0A8C0NVX7_CANLF UniProtKB/TrEMBL
  A0A8C0RLG8_CANLF UniProtKB/TrEMBL
  A0A8I3NLI3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3NNJ5_CANLF UniProtKB/TrEMBL
  A0A8I3P0Y7_CANLF UniProtKB/TrEMBL
  A0A8I3RXS0_CANLF UniProtKB/TrEMBL
  A0A8P0NK86_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:48297 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-01-30 VPS53  VPS53 subunit of GARP complex    VPS53, GARP complex subunit  Symbol and/or name change 5135510 APPROVED