VPS50 (VPS50 subunit of EARP/GARPII 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   new 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
Gene: VPS50 (VPS50 subunit of EARP/GARPII complex) Pan paniscus
Analyze
Symbol: VPS50
Name: VPS50 subunit of EARP/GARPII complex
RGD ID: 11841256
Description: ENCODES a protein that exhibits SNARE binding (inferred); INVOLVED IN endocytic recycling (ortholog); retrograde transport, endosome to Golgi (ortholog); ASSOCIATED WITH genetic disease (ortholog); NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, SEIZURES, AND NEONATAL CHOLESTASIS (ortholog); pleomorphic xanthoastrocytoma (ortholog); FOUND IN EARP complex (ortholog); membrane (ortholog); perinuclear region of cytoplasm (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: CCDC132; coiled-coil domain containing 132; syndetin; VPS50, EARP/GARPII complex subunit
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly
Position:
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26111,074,309 - 111,202,358 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17159,340,873 - 159,467,006 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0785,188,960 - 85,315,452 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1798,783,520 - 98,909,208 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl798,786,809 - 98,908,113 (+)Ensemblpanpan1.1panPan2
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
VPS50
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26111,074,309 - 111,202,358 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17159,340,873 - 159,467,006 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0785,188,960 - 85,315,452 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1798,783,520 - 98,909,208 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl798,786,809 - 98,908,113 (+)Ensemblpanpan1.1panPan2
VPS50
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38793,232,366 - 93,361,123 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl793,232,340 - 93,361,123 (+)EnsemblGRCh38hg38GRCh38
GRCh37792,861,679 - 92,990,435 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36792,699,589 - 92,826,274 (+)NCBINCBI36Build 36hg18NCBI36
Celera787,566,164 - 87,692,840 (+)NCBICelera
Cytogenetic Map7q21.2-q21.3NCBI
HuRef787,470,455 - 87,601,198 (+)NCBIHuRef
CHM1_1792,791,700 - 92,920,441 (+)NCBICHM1_1
T2T-CHM13v2.0794,474,420 - 94,603,577 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2792,190,974 - 92,319,745 (+)NCBI
Vps50
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3963,498,393 - 3,603,531 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl63,498,382 - 3,603,531 (+)EnsemblGRCm39 Ensembl
GRCm3863,498,393 - 3,603,531 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl63,498,382 - 3,603,531 (+)EnsemblGRCm38mm10GRCm38
MGSCv3763,448,393 - 3,553,531 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3663,448,405 - 3,553,307 (+)NCBIMGSCv36mm8
Celera63,656,648 - 3,761,558 (+)NCBICelera
Cytogenetic Map6A1NCBI
cM Map61.81NCBI
Vps50
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8432,439,101 - 32,540,299 (+)NCBIGRCr8
mRatBN7.2431,484,424 - 31,585,617 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl431,484,463 - 31,585,617 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx436,457,167 - 36,558,319 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0432,383,277 - 32,484,430 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0430,741,292 - 30,842,473 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0428,441,255 - 28,551,784 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl428,441,301 - 28,551,784 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0428,344,487 - 28,455,450 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4428,304,788 - 28,410,697 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1428,318,488 - 28,424,228 (+)NCBI
Celera426,870,657 - 26,971,611 (+)NCBICelera
Cytogenetic Map4q13NCBI
Vps50
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543210,134,141 - 10,245,895 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543210,134,280 - 10,244,390 (+)NCBIChiLan1.0ChiLan1.0
VPS50
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11418,742,214 - 18,874,779 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1418,742,349 - 18,874,776 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1418,302,677 - 18,435,316 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01418,550,501 - 18,683,063 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1418,550,139 - 18,683,566 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11418,709,720 - 18,842,184 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01418,445,282 - 18,578,116 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01418,696,225 - 18,828,745 (+)NCBIUU_Cfam_GSD_1.0
Vps50
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511832,148,433 - 32,269,351 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936803530,402 - 651,502 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936803530,543 - 651,461 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS50
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl973,074,906 - 73,217,053 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1973,074,878 - 73,215,833 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2979,841,292 - 79,965,954 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS50
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12155,660,565 - 55,782,188 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2155,660,311 - 55,782,167 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604248,524,305 - 48,645,505 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps50
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462481359,528 - 189,169 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462481359,560 - 187,743 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSPPAT00000065041   ⟹   ENSPPAP00000042112
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl798,786,809 - 98,908,113 (+)Ensembl
RefSeq Acc Id: ENSPPAT00000065042   ⟹   ENSPPAP00000042113
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl798,789,340 - 98,908,113 (+)Ensembl
RefSeq Acc Id: ENSPPAT00000065043   ⟹   ENSPPAP00000042114
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl798,789,340 - 98,908,113 (+)Ensembl
RefSeq Acc Id: ENSPPAT00000065046   ⟹   ENSPPAP00000042117
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl798,801,929 - 98,908,113 (+)Ensembl
RefSeq Acc Id: ENSPPAT00000065048   ⟹   ENSPPAP00000042119
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl798,810,458 - 98,899,620 (+)Ensembl
RefSeq Acc Id: XM_003809726   ⟹   XP_003809774
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v26111,074,309 - 111,202,358 (+)NCBI
NHGRI_mPanPan17159,340,873 - 159,467,006 (+)NCBI
Mhudiblu_PPA_v0785,188,969 - 85,315,452 (+)NCBI
PanPan1.1798,783,520 - 98,908,704 (+)NCBI
Sequence:
RefSeq Acc Id: XM_034964460   ⟹   XP_034820351
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v26111,076,562 - 111,202,358 (+)NCBI
NHGRI_mPanPan17159,341,200 - 159,467,006 (+)NCBI
Mhudiblu_PPA_v0785,188,960 - 85,315,452 (+)NCBI
Protein Sequences
Protein RefSeqs XP_003809774 (Get FASTA)   NCBI Sequence Viewer  
  XP_034820351 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSPPAP00000042112.1
  ENSPPAP00000042113
  ENSPPAP00000042113.1
  ENSPPAP00000042114.1
  ENSPPAP00000042117.1
  ENSPPAP00000042119.1
Reference Protein Sequences
RefSeq Acc Id: XP_003809774   ⟸   XM_003809726
- Peptide Label: isoform X1
- UniProtKB: A0A2R9CM63 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_034820351   ⟸   XM_034964460
- Peptide Label: isoform X2
- UniProtKB: A0A2R9CSA7 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSPPAP00000042117   ⟸   ENSPPAT00000065046
RefSeq Acc Id: ENSPPAP00000042114   ⟸   ENSPPAT00000065043
RefSeq Acc Id: ENSPPAP00000042113   ⟸   ENSPPAT00000065042
RefSeq Acc Id: ENSPPAP00000042112   ⟸   ENSPPAT00000065041
RefSeq Acc Id: ENSPPAP00000042119   ⟸   ENSPPAT00000065048
Protein Domains
Syndetin C-terminal   Vacuolar protein sorting-associated protein 54 N-


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSPPAG00000043615 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSPPAT00000065041.1 UniProtKB/TrEMBL
  ENSPPAT00000065042.1 UniProtKB/TrEMBL
  ENSPPAT00000065043.1 UniProtKB/TrEMBL
  ENSPPAT00000065046.1 UniProtKB/TrEMBL
  ENSPPAT00000065048.1 UniProtKB/TrEMBL
InterPro Syndetin_C UniProtKB/TrEMBL
  VPS50 UniProtKB/TrEMBL
  VPS54_N UniProtKB/TrEMBL
NCBI Gene VPS50 ENTREZGENE
PANTHER PTHR13258 UniProtKB/TrEMBL
  SYNDETIN UniProtKB/TrEMBL
Pfam DUF2451 UniProtKB/TrEMBL
  Vps54_N UniProtKB/TrEMBL
UniProt A0A2R9CJI8_PANPA UniProtKB/TrEMBL
  A0A2R9CJJ2_PANPA UniProtKB/TrEMBL
  A0A2R9CM63 ENTREZGENE, UniProtKB/TrEMBL
  A0A2R9CSA6_PANPA UniProtKB/TrEMBL
  A0A2R9CSA7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-01-29 VPS50  VPS50 subunit of EARP/GARPII complex    VPS50, EARP/GARPII complex subunit  Symbol and/or name change 5135510 APPROVED