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 Behavioral & Substance Use Disorder 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: Vps50 (VPS50 subunit of EARP/GARPII complex) Rattus norvegicus
Analyze
Symbol: Vps50
Name: VPS50 subunit of EARP/GARPII complex
RGD ID: 1304751
Description: Predicted to enable SNARE binding activity. Predicted to be involved in endocytic recycling. Located in membrane; perinuclear region of cytoplasm; and recycling endosome. Orthologous to human VPS50 (VPS50 subunit of EARP/GARPII complex); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Ccdc132; coiled-coil domain containing 132; coiled-coil domain-containing protein 132; coiled-coil domain-containing protein 132-like; EARP/GARPII complex subunit VPS50; LOC100911994; LOC312083; RGD1304751; similar to RIKEN cDNA 1700034M03 gene; syndetin; syndetin-like; VPS50 EARP/GARPII complex subunit
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8432,439,101 - 32,540,299 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl432,439,138 - 32,540,538 (+)EnsemblGRCr8
mRatBN7.2431,484,424 - 31,585,617 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl431,484,463 - 31,585,617 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx436,457,167 - 36,558,319 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0432,383,277 - 32,484,430 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0430,741,292 - 30,842,473 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0428,441,255 - 28,551,784 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl428,441,301 - 28,551,784 (+)Ensemblrn6Rnor6.0
Rnor_5.0428,344,487 - 28,455,450 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4428,304,788 - 28,410,697 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera426,870,657 - 26,971,611 (+)NCBICelera
RGSC_v3.1428,318,488 - 28,424,228 (+)NCBI
Cytogenetic Map4q13NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IEA)
EARP complex  (IBA,IEA,ISO,ISS)
membrane  (IDA,IEA)
perinuclear region of cytoplasm  (IDA)
recycling endosome  (IDA,IEA,ISO,ISS)

Molecular Function
protein binding  (IPI,ISO)
SNARE binding  (IBA,IEA,ISO)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. 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.
5. 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.
Additional References at PubMed
PMID:12477932   PMID:19056867   PMID:19946888   PMID:27440922  


Genomics

Comparative Map Data
Vps50
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8432,439,101 - 32,540,299 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl432,439,138 - 32,540,538 (+)EnsemblGRCr8
mRatBN7.2431,484,424 - 31,585,617 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl431,484,463 - 31,585,617 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx436,457,167 - 36,558,319 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0432,383,277 - 32,484,430 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0430,741,292 - 30,842,473 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0428,441,255 - 28,551,784 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl428,441,301 - 28,551,784 (+)Ensemblrn6Rnor6.0
Rnor_5.0428,344,487 - 28,455,450 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4428,304,788 - 28,410,697 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera426,870,657 - 26,971,611 (+)NCBICelera
RGSC_v3.1428,318,488 - 28,424,228 (+)NCBI
Cytogenetic Map4q13NCBI
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 (+)Ensemblhg38GRCh38
GRCh37792,861,679 - 92,990,435 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36792,699,589 - 92,826,274 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm3863,498,393 - 3,603,531 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl63,498,382 - 3,603,531 (+)Ensemblmm10GRCm38
MGSCv3763,448,393 - 3,553,531 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3663,448,405 - 3,553,307 (+)NCBIMGSCv36mm8
Celera63,656,648 - 3,761,558 (+)NCBICelera
Cytogenetic Map6A1NCBI
cM Map61.81NCBI
Vps50
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543210,134,141 - 10,245,895 (+)Ensembl
ChiLan1.0NW_00495543210,134,280 - 10,244,390 (+)NCBIChiLan1.0ChiLan1.0
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 (+)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1418,302,677 - 18,435,316 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01418,550,501 - 18,683,063 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (-)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462481359,560 - 187,743 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Vps50
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v16135,011,654 - 135,114,947 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Vps50
701 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:229
Count of miRNA genes:155
Interacting mature miRNAs:173
Transcripts:ENSRNOT00000067087
Prediction methods:Microtar, Miranda, Rnahybrid
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
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)41308014658080146Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41564430960644309Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4132668025Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4132668025Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41103870656038706Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4134142783Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)427730518170099664Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4134142783Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)4135396961Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41103870656038706Rat
70222Eae2Experimental allergic encephalomyelitis QTL 24.3nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)42228845340471598Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)426234499134199155Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4589457557613242Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41103870656038706Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41170660492690519Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41890069763900697Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4145429897Rat
8552803Bw144Body weight QTL 14416body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)4135396961Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)427862204126119996Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41103870656038706Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)4135396961Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45889999148002343Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4132668025Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42228845363245191Rat
8552807Vie4Viral induced encephalitis QTL 47.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)41890069763900697Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41103870656038706Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)43044896182336920Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4140471598Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4588999950889999Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)4135396961Rat
7387227Uae40Urinary albumin excretion QTL 402.90.0052urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)41891315163913151Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42786220462997402Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4133538816Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42192515166925151Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)4163900697Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41103870656038706Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4132668025Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)412212457182430611Rat
1354665Stl10Serum triglyceride level QTL 103.57blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42228845345429897Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41075870140490708Rat

Markers in Region
D4Mgh26  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8432,486,990 - 32,487,202 (+)Marker Load Pipeline
mRatBN7.2431,532,304 - 31,532,516 (+)MAPPERmRatBN7.2
Rnor_6.0428,489,143 - 28,489,354NCBIRnor6.0
Rnor_5.0428,392,361 - 28,392,572UniSTSRnor5.0
RGSC_v3.4428,356,124 - 28,356,335UniSTSRGSC3.4
RGSC_v3.4428,356,123 - 28,356,334RGDRGSC3.4
Celera426,918,495 - 26,918,706UniSTS
RGSC_v3.1428,369,857 - 28,370,068RGD
Cytogenetic Map4q13UniSTS
D4Got285  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2431,551,572 - 31,551,723 (+)MAPPERmRatBN7.2
Rnor_6.0428,517,742 - 28,517,892NCBIRnor6.0
Rnor_5.0428,421,408 - 28,421,558UniSTSRnor5.0
RGSC_v3.4428,375,426 - 28,375,576UniSTSRGSC3.4
Celera426,937,574 - 26,937,724UniSTS
Cytogenetic Map4q13UniSTS
RH127690  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2431,585,353 - 31,585,548 (+)MAPPERmRatBN7.2
Rnor_6.0431,352,233 - 31,352,427NCBIRnor6.0
Rnor_6.0428,551,521 - 28,551,715NCBIRnor6.0
Rnor_5.0428,455,187 - 28,455,381UniSTSRnor5.0
Rnor_5.0431,256,040 - 31,256,234UniSTSRnor5.0
RGSC_v3.4428,410,258 - 28,410,452UniSTSRGSC3.4
Celera426,971,348 - 26,971,542UniSTS
Cytogenetic Map4q13UniSTS
AA818446  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2431,585,195 - 31,585,380 (+)MAPPERmRatBN7.2
Rnor_6.0431,352,075 - 31,352,259NCBIRnor6.0
Rnor_6.0428,551,363 - 28,551,547NCBIRnor6.0
Rnor_5.0431,255,882 - 31,256,066UniSTSRnor5.0
Rnor_5.0428,455,029 - 28,455,213UniSTSRnor5.0
RGSC_v3.4428,410,100 - 28,410,284UniSTSRGSC3.4
Celera426,971,190 - 26,971,374UniSTS
RH 3.4 Map4170.1UniSTS
Cytogenetic Map4q13UniSTS


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
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000064866   ⟹   ENSRNOP00000061982
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl432,439,138 - 32,540,538 (+)Ensembl
mRatBN7.2 Ensembl431,484,463 - 31,585,617 (+)Ensembl
Rnor_6.0 Ensembl431,333,970 - 31,351,942 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000067087   ⟹   ENSRNOP00000059003
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl432,439,138 - 32,540,538 (+)Ensembl
mRatBN7.2 Ensembl431,484,463 - 31,585,617 (+)Ensembl
Rnor_6.0 Ensembl428,441,301 - 28,551,784 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000095718   ⟹   ENSRNOP00000086543
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl432,439,138 - 32,540,538 (+)Ensembl
mRatBN7.2 Ensembl431,484,463 - 31,585,617 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000096203   ⟹   ENSRNOP00000093011
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl432,444,675 - 32,540,538 (+)Ensembl
mRatBN7.2 Ensembl431,489,989 - 31,585,617 (+)Ensembl
RefSeq Acc Id: NM_001173511   ⟹   NP_001166982
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8432,439,149 - 32,540,299 (+)NCBI
mRatBN7.2431,484,463 - 31,585,617 (+)NCBI
Rnor_6.0428,441,301 - 28,551,784 (+)NCBI
Rnor_5.0428,344,487 - 28,455,450 (+)NCBI
Celera426,870,657 - 26,971,611 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006236037   ⟹   XP_006236099
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8432,439,110 - 32,540,279 (+)NCBI
mRatBN7.2431,484,424 - 31,585,600 (+)NCBI
Rnor_6.0428,441,255 - 28,551,764 (+)NCBI
Rnor_5.0428,344,487 - 28,455,450 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008762704   ⟹   XP_008760926
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8432,439,101 - 32,540,279 (+)NCBI
mRatBN7.2431,484,424 - 31,585,600 (+)NCBI
Rnor_6.0428,441,255 - 28,551,764 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001166982 (Get FASTA)   NCBI Sequence Viewer  
  XP_006236099 (Get FASTA)   NCBI Sequence Viewer  
  XP_008760926 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH91288 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000059003
  ENSRNOP00000059003.1
GenBank Protein F1LSG8 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001166982   ⟸   NM_001173511
- UniProtKB: F1LSG8 (UniProtKB/Swiss-Prot),   A0A8I6GK25 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006236099   ⟸   XM_006236037
- Peptide Label: isoform X2
- UniProtKB: A0A8I6GK25 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760926   ⟸   XM_008762704
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GK25 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000059003   ⟸   ENSRNOT00000067087
Ensembl Acc Id: ENSRNOP00000061982   ⟸   ENSRNOT00000064866
Ensembl Acc Id: ENSRNOP00000093011   ⟸   ENSRNOT00000096203
Ensembl Acc Id: ENSRNOP00000086543   ⟸   ENSRNOT00000095718
Protein Domains
Syndetin C-terminal   Vacuolar protein sorting-associated protein 54 N-

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZTE2-F1-model_v2 AlphaFold D3ZTE2 1-343 view protein structure
AF-F1LSG8-F1-model_v2 AlphaFold F1LSG8 1-964 view protein structure

Transcriptome

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

Promoters
RGD ID:13692853
Promoter ID:EPDNEW_R3377
Type:multiple initiation site
Name:Vps50_1
Description:VPS50 EARP/GARPII complex subunit
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0428,441,290 - 28,441,350EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304751 AgrOrtholog
BioCyc Gene G2FUF-45738 BioCyc
Ensembl Genes ENSRNOG00000009894 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00000050855 Ensembl
Ensembl Transcript ENSRNOT00000067087 ENTREZGENE
  ENSRNOT00000067087.3 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7304986 IMAGE-MGC_LOAD
InterPro Syndetin_C UniProtKB/Swiss-Prot
  VPS50 UniProtKB/Swiss-Prot
  VPS54_N UniProtKB/Swiss-Prot
KEGG Report rno:312083 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109185 IMAGE-MGC_LOAD
NCBI Gene 312083 ENTREZGENE
PANTHER PTHR13258 UniProtKB/Swiss-Prot
  SYNDETIN UniProtKB/Swiss-Prot
Pfam DUF2451 UniProtKB/Swiss-Prot
  Vps54_N UniProtKB/Swiss-Prot
PhenoGen Vps50 PhenoGen
RatGTEx ENSRNOG00000009894 RatGTEx
  ENSRNOG00000050855 RatGTEx
UniProt A0A8I6GE55_RAT UniProtKB/TrEMBL
  A0A8I6GK25 ENTREZGENE, UniProtKB/TrEMBL
  D3ZTE2_RAT UniProtKB/TrEMBL
  F1LSG8 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Vps50  VPS50 subunit of EARP/GARPII complex  LOC100911994  coiled-coil domain-containing protein 132-like  Data merged from RGD:6489220 737654 PROVISIONAL
2019-04-02 Vps50  VPS50 subunit of EARP/GARPII complex  Vps50  VPS50 EARP/GARPII complex subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-09 Vps50  VPS50 EARP/GARPII complex subunit  Ccdc132  coiled-coil domain containing 132  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100911994  coiled-coil domain-containing protein 132-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-04 Ccdc132  coiled-coil domain containing 132  RGD1304751  similar to RIKEN cDNA 1700034M03 gene  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1304751  similar to RIKEN cDNA 1700034M03 gene  RGD1304751_predicted  similar to RIKEN cDNA 1700034M03 gene (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1304751_predicted  similar to RIKEN cDNA 1700034M03 gene (predicted)  LOC312083_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC312083_predicted  similar to RIKEN cDNA 1700034M03 gene (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL