Vps52 (VPS52 subunit of GARP complex) - Rat Genome Database

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Gene: Vps52 (VPS52 subunit of GARP complex) Rattus norvegicus
Analyze
Symbol: Vps52
Name: VPS52 subunit of GARP complex
RGD ID: 3618
Description: Predicted to enable syntaxin binding activity. Predicted to be involved in several processes, including cytosolic transport; endocytic recycling; and vacuolar transport. Predicted to act upstream of or within ectodermal cell differentiation and embryonic ectodermal digestive tract development. Predicted to be located in several cellular components, including Golgi apparatus; perinuclear region of cytoplasm; and recycling endosome. Predicted to be part of EARP complex and GARP complex. Predicted to be active in postsynapse and presynapse. Orthologous to human VPS52 (VPS52 subunit of GARP complex); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Are1; SAC2 (suppressor of actin mutations 2 homolog)-like (S. cerevisiae); SAC2 (supressor of actin mutations 2, homolog)-like (S. cerevisiae) ; SAC2 suppressor of actin mutation 2-like; SAC2 suppressor of actin mutations 2-like protein; Sacm2l; suppressor of actin mutation 2-like; vacuolar protein sorting 52 (yeast); vacuolar protein sorting 52 homolog; vacuolar protein sorting 52 homolog (S. cerevisiae); vacuolar protein sorting-associated protein 52 homolog; VPS52 GARP complex subunit
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Sacm2l-ps3  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,922,599 - 4,933,458 (-)NCBIGRCr8
mRatBN7.2204,920,715 - 4,931,685 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,860,843 - 4,931,665 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx205,645,463 - 5,655,060 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0205,007,208 - 5,016,805 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0205,487,922 - 5,497,595 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0205,431,997 - 5,441,736 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,432,004 - 5,441,706 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0207,490,616 - 7,500,348 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,073,753 - 5,083,339 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1205,074,730 - 5,083,444 (-)NCBI
Celera206,506,237 - 6,515,816 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function
protein binding  (IPI,ISO)
syntaxin binding  (IBA,ISO)

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
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. 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.
7. Identification of a novel highly conserved gene in the centromeric part of the major histocompatibility complex. Walter L and Gunther E, Genomics 1998 Sep 15;52(3):298-304.
Additional References at PubMed
PMID:12477932   PMID:15060004   PMID:15878329   PMID:22871113   PMID:23142660   PMID:25799061   PMID:27440922  


Genomics

Comparative Map Data
Vps52
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,922,599 - 4,933,458 (-)NCBIGRCr8
mRatBN7.2204,920,715 - 4,931,685 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,860,843 - 4,931,665 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx205,645,463 - 5,655,060 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0205,007,208 - 5,016,805 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0205,487,922 - 5,497,595 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0205,431,997 - 5,441,736 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,432,004 - 5,441,706 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0207,490,616 - 7,500,348 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,073,753 - 5,083,339 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1205,074,730 - 5,083,444 (-)NCBI
Celera206,506,237 - 6,515,816 (-)NCBICelera
Cytogenetic Map20p12NCBI
VPS52
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38633,250,272 - 33,271,965 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl633,250,272 - 33,272,047 (-)EnsemblGRCh38hg38GRCh38
GRCh37633,218,049 - 33,239,742 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36633,326,027 - 33,347,640 (-)NCBINCBI36Build 36hg18NCBI36
Celera634,772,418 - 34,794,017 (-)NCBICelera
Cytogenetic Map6p21.32NCBI
HuRef632,960,078 - 32,981,319 (-)NCBIHuRef
CHM1_1633,220,041 - 33,241,595 (-)NCBICHM1_1
T2T-CHM13v2.0633,071,634 - 33,093,327 (-)NCBIT2T-CHM13v2.0
Vps52
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,174,753 - 34,186,012 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1734,174,786 - 34,186,009 (+)EnsemblGRCm39 Ensembl
GRCm381733,955,779 - 33,967,038 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1733,955,812 - 33,967,035 (+)EnsemblGRCm38mm10GRCm38
MGSCv371734,092,827 - 34,103,433 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361733,566,266 - 33,577,438 (+)NCBIMGSCv36mm8
Celera1736,708,772 - 36,718,743 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.98NCBI
Vps52
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554371,820,817 - 1,833,363 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554371,820,355 - 1,833,615 (-)NCBIChiLan1.0ChiLan1.0
VPS52
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2547,728,005 - 47,749,819 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1643,599,681 - 43,621,467 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0632,822,394 - 32,844,120 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1633,936,683 - 33,958,404 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl633,936,683 - 33,958,404 (-)Ensemblpanpan1.1panPan2
VPS52
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1122,697,508 - 2,712,831 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl122,697,508 - 2,712,831 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha122,778,649 - 2,793,972 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0123,028,483 - 3,043,812 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl123,028,488 - 3,043,823 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1122,696,593 - 2,711,699 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0122,777,932 - 2,793,204 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0122,852,572 - 2,867,899 (-)NCBIUU_Cfam_GSD_1.0
Vps52
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494638,348,223 - 38,366,057 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647625,594,114 - 25,612,066 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647625,594,168 - 25,612,044 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS52
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl729,624,230 - 29,639,140 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1729,624,224 - 29,639,168 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2734,127,990 - 34,142,475 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VPS52
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11738,805,072 - 38,824,526 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1738,805,355 - 38,825,383 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604433,087,431 - 33,107,067 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps52
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475423,548,998 - 23,563,931 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475423,549,033 - 23,563,756 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vps52
439 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:331
Count of miRNA genes:191
Interacting mature miRNAs:212
Transcripts:ENSRNOT00000000549
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2046066076691706Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
7175096Tcs1T cell selection QTL 1T cell selectionexpression2047270785024580Rat

Markers in Region
D20Yum82  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,929,504 - 4,929,655 (+)MAPPERmRatBN7.2
Rnor_6.0205,439,520 - 5,439,670NCBIRnor6.0
Rnor_5.0207,498,132 - 7,498,282UniSTSRnor5.0
RGSC_v3.4205,081,271 - 5,081,421UniSTSRGSC3.4
Celera206,513,748 - 6,513,898UniSTS
Cytogenetic Map20p12UniSTS
RH141313  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,921,983 - 4,922,189 (+)MAPPERmRatBN7.2
Rnor_6.0205,431,998 - 5,432,203NCBIRnor6.0
Rnor_5.0207,490,610 - 7,490,815UniSTSRnor5.0
RGSC_v3.4205,073,747 - 5,073,952UniSTSRGSC3.4
Celera206,506,231 - 6,506,436UniSTS
RH 3.4 Map2053.53UniSTS
Cytogenetic Map20p12UniSTS
RH141868  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,922,591 - 4,922,798 (+)MAPPERmRatBN7.2
Rnor_6.0205,432,606 - 5,432,812NCBIRnor6.0
Rnor_5.0207,491,218 - 7,491,424UniSTSRnor5.0
RGSC_v3.4205,074,355 - 5,074,561UniSTSRGSC3.4
Celera206,506,839 - 6,507,045UniSTS
RH 3.4 Map2057.0UniSTS
Cytogenetic Map20p12UniSTS
UniSTS:463437  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,924,733 - 4,926,220 (+)MAPPERmRatBN7.2
Rnor_6.0205,434,748 - 5,436,234NCBIRnor6.0
Rnor_5.0207,493,360 - 7,494,846UniSTSRnor5.0
RGSC_v3.4205,076,497 - 5,077,983UniSTSRGSC3.4
Celera206,508,981 - 6,510,467UniSTS
Cytogenetic Map20p12UniSTS


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 43 51 35 19 35 8 11 74 35 40 11 8
Low 6 6 6 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_033097 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772707 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772709 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098438 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497173 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497174 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497175 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC128962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ223830 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ223831 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC166419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX883042 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSRNOT00000000549   ⟹   ENSRNOP00000000549
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,921,992 - 4,931,573 (-)Ensembl
Rnor_6.0 Ensembl205,432,004 - 5,441,706 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092306
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,433,623 - 5,435,494 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092458
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,433,629 - 5,434,234 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092539
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,439,980 - 5,440,690 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092605
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,439,671 - 5,440,146 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092640
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,439,026 - 5,440,231 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096948   ⟹   ENSRNOP00000087040
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,920,743 - 4,931,665 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107087   ⟹   ENSRNOP00000080803
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,860,843 - 4,931,462 (-)Ensembl
RefSeq Acc Id: NM_033097   ⟹   NP_149088
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,923,874 - 4,933,458 (-)NCBI
mRatBN7.2204,921,990 - 4,931,573 (-)NCBI
Rnor_6.0205,432,004 - 5,441,588 (-)NCBI
Rnor_5.0207,490,616 - 7,500,348 (-)NCBI
RGSC_v3.4205,073,753 - 5,083,339 (-)RGD
Celera206,506,237 - 6,515,816 (-)RGD
Sequence:
RefSeq Acc Id: XM_008772707   ⟹   XP_008770929
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,922,599 - 4,933,386 (-)NCBI
mRatBN7.2204,920,715 - 4,931,681 (-)NCBI
Rnor_6.0205,431,997 - 5,441,736 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098438   ⟹   XP_038954366
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,924,901 - 4,933,386 (-)NCBI
mRatBN7.2204,922,990 - 4,931,684 (-)NCBI
RefSeq Acc Id: XM_039098440   ⟹   XP_038954368
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,928,051 - 4,933,386 (-)NCBI
mRatBN7.2204,926,172 - 4,931,679 (-)NCBI
RefSeq Acc Id: XM_063278973   ⟹   XP_063135043
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,922,599 - 4,931,853 (-)NCBI
RefSeq Acc Id: XR_005497173
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,927,020 - 4,933,386 (-)NCBI
mRatBN7.2204,923,703 - 4,931,683 (-)NCBI
RefSeq Acc Id: XR_005497174
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,927,020 - 4,933,386 (-)NCBI
mRatBN7.2204,925,136 - 4,931,682 (-)NCBI
RefSeq Acc Id: XR_005497175
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,927,020 - 4,933,386 (-)NCBI
mRatBN7.2204,925,136 - 4,931,677 (-)NCBI
RefSeq Acc Id: NP_149088   ⟸   NM_033097
- UniProtKB: O55166 (UniProtKB/Swiss-Prot),   B2GUV2 (UniProtKB/TrEMBL),   A0A8I6A724 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770929   ⟸   XM_008772707
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A724 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000549   ⟸   ENSRNOT00000000549
RefSeq Acc Id: XP_038954366   ⟸   XM_039098438
- Peptide Label: isoform X2
- UniProtKB: A0A8I6A724 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954368   ⟸   XM_039098440
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000087040   ⟸   ENSRNOT00000096948
RefSeq Acc Id: ENSRNOP00000080803   ⟸   ENSRNOT00000107087
RefSeq Acc Id: XP_063135043   ⟸   XM_063278973
- Peptide Label: isoform X3
- UniProtKB: A0A8I6A724 (UniProtKB/TrEMBL)
Protein Domains
Vps52 C-terminal   Vps52 coiled-coil

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O55166-F1-model_v2 AlphaFold O55166 1-723 view protein structure

Transcriptome

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

Promoters
RGD ID:13701409
Promoter ID:EPDNEW_R11932
Type:initiation region
Name:Vps52_1
Description:VPS52 GARP 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_6.0205,441,674 - 5,441,734EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3618 AgrOrtholog
BioCyc Gene G2FUF-4522 BioCyc
Ensembl Genes ENSRNOG00000000470 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055007549 UniProtKB/Swiss-Prot
  ENSRNOG00060004873 UniProtKB/Swiss-Prot
  ENSRNOG00065031276 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000000549 ENTREZGENE
  ENSRNOT00000000549.6 UniProtKB/Swiss-Prot
  ENSRNOT00000096948.1 UniProtKB/TrEMBL
  ENSRNOT00000107087.1 UniProtKB/TrEMBL
  ENSRNOT00055012610 UniProtKB/Swiss-Prot
  ENSRNOT00060008110 UniProtKB/Swiss-Prot
  ENSRNOT00065053942 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:9029985 IMAGE-MGC_LOAD
InterPro Vps52 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vps52_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vps52_CC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25218 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:187352 IMAGE-MGC_LOAD
NCBI Gene 25218 ENTREZGENE
PANTHER PTHR14190 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 52 HOMOLOG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Vps52 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vps52_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vps52 PhenoGen
RatGTEx ENSRNOG00000000470 RatGTEx
  ENSRNOG00055007549 RatGTEx
  ENSRNOG00060004873 RatGTEx
  ENSRNOG00065031276 RatGTEx
UniProt A0A8I6A724 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6G757_RAT UniProtKB/TrEMBL
  A6JJH5_RAT UniProtKB/TrEMBL
  B2GUV2 ENTREZGENE, UniProtKB/TrEMBL
  O55166 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-02 Vps52  VPS52 subunit of GARP complex  Vps52  VPS52 GARP complex subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-25 Vps52  VPS52 GARP complex subunit  Vps52  vacuolar protein sorting 52 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Vps52  vacuolar protein sorting 52 homolog (S. cerevisiae)  Vps52  vacuolar protein sorting 52 (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Vps52  vacuolar protein sorting 52 (yeast)  Sacm2l  SAC2 (supressor of actin mutations 2, homolog)-like (S. cerevisiae)   Symbol and Name updated 1299863 APPROVED
2002-06-10 Sacm2l  SAC2 (supressor of actin mutations 2, homolog)-like (S. cerevisiae)       Name updated 70584 APPROVED
2002-02-20 Sacm2l  SAC2 (suppressor of actin mutations 2 homolog)-like (S. cerevisiae)      Name updated to reflect Human and Mouse nomenclature 70282 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains a putative coiled-coil region and significant homology 633999