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 have syntaxin binding activity. Predicted to be involved in several processes, including Golgi to vacuole transport; embryonic ectodermal digestive tract development; and endosomal transport. Predicted to localize to cytoplasmic vesicle; membrane; and perinuclear region of cytoplasm. Orthologous to human VPS52 (VPS52 subunit of GARP complex); INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also 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 Genes
More Info more info ...
Related Pseudogenes: Sacm2l-ps3  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,920,715 - 4,931,685 (-)NCBI
Rnor_6.0 Ensembl205,432,004 - 5,441,706 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0205,431,997 - 5,441,736 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0207,490,616 - 7,500,348 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,073,753 - 5,083,339 (-)NCBIRGSC3.4rn4RGSC3.4
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


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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

References

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
mRatBN7.2204,920,715 - 4,931,685 (-)NCBI
Rnor_6.0 Ensembl205,432,004 - 5,441,706 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0205,431,997 - 5,441,736 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0207,490,616 - 7,500,348 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,073,753 - 5,083,339 (-)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl633,250,272 - 33,272,047 (-)EnsemblGRCh38hg38GRCh38
GRCh38633,250,272 - 33,271,965 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37633,218,049 - 33,239,742 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36633,326,027 - 33,347,640 (-)NCBINCBI36hg18NCBI36
Celera634,772,418 - 34,794,017 (-)NCBI
Cytogenetic Map6p21.32NCBI
HuRef632,960,078 - 32,981,319 (-)NCBIHuRef
CHM1_1633,220,041 - 33,241,675 (-)NCBICHM1_1
Vps52
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,174,753 - 34,186,012 (+)NCBIGRCm39mm39
GRCm39 Ensembl1734,174,786 - 34,186,009 (+)Ensembl
GRCm381733,955,779 - 33,967,038 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1733,955,812 - 33,967,035 (+)EnsemblGRCm38mm10GRCm38
MGSCv371734,092,827 - 34,103,433 (+)NCBIGRCm37mm9NCBIm37
MGSCv361733,566,266 - 33,577,438 (+)NCBImm8
Celera1736,708,772 - 36,718,743 (+)NCBICelera
Cytogenetic Map17B1NCBI
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
PanPan1.1633,936,683 - 33,958,404 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl633,936,683 - 33,958,404 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0632,822,394 - 32,844,120 (-)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.0123,028,483 - 3,043,812 (-)NCBI
UMICH_Zoey_3.1122,696,593 - 2,711,699 (-)NCBI
UNSW_CanFamBas_1.0122,777,932 - 2,793,204 (-)NCBI
UU_Cfam_GSD_1.0122,852,572 - 2,867,899 (-)NCBI
Vps52
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494638,348,223 - 38,366,057 (-)NCBI
SpeTri2.0NW_00493647625,594,168 - 25,612,044 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS52
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl729,624,224 - 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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11738,805,072 - 38,824,526 (+)NCBI
ChlSab1.1 Ensembl1738,805,355 - 38,825,383 (+)Ensembl
Vps52
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475423,549,033 - 23,563,756 (+)NCBI

Position Markers
D20Yum82  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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
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
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


QTLs in Region (Rnor_6.0)
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)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2020187706567419Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2031518156896013Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2031518156896013Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
7175096Tcs1T cell selection QTL 1T cell selectionexpression2039105555533640Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2040391135875448Rat
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)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2048554689899946Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RChigh CD8 T cell count to CD45RClow CD8 T cell count ratio (CMO:0001990)20485546810800530Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat

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.


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_008772706 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772707 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772708 (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_039098439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497172 (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
  JACYVU010000324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000000549   ⟹   ENSRNOP00000000549
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,432,004 - 5,441,706 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092306
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,433,623 - 5,435,494 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092458
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,433,629 - 5,434,234 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092539
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,439,980 - 5,440,690 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092605
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,439,671 - 5,440,146 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092640
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,439,026 - 5,440,231 (-)Ensembl
RefSeq Acc Id: NM_033097   ⟹   NP_149088
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_008772706   ⟹   XP_008770928
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,921,984 - 4,931,685 (-)NCBI
Rnor_6.0205,431,997 - 5,441,736 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772707   ⟹   XP_008770929
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,920,715 - 4,931,681 (-)NCBI
Rnor_6.0205,431,997 - 5,441,736 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772708   ⟹   XP_008770930
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,921,984 - 4,931,683 (-)NCBI
Rnor_6.0205,431,997 - 5,441,736 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772709   ⟹   XP_008770931
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0205,433,284 - 5,441,736 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098438   ⟹   XP_038954366
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,922,990 - 4,931,684 (-)NCBI
RefSeq Acc Id: XM_039098439   ⟹   XP_038954367
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,921,961 - 4,929,963 (-)NCBI
RefSeq Acc Id: XM_039098440   ⟹   XP_038954368
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,926,172 - 4,931,679 (-)NCBI
RefSeq Acc Id: XR_005497171
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,922,870 - 4,931,684 (-)NCBI
RefSeq Acc Id: XR_005497172
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,922,988 - 4,931,684 (-)NCBI
RefSeq Acc Id: XR_005497173
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,923,703 - 4,931,683 (-)NCBI
RefSeq Acc Id: XR_005497174
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,925,136 - 4,931,682 (-)NCBI
RefSeq Acc Id: XR_005497175
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,925,136 - 4,931,677 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_149088   ⟸   NM_033097
- UniProtKB: O55166 (UniProtKB/Swiss-Prot),   B2GUV2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770930   ⟸   XM_008772708
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008770929   ⟸   XM_008772707
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008770928   ⟸   XM_008772706
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008770931   ⟸   XM_008772709
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000000549   ⟸   ENSRNOT00000000549
RefSeq Acc Id: XP_038954367   ⟸   XM_039098439
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038954366   ⟸   XM_039098438
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038954368   ⟸   XM_039098440
- Peptide Label: isoform X6

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 7493198 7493199 C G snv SBH/Ygl (MCW), GH/OmrMcwi (MCW)
20 7493207 7493208 C G snv SBH/Ygl (MCW)
20 7493209 7493210 C T snv SBH/Ygl (MCW), GH/OmrMcwi (MCW)
20 7497250 7497251 T A snv RCS/Kyo (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 5433380 5433381 G A snv SBH/Ygl (MCW), CDR, CDS, Buf/N (MCW), M520/N (MCW), SHRSP/Gcrc (RGD), LE/Stm (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), SBH/Ygl (RGD), SHR/NHsd (RGD), GK/Ox (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 5076292 5076293 C T snv GH/OmrMcwi (MCW)
20 5076335 5076336 C G snv SHRSP/Gcrc (MDC), GH/OmrMcwi (MCW)
20 5076346 5076347 C T snv GH/OmrMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3618 AgrOrtholog
Ensembl Genes ENSRNOG00000000470 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000000549 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000000549 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:9029985 IMAGE-MGC_LOAD
InterPro Vps52 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
Pfam Vps52 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vps52 PhenoGen
UniProt 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