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

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Gene: VPS52 (VPS52 subunit of GARP complex) Sus scrofa
Analyze
Symbol: VPS52
Name: VPS52 subunit of GARP complex
RGD ID: 14086105
Description: ENCODES a protein that exhibits syntaxin binding (inferred); INVOLVED IN ectodermal cell differentiation (ortholog); embryonic ectodermal digestive tract development (ortholog); lysosomal transport (ortholog); ASSOCIATED WITH autosomal dominant intellectual developmental disorder 5 (ortholog); genetic disease (ortholog); Prostatic Neoplasms (ortholog); FOUND IN EARP complex (ortholog); postsynapse (ortholog); presynapse (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: vacuolar protein sorting-associated protein 52 homolog; VPS52, GARP complex subunit
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:14681463   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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
(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
481 total Variants

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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 5 1 1 3 15 2
Low 5 3 2 2 2 8 2 1 3
Below cutoff

Sequence


RefSeq Acc Id: ENSSSCT00000001674   ⟹   ENSSSCP00000001630
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl729,624,232 - 29,638,466 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000062106   ⟹   ENSSSCP00000058359
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl729,624,232 - 29,639,140 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000068945   ⟹   ENSSSCP00000072475
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl729,624,230 - 29,638,598 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000080320   ⟹   ENSSSCP00000061288
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl729,624,232 - 29,639,140 (-)Ensembl
RefSeq Acc Id: XM_001925393   ⟹   XP_001925428
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1729,624,224 - 29,639,168 (-)NCBI
Sequence:
RefSeq Acc Id: XM_013977772   ⟹   XP_013833226
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1729,624,224 - 29,638,548 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021098592   ⟹   XP_020954251
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1729,624,224 - 29,638,451 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_001925428 (Get FASTA)   NCBI Sequence Viewer  
  XP_013833226 (Get FASTA)   NCBI Sequence Viewer  
  XP_020954251 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSSCP00000001630.3
  ENSSSCP00000058359
  ENSSSCP00000058359.2
  ENSSSCP00000061288.1
  ENSSSCP00000072475
  ENSSSCP00000072475.2
  ENSSSCP00005028745.1
  ENSSSCP00005028784.1
  ENSSSCP00005028799.1
  ENSSSCP00005028843.1
  ENSSSCP00015016668.1
  ENSSSCP00015016705.1
  ENSSSCP00015016834.1
  ENSSSCP00015016872.1
  ENSSSCP00015016997.1
  ENSSSCP00025028615.1
  ENSSSCP00025028737.1
  ENSSSCP00025028880.1
  ENSSSCP00025029008.1
  ENSSSCP00025029160.1
  ENSSSCP00030049044.1
  ENSSSCP00030049045.1
  ENSSSCP00030049046.1
  ENSSSCP00030049049.1
  ENSSSCP00035004267.1
  ENSSSCP00035004268.1
  ENSSSCP00035004270.1
  ENSSSCP00035004271.1
  ENSSSCP00040046363.1
  ENSSSCP00040046413.1
  ENSSSCP00040046461.1
  ENSSSCP00040046473.1
  ENSSSCP00040046508.1
  ENSSSCP00045010304.1
  ENSSSCP00045010389.1
  ENSSSCP00045010466.1
  ENSSSCP00045010543.1
  ENSSSCP00050041007.1
  ENSSSCP00050041010.1
  ENSSSCP00050041015.1
  ENSSSCP00050041017.1
  ENSSSCP00055031696.1
  ENSSSCP00055031830.1
  ENSSSCP00055031950.1
  ENSSSCP00055032062.1
  ENSSSCP00055032202.1
  ENSSSCP00060041450.1
  ENSSSCP00060041454.1
  ENSSSCP00060041489.1
  ENSSSCP00060041504.1
  ENSSSCP00060041536.1
  ENSSSCP00065027875.1
  ENSSSCP00065027887.1
  ENSSSCP00065027898.1
  ENSSSCP00065027900.1
  ENSSSCP00065027902.1
  ENSSSCP00065027907.1
RefSeq Acc Id: XP_001925428   ⟸   XM_001925393
- Peptide Label: isoform X1
- UniProtKB: A0A8D1Z286 (UniProtKB/TrEMBL),   A0A8D0JUH2 (UniProtKB/TrEMBL),   A0A8D1G831 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013833226   ⟸   XM_013977772
- Peptide Label: isoform X3
- UniProtKB: A0A8D0SDH4 (UniProtKB/TrEMBL),   A0A8D1TNQ8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020954251   ⟸   XM_021098592
- Peptide Label: isoform X2
- UniProtKB: A0A480IWZ9 (UniProtKB/TrEMBL),   A0A8D1YZW7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000072475   ⟸   ENSSSCT00000068945
RefSeq Acc Id: ENSSSCP00000001630   ⟸   ENSSSCT00000001674
RefSeq Acc Id: ENSSSCP00000061288   ⟸   ENSSSCT00000080320
RefSeq Acc Id: ENSSSCP00000058359   ⟸   ENSSSCT00000062106
Protein Domains
Vps52 C-terminal   Vps52 coiled-coil


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000001501 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00005028642 UniProtKB/TrEMBL
  ENSSSCG00015031866 UniProtKB/TrEMBL
  ENSSSCG00025049084 UniProtKB/TrEMBL
  ENSSSCG00030074968 UniProtKB/TrEMBL
  ENSSSCG00035010101 UniProtKB/TrEMBL
  ENSSSCG00040073935 UniProtKB/TrEMBL
  ENSSSCG00045008766 UniProtKB/TrEMBL
  ENSSSCG00050069830 UniProtKB/TrEMBL
  ENSSSCG00055020295 UniProtKB/TrEMBL
  ENSSSCG00060070200 UniProtKB/TrEMBL
  ENSSSCG00065046969 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000001674.5 UniProtKB/TrEMBL
  ENSSSCT00000062106 ENTREZGENE
  ENSSSCT00000062106.2 UniProtKB/TrEMBL
  ENSSSCT00000068945 ENTREZGENE
  ENSSSCT00000068945.2 UniProtKB/TrEMBL
  ENSSSCT00000080320.1 UniProtKB/TrEMBL
  ENSSSCT00005046743.1 UniProtKB/TrEMBL
  ENSSSCT00005046808.1 UniProtKB/TrEMBL
  ENSSSCT00005046827.1 UniProtKB/TrEMBL
  ENSSSCT00005046879.1 UniProtKB/TrEMBL
  ENSSSCT00015042189.1 UniProtKB/TrEMBL
  ENSSSCT00015042264.1 UniProtKB/TrEMBL
  ENSSSCT00015042565.1 UniProtKB/TrEMBL
  ENSSSCT00015042684.1 UniProtKB/TrEMBL
  ENSSSCT00015043010.1 UniProtKB/TrEMBL
  ENSSSCT00025066912.1 UniProtKB/TrEMBL
  ENSSSCT00025067178.1 UniProtKB/TrEMBL
  ENSSSCT00025067450.1 UniProtKB/TrEMBL
  ENSSSCT00025067669.1 UniProtKB/TrEMBL
  ENSSSCT00025067912.1 UniProtKB/TrEMBL
  ENSSSCT00030105372.1 UniProtKB/TrEMBL
  ENSSSCT00030105373.1 UniProtKB/TrEMBL
  ENSSSCT00030105374.1 UniProtKB/TrEMBL
  ENSSSCT00030105377.1 UniProtKB/TrEMBL
  ENSSSCT00035012634.1 UniProtKB/TrEMBL
  ENSSSCT00035012638.1 UniProtKB/TrEMBL
  ENSSSCT00035012640.1 UniProtKB/TrEMBL
  ENSSSCT00035012647.1 UniProtKB/TrEMBL
  ENSSSCT00040102557.1 UniProtKB/TrEMBL
  ENSSSCT00040102644.1 UniProtKB/TrEMBL
  ENSSSCT00040102736.1 UniProtKB/TrEMBL
  ENSSSCT00040102758.1 UniProtKB/TrEMBL
  ENSSSCT00040102827.1 UniProtKB/TrEMBL
  ENSSSCT00045014846.1 UniProtKB/TrEMBL
  ENSSSCT00045014963.1 UniProtKB/TrEMBL
  ENSSSCT00045015074.1 UniProtKB/TrEMBL
  ENSSSCT00045015177.1 UniProtKB/TrEMBL
  ENSSSCT00050095223.1 UniProtKB/TrEMBL
  ENSSSCT00050095229.1 UniProtKB/TrEMBL
  ENSSSCT00050095242.1 UniProtKB/TrEMBL
  ENSSSCT00050095244.1 UniProtKB/TrEMBL
  ENSSSCT00055039862.1 UniProtKB/TrEMBL
  ENSSSCT00055040013.1 UniProtKB/TrEMBL
  ENSSSCT00055040153.1 UniProtKB/TrEMBL
  ENSSSCT00055040300.1 UniProtKB/TrEMBL
  ENSSSCT00055040468.1 UniProtKB/TrEMBL
  ENSSSCT00060095835.1 UniProtKB/TrEMBL
  ENSSSCT00060095848.1 UniProtKB/TrEMBL
  ENSSSCT00060095922.1 UniProtKB/TrEMBL
  ENSSSCT00060095964.1 UniProtKB/TrEMBL
  ENSSSCT00060096033.1 UniProtKB/TrEMBL
  ENSSSCT00065064362.1 UniProtKB/TrEMBL
  ENSSSCT00065064386.1 UniProtKB/TrEMBL
  ENSSSCT00065064409.1 UniProtKB/TrEMBL
  ENSSSCT00065064415.1 UniProtKB/TrEMBL
  ENSSSCT00065064419.1 UniProtKB/TrEMBL
  ENSSSCT00065064425.1 UniProtKB/TrEMBL
InterPro Vps52 UniProtKB/TrEMBL
  Vps52_C UniProtKB/TrEMBL
  Vps52_CC UniProtKB/TrEMBL
KEGG Report ssc:100152596 UniProtKB/TrEMBL
NCBI Gene VPS52 ENTREZGENE
PANTHER PTHR14190 UniProtKB/TrEMBL
  VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 52 HOMOLOG UniProtKB/TrEMBL
Pfam Vps52 UniProtKB/TrEMBL
  Vps52_C UniProtKB/TrEMBL
UniProt A0A287BQH1_PIG UniProtKB/TrEMBL
  A0A480IWZ9 ENTREZGENE, UniProtKB/TrEMBL
  A0A5G2QGZ6_PIG UniProtKB/TrEMBL
  A0A5G2R5G5_PIG UniProtKB/TrEMBL
  A0A8D0JUH2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0NCZ4_PIG UniProtKB/TrEMBL
  A0A8D0NHL1_PIG UniProtKB/TrEMBL
  A0A8D0SDH4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0U144_PIG UniProtKB/TrEMBL
  A0A8D0YR78_PIG UniProtKB/TrEMBL
  A0A8D1G831 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1GX60_PIG UniProtKB/TrEMBL
  A0A8D1GXN6_PIG UniProtKB/TrEMBL
  A0A8D1GY51_PIG UniProtKB/TrEMBL
  A0A8D1TNQ8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1YZW7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1Z286 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F1RZT5 UniProtKB/TrEMBL
VGNC ID VGNC:94860 ENTREZGENE