Vps53 (VPS53 subunit of GARP complex) - Rat Genome Database

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Gene: Vps53 (VPS53 subunit of GARP complex) Heterocephalus glaber
Analyze
Symbol: Vps53
Name: VPS53 subunit of GARP complex
RGD ID: 18915200
Description: INVOLVED IN endocytic recycling (ortholog); lysosomal transport (ortholog); protein targeting to lysosome (ortholog); ASSOCIATED WITH genetic disease (ortholog); microcephaly (ortholog); Neurodevelopmental Disorders (ortholog); FOUND IN EARP complex (ortholog); intracellular membrane-bounded organelle (ortholog); perinuclear region of cytoplasm (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: vacuolar protein sorting-associated protein 53 homolog; VPS53, GARP complex subunit
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247863,614,811 - 3,778,069 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247863,614,775 - 3,779,644 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
Vps53
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247863,614,811 - 3,778,069 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247863,614,775 - 3,779,644 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2
VPS53
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3817508,668 - 714,839 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl17508,503 - 721,717 (-)EnsemblGRCh38hg38GRCh38
GRCh3717411,908 - 618,079 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3617382,698 - 564,758 (-)NCBINCBI36Build 36hg18NCBI36
Celera17423,924 - 629,862 (-)NCBICelera
Cytogenetic Map17p13.3NCBI
HuRef17325,008 - 528,642 (-)NCBIHuRef
CHM1_117418,907 - 623,396 (-)NCBICHM1_1
T2T-CHM13v2.017391,960 - 599,311 (-)NCBIT2T-CHM13v2.0
Vps53
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391175,937,052 - 76,070,464 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1175,937,052 - 76,070,473 (-)EnsemblGRCm39 Ensembl
GRCm381176,046,226 - 76,179,638 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1176,046,226 - 76,179,647 (-)EnsemblGRCm38mm10GRCm38
MGSCv371175,859,728 - 75,993,132 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361175,862,421 - 75,995,825 (-)NCBIMGSCv36mm8
Celera1183,555,285 - 83,692,488 (-)NCBICelera
Cytogenetic Map11B5NCBI
cM Map1145.92NCBI
Vps53
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81061,418,076 - 61,536,912 (-)NCBIGRCr8
mRatBN7.21060,919,820 - 61,038,674 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1060,919,820 - 61,038,676 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1065,561,939 - 65,680,825 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01065,067,390 - 65,186,273 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01060,537,918 - 60,656,979 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01064,218,596 - 64,341,064 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1064,222,276 - 64,341,109 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01063,672,733 - 63,793,858 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41063,410,886 - 63,535,682 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11063,424,683 - 63,543,200 (-)NCBI
Celera1059,935,404 - 60,054,107 (-)NCBICelera
Cytogenetic Map10q24NCBI
Vps53
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554812,130,888 - 2,264,924 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554812,130,669 - 2,265,065 (-)NCBIChiLan1.0ChiLan1.0
VPS53
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2198,042,929 - 8,261,718 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1179,602,776 - 9,812,194 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v017400,048 - 576,119 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.117416,136 - 604,705 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl17414,782 - 604,705 (-)Ensemblpanpan1.1panPan2
VPS53
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1945,074,066 - 45,239,569 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl945,074,100 - 45,214,066 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha944,224,566 - 44,391,993 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0945,892,548 - 46,060,240 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl945,892,566 - 46,035,516 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1944,670,971 - 44,838,890 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0944,964,695 - 45,132,085 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0945,043,233 - 45,211,135 (+)NCBIUU_Cfam_GSD_1.0
Vps53
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560244,189,381 - 44,329,957 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365387,067,327 - 7,205,768 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365387,067,332 - 7,207,852 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS53
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1247,143,098 - 47,291,161 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11247,141,749 - 47,291,169 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21249,308,850 - 49,456,068 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS53
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.116302,771 - 464,572 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl16303,414 - 464,574 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605921,622,848 - 21,752,483 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSHGLT00000016616   ⟹   ENSHGLP00000016447
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046247863,614,811 - 3,778,069 (+)Ensembl
RefSeq Acc Id: ENSHGLT00000016617   ⟹   ENSHGLP00000016448
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046247863,614,931 - 3,775,361 (+)Ensembl
RefSeq Acc Id: ENSHGLT00000016618   ⟹   ENSHGLP00000016449
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046247863,614,931 - 3,775,361 (+)Ensembl
RefSeq Acc Id: ENSHGLT00000016619   ⟹   ENSHGLP00000016450
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046247863,614,931 - 3,616,656 (+)Ensembl
RefSeq Acc Id: XM_004857106   ⟹   XP_004857163
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046247863,614,934 - 3,779,644 (+)NCBI
RefSeq Acc Id: XM_021238039   ⟹   XP_021093698
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046247863,614,775 - 3,779,644 (+)NCBI
Protein Sequences
Protein RefSeqs XP_004857163 (Get FASTA)   NCBI Sequence Viewer  
  XP_021093698 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSHGLP00000016447
Reference Protein Sequences
RefSeq Acc Id: XP_021093698   ⟸   XM_021238039
- Peptide Label: isoform X2
- UniProtKB: G5BVK7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_004857163   ⟸   XM_004857106
- Peptide Label: isoform X1
- UniProtKB: G5BVK7 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSHGLP00000016448   ⟸   ENSHGLT00000016617
RefSeq Acc Id: ENSHGLP00000016449   ⟸   ENSHGLT00000016618
RefSeq Acc Id: ENSHGLP00000016450   ⟸   ENSHGLT00000016619
RefSeq Acc Id: ENSHGLP00000016447   ⟸   ENSHGLT00000016616


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000011774 Ensembl, ENTREZGENE
Ensembl Transcript ENSHGLT00000016616 ENTREZGENE
Gene3D-CATH Methyl-accepting chemotaxis protein UniProtKB/TrEMBL
  Vacuolar protein sorting-associated protein 53, C-terminus UniProtKB/TrEMBL
InterPro Vps53 UniProtKB/TrEMBL
  Vps53_C UniProtKB/TrEMBL
  Vps53_C_sf UniProtKB/TrEMBL
  Vps53_N UniProtKB/TrEMBL
NCBI Gene Vps53 ENTREZGENE
PANTHER VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 53 HOMOLOG UniProtKB/TrEMBL
  VACUOLAR SORTING PROTEIN 53 UniProtKB/TrEMBL
Pfam VPS53_C UniProtKB/TrEMBL
  Vps53_N UniProtKB/TrEMBL
UniProt G5BVK7 ENTREZGENE, UniProtKB/TrEMBL