Human Gene VPS54 (ENST00000272322.9) from GENCODE V39
Description: Homo sapiens VPS54 subunit of GARP complex (VPS54), transcript variant 1, mRNA. (from RefSeq NM_016516) RefSeq Summary (NM_016516): This gene encodes for a protein that in yeast forms part of a trimeric vacuolar-protein-sorting complex that is required for retrograde transport of proteins from prevacuoles to the late Golgi compartment. As in yeast, mammalian Vps54 proteins contain a coiled-coil region and dileucine motifs. Alternative splicing results in multiple transcript variants encoding different isoforms [provided by RefSeq, Jul 2008]. Gencode Transcript: ENST00000272322.9 Gencode Gene: ENSG00000143952.20 Transcript (Including UTRs) Position: hg38 chr2:63,892,150-64,019,428 Size: 127,279 Total Exon Count: 23 Strand: - Coding Region Position: hg38 chr2:63,893,430-63,983,999 Size: 90,570 Coding Exon Count: 22
ID:VPS54_HUMAN DESCRIPTION: RecName: Full=Vacuolar protein sorting-associated protein 54; AltName: Full=Hepatocellular carcinoma protein 8; AltName: Full=Tumor antigen HOM-HCC-8; AltName: Full=Tumor antigen SLP-8p; FUNCTION: May be involved in retrograde transport from early and late endosomes to the late Golgi. The GARP complex is required for the maintenance of the cycling of mannose 6-phosphate receptors between the TGN and endosomes, this cycling is necessary for proper lysosomal sorting of acid hydrolases such as CTSD. SUBUNIT: Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS51, VPS52, VPS53 and VPS54. SIMILARITY: Belongs to the VPS54 family. SEQUENCE CAUTION: Sequence=BAA92134.1; Type=Erroneous initiation;
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
Pfam Domains: PF10475 - Vacuolar-sorting protein 54, of GARP complex PF07928 - Vps54-like protein
ModBase Predicted Comparative 3D Structure on Q9P1Q0
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Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
Biological Process: GO:0006896 Golgi to vacuole transport GO:0007041 lysosomal transport GO:0015031 protein transport GO:0040007 growth GO:0042147 retrograde transport, endosome to Golgi GO:0048873 homeostasis of number of cells within a tissue GO:0050881 musculoskeletal movement GO:0060052 neurofilament cytoskeleton organization
BC041868 - Homo sapiens vacuolar protein sorting 54 homolog (S. cerevisiae), mRNA (cDNA clone MGC:43704 IMAGE:5271464), complete cds. AF102177 - Homo sapiens tumor antigen SLP-8p (HCC8) mRNA, complete cds. BC030275 - Homo sapiens vacuolar protein sorting 54 homolog (S. cerevisiae), mRNA (cDNA clone MGC:39932 IMAGE:3917367), complete cds. AK292889 - Homo sapiens cDNA FLJ78648 complete cds, highly similar to Homo sapiens vacuolar protein sorting 54 (yeast) (VPS54), transcript variant 2, mRNA. AK292669 - Homo sapiens cDNA FLJ77625 complete cds, highly similar to Homo sapiens vacuolar protein sorting 54 (VPS54), transcript variant 1, mRNA. KJ893937 - Synthetic construct Homo sapiens clone ccsbBroadEn_03331 VPS54 gene, encodes complete protein. AY444798 - Homo sapiens vacuolar sorting protein 54 long isoform (VPS54) mRNA, complete cds, alternatively spliced. DQ891080 - Synthetic construct clone IMAGE:100003710; FLH169138.01X; RZPDo839G1194D vacuolar protein sorting 54 (S. cerevisiae) (VPS54) gene, encodes complete protein. DQ894262 - Synthetic construct Homo sapiens clone IMAGE:100008722; FLH169134.01L; RZPDo839G1193D vacuolar protein sorting 54 (S. cerevisiae) (VPS54) gene, encodes complete protein. AK002205 - Homo sapiens cDNA FLJ11343 fis, clone PLACE1010811. AL137604 - Homo sapiens mRNA; cDNA DKFZp434F0411 (from clone DKFZp434F0411); partial cds. AK094019 - Homo sapiens cDNA FLJ36700 fis, clone UTERU2009131, highly similar to Rattus norvegicus mRNA for Vps54-like protein. AK124436 - Homo sapiens cDNA FLJ42445 fis, clone BLADE2008539, highly similar to Homo sapiens tumor antigen SLP-8p (HCC8). JD137424 - Sequence 118448 from Patent EP1572962. JD087466 - Sequence 68490 from Patent EP1572962. AL359939 - Homo sapiens mRNA; cDNA DKFZp434I1019 (from clone DKFZp434I1019). CR749701 - Homo sapiens mRNA; cDNA DKFZp434I1019 (from clone DKFZp434I1019). AK025545 - Homo sapiens cDNA: FLJ21892 fis, clone HEP03336, highly similar to AF102177 Homo sapiens tumor antigen SLP-8p (HCC8) mRNA. JD297319 - Sequence 278343 from Patent EP1572962. JD299901 - Sequence 280925 from Patent EP1572962. JD281868 - Sequence 262892 from Patent EP1572962. JD347708 - Sequence 328732 from Patent EP1572962. JD041777 - Sequence 22801 from Patent EP1572962. JD376353 - Sequence 357377 from Patent EP1572962. AK126141 - Homo sapiens cDNA FLJ44153 fis, clone THYMU2031579.
Biochemical and Signaling Pathways
Reactome (by CSHL, EBI, and GO)
Protein Q9P1Q0 (Reactome details) participates in the following event(s):
R-HSA-6811431 RAB6:GTP binds the GARP and COG complexes, t-SNAREs and endosome-derived vesicles R-HSA-6814674 Tethering of late endosome-derived vesicles by GARP, STX10:ST16:VTI1A and Golgins R-HSA-6811440 Retrograde transport at the Trans-Golgi-Network R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic R-HSA-199991 Membrane Trafficking R-HSA-5653656 Vesicle-mediated transport
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