Human Gene VTA1 (ENST00000367630.9) from GENCODE V44
  Description: Homo sapiens vesicle trafficking 1 (VTA1), transcript variant 1, mRNA. (from RefSeq NM_016485)
RefSeq Summary (NM_016485): C6ORF55 encodes a protein involved in trafficking of the multivesicular body, an endosomal compartment involved in sorting membrane proteins for degradation in lysosomes (Ward et al., 2005 [PubMed 15644320]).[supplied by OMIM, Mar 2008].
Gencode Transcript: ENST00000367630.9
Gencode Gene: ENSG00000009844.16
Transcript (Including UTRs)
   Position: hg38 chr6:142,147,263-142,224,685 Size: 77,423 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg38 chr6:142,147,288-142,218,643 Size: 71,356 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:142,147,263-142,224,685)mRNA (may differ from genome)Protein (307 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VTA1_HUMAN
DESCRIPTION: RecName: Full=Vacuolar protein sorting-associated protein VTA1 homolog; AltName: Full=Dopamine-responsive gene 1 protein; Short=DRG-1; AltName: Full=LYST-interacting protein 5; Short=LIP5; AltName: Full=SKD1-binding protein 1; Short=SBP1;
FUNCTION: Involved in the endosomal multivesicular bodies (MVB) pathway. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. Thought to be a cofactor of VPS4A/B, which catalyzes disassembles membrane-associated ESCRT-III assemblies. Involved in the sorting and down-regulation of EGFR (By similarity). Involved in HIV-1 budding.
SUBUNIT: Interacts with VPS4B. Interacts with CHMP1B. Interacts with CHMP2A; the interaction probably involves the open conformation of (polymerized) CHMP2A. May interact with CHMP3. Interacts with CHMP5; the interaction involves soluble CHMP5. Interacts with IST1.
SUBCELLULAR LOCATION: Cytoplasm. Endosome membrane; Peripheral membrane protein (Probable).
SIMILARITY: Belongs to the VTA1 family.
SEQUENCE CAUTION: Sequence=AAF36148.1; Type=Frameshift; Positions=131, 140; Sequence=AAG43125.1; Type=Frameshift; Positions=269;

-  Primer design for this transcript
 

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-  MalaCards Disease Associations
  MalaCards Gene Search: VTA1
Diseases sorted by gene-association score: amyotrophic lateral sclerosis 15, with or without frontotemporal dementia (6), amyotrophic lateral sclerosis 9 (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.06 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 222.57 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -1.5025-0.060 Picture PostScript Text
3' UTR -1572.706042-0.260 Picture PostScript Text

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.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR023175 - VPS_Vta1_N

ModBase Predicted Comparative 3D Structure on Q9NP79
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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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsemblWormBase 
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence 
AlignmentAlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008022 protein C-terminus binding

Biological Process:
GO:0015031 protein transport
GO:0016236 macroautophagy
GO:0019058 viral life cycle
GO:0036258 multivesicular body assembly
GO:0046755 viral budding
GO:0071985 multivesicular body sorting pathway
GO:1904903 ESCRT III complex disassembly

Cellular Component:
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005829 cytosol
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0043231 intracellular membrane-bounded organelle
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AF151062 - Homo sapiens HSPC228 mRNA, complete cds.
AK301376 - Homo sapiens cDNA FLJ50889 complete cds.
BC006989 - Homo sapiens Vps20-associated 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:12227 IMAGE:3961637), complete cds.
BC022536 - Homo sapiens Vps20-associated 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:26689 IMAGE:4817057), complete cds.
AL136684 - Homo sapiens mRNA; cDNA DKFZp564E1878 (from clone DKFZp564E1878).
AK130738 - Homo sapiens cDNA FLJ27228 fis, clone SYN05650.
AK000051 - Homo sapiens cDNA FLJ20044 fis, clone COL00456.
AF060225 - Homo sapiens clone 009c06 My012 protein mRNA, complete cds.
AF271994 - Homo sapiens dopamine responsive protein DRG-1 mRNA, complete cds.
LF384620 - JP 2014500723-A/192123: Polycomb-Associated Non-Coding RNAs.
MA620197 - JP 2018138019-A/192123: Polycomb-Associated Non-Coding RNAs.
BC005937 - Homo sapiens Vps20-associated 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:14555 IMAGE:4081455), complete cds.
AF141341 - Homo sapiens LYST-interacting protein LIP5 mRNA, partial cds.
CR457207 - Homo sapiens full open reading frame cDNA clone RZPDo834G0212D for gene C6orf55, chromosome 6 open reading frame 55; complete cds, incl. stopcodon.
AB464348 - Synthetic construct DNA, clone: pF1KB6409, Homo sapiens VTA1 gene for Vps20-associated 1 homolog, without stop codon, in Flexi system.
DQ893520 - Synthetic construct clone IMAGE:100006150; FLH194939.01X; RZPDo839G0880D chromosome 6 open reading frame 55 (C6orf55) gene, encodes complete protein.
DQ896504 - Synthetic construct Homo sapiens clone IMAGE:100010964; FLH194935.01L; RZPDo839G0870D chromosome 6 open reading frame 55 (C6orf55) gene, encodes complete protein.
KJ898916 - Synthetic construct Homo sapiens clone ccsbBroadEn_08310 VTA1 gene, encodes complete protein.
AJ420507 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 2130179.
AY007093 - Homo sapiens clone TCCCIA00133 mRNA sequence.
BC013217 - Homo sapiens Vps20-associated 1 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3452793).
CU692682 - Synthetic construct Homo sapiens gateway clone IMAGE:100018810 5' read VTA1 mRNA.
LF321886 - JP 2014500723-A/129389: Polycomb-Associated Non-Coding RNAs.
MA557463 - JP 2018138019-A/129389: Polycomb-Associated Non-Coding RNAs.
LF321885 - JP 2014500723-A/129388: Polycomb-Associated Non-Coding RNAs.
MA557462 - JP 2018138019-A/129388: Polycomb-Associated Non-Coding RNAs.
JD347900 - Sequence 328924 from Patent EP1572962.
JD404066 - Sequence 385090 from Patent EP1572962.
LF321879 - JP 2014500723-A/129382: Polycomb-Associated Non-Coding RNAs.
MA557456 - JP 2018138019-A/129382: Polycomb-Associated Non-Coding RNAs.
JD023841 - Sequence 4865 from Patent EP1572962.
JD334002 - Sequence 315026 from Patent EP1572962.
JD550923 - Sequence 531947 from Patent EP1572962.
JD026992 - Sequence 8016 from Patent EP1572962.
JD082863 - Sequence 63887 from Patent EP1572962.
JD184377 - Sequence 165401 from Patent EP1572962.
DL491547 - Novel nucleic acids.
DL490152 - Novel nucleic acids.
JD313046 - Sequence 294070 from Patent EP1572962.
JD286079 - Sequence 267103 from Patent EP1572962.
JD114114 - Sequence 95138 from Patent EP1572962.
JD417407 - Sequence 398431 from Patent EP1572962.
JD354337 - Sequence 335361 from Patent EP1572962.
JD246460 - Sequence 227484 from Patent EP1572962.
JD180620 - Sequence 161644 from Patent EP1572962.
JD235336 - Sequence 216360 from Patent EP1572962.
JD563659 - Sequence 544683 from Patent EP1572962.
JD296625 - Sequence 277649 from Patent EP1572962.
JD509278 - Sequence 490302 from Patent EP1572962.
JD380942 - Sequence 361966 from Patent EP1572962.
JD074947 - Sequence 55971 from Patent EP1572962.
JD453103 - Sequence 434127 from Patent EP1572962.
JD106416 - Sequence 87440 from Patent EP1572962.
JD462370 - Sequence 443394 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04144 - Endocytosis

Reactome (by CSHL, EBI, and GO)

Protein Q9NP79 (Reactome details) participates in the following event(s):

R-HSA-3159232 Recruitment Of HIV Virion Budding Machinery
R-HSA-917693 ESCRT Disassembly
R-HSA-162588 Budding and maturation of HIV virion
R-HSA-162599 Late Phase of HIV Life Cycle
R-HSA-917729 Endosomal Sorting Complex Required For Transport (ESCRT)
R-HSA-162587 HIV Life Cycle
R-HSA-199991 Membrane Trafficking
R-HSA-162906 HIV Infection
R-HSA-5653656 Vesicle-mediated transport
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: C6orf55, E1P594, ENST00000367630.1, ENST00000367630.2, ENST00000367630.3, ENST00000367630.4, ENST00000367630.5, ENST00000367630.6, ENST00000367630.7, ENST00000367630.8, HSPC228, My012, NM_016485, Q5TGM1, Q6IAE8, Q9H0R2, Q9H3K9, Q9NP79, Q9P0Q0, uc003qiw.1, uc003qiw.2, uc003qiw.3, uc003qiw.4, uc003qiw.5, uc003qiw.6, VTA1_HUMAN
UCSC ID: ENST00000367630.9
RefSeq Accession: NM_016485
Protein: Q9NP79 (aka VTA1_HUMAN)
CCDS: CCDS5197.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.