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Entry version 133 (11 Dec 2019)
Sequence version 1 (07 Dec 2004)
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Protein

Vacuolar protein sorting-associated protein 53 homolog

Gene

VPS53

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). 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 (PubMed:15878329, PubMed:18367545). Acts as component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane (PubMed:25799061).3 Publications

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Biological processProtein transport, Transport

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-HSA-6811440 Retrograde transport at the Trans-Golgi-Network

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 53 homolog
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:VPS53
ORF Names:PP13624
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiHomo sapiens (Human)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri9606 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000005640 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 17

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
HostDB:ENSG00000141252.19

Human Gene Nomenclature Database

More...
HGNCi
HGNC:25608 VPS53

Online Mendelian Inheritance in Man (OMIM)

More...
MIMi
615850 gene

neXtProt; the human protein knowledge platform

More...
neXtProti
NX_Q5VIR6

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Endosome, Golgi apparatus, Membrane

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the ‘Pathology and Biotech’ section provides information on the disease(s) associated with genetic variations in a given protein. The information is extracted from the scientific literature and diseases that are also described in the <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim">OMIM</a> database are represented with a <a href="http://www.uniprot.org/diseases">controlled vocabulary</a> in the following way:<p><a href='/help/involvement_in_disease' target='_top'>More...</a></p>Involvement in diseasei

Pontocerebellar hypoplasia 2E (PCH2E)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA neurodegenerative disorder characterized by progressive cerebello-cerebral atrophy, profound mental retardation, progressive microcephaly, spasticity, and early-onset epilepsy.
Related information in OMIM
Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section describes natural variant(s) of the protein sequence.<p><a href='/help/variant' target='_top'>More...</a></p>Natural variantiVAR_071803695Q → R in PCH2E. 1 PublicationCorresponds to variant dbSNP:rs587777465EnsemblClinVar.1
Isoform 4 (identifier: Q5VIR6-4)
Natural variantiVAR_082933695Q → R in PCH2E. 1 Publication1

Keywords - Diseasei

Disease mutation, Epilepsy, Mental retardation, Neurodegeneration

Organism-specific databases

DisGeNET

More...
DisGeNETi
55275

MalaCards human disease database

More...
MalaCardsi
VPS53
MIMi615851 phenotype

Open Targets

More...
OpenTargetsi
ENSG00000141252

Orphanet; a database dedicated to information on rare diseases and orphan drugs

More...
Orphaneti
247198 Progressive cerebello-cerebral atrophy

The Pharmacogenetics and Pharmacogenomics Knowledge Base

More...
PharmGKBi
PA142670618

Miscellaneous databases

Pharos NIH Druggable Genome Knowledgebase

More...
Pharosi
Q5VIR6 Tbio

Polymorphism and mutation databases

BioMuta curated single-nucleotide variation and disease association database

More...
BioMutai
VPS53

Domain mapping of disease mutations (DMDM)

More...
DMDMi
74746777

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002151891 – 699Vacuolar protein sorting-associated protein 53 homologAdd BLAST699

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei110N6-acetyllysineCombined sources1
Modified residuei360N6-acetyllysineCombined sources1
Modified residuei377PhosphoserineCombined sources1
Modified residuei391PhosphothreonineCombined sources1
Modified residuei580PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
Q5VIR6

MassIVE - Mass Spectrometry Interactive Virtual Environment

More...
MassIVEi
Q5VIR6

MaxQB - The MaxQuant DataBase

More...
MaxQBi
Q5VIR6

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
Q5VIR6

PeptideAtlas

More...
PeptideAtlasi
Q5VIR6

PRoteomics IDEntifications database

More...
PRIDEi
Q5VIR6

ProteomicsDB: a multi-organism proteome resource

More...
ProteomicsDBi
65251 [Q5VIR6-1]
65252 [Q5VIR6-2]
65253 [Q5VIR6-3]
65254 [Q5VIR6-4]

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
Q5VIR6

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

More...
PhosphoSitePlusi
Q5VIR6

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...
Bgeei
ENSG00000141252 Expressed in 187 organ(s), highest expression level in frontal cortex

ExpressionAtlas, Differential and Baseline Expression

More...
ExpressionAtlasi
Q5VIR6 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q5VIR6 HS

Organism-specific databases

Human Protein Atlas

More...
HPAi
HPA022988
HPA024446

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS51, VPS52, VPS53 and VPS54 (PubMed:27440922, PubMed:15878329).

Component of the endosome-associated retrograde protein (EARP) complex, composed of VPS51, VPS52, VPS53 and VPS50/Syndetin (PubMed:25799061, PubMed:27440922). EIPR1 interacts with both EARP and GARP complexes and mediates the recruitment of the GARP complex to the trans-Golgi network (PubMed:27440922).

3 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

WithEntry#Exp.IntActNotes
Q96JG68EBI-2850511,EBI-11044388

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
120563, 101 interactors

CORUM comprehensive resource of mammalian protein complexes

More...
CORUMi
Q5VIR6

Database of interacting proteins

More...
DIPi
DIP-59352N

Protein interaction database and analysis system

More...
IntActi
Q5VIR6, 19 interactors

STRING: functional protein association networks

More...
STRINGi
9606.ENSP00000401435

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...
RNActi
Q5VIR6 protein

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
Q5VIR6

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and domains’ section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>Coiled coili55 – 142Sequence analysisAdd BLAST88

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the VPS53 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG2180 Eukaryota
ENOG410XNMT LUCA

Ensembl GeneTree

More...
GeneTreei
ENSGT00390000015165

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000265899

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q5VIR6

KEGG Orthology (KO)

More...
KOi
K20299

Identification of Orthologs from Complete Genome Data

More...
OMAi
YRQVFRG

Database of Orthologous Groups

More...
OrthoDBi
1379600at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q5VIR6

TreeFam database of animal gene trees

More...
TreeFami
TF106150

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR039766 Vps53
IPR007234 Vps53_N

The PANTHER Classification System

More...
PANTHERi
PTHR12820 PTHR12820, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF04100 Vps53_N, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequences (4+)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

This entry describes 4 <p>This subsection of the ‘Sequence’ section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 4 described isoforms and 6 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q5VIR6-1) [UniParc]FASTAAdd to basket
Also known as: long

This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MMEEEELEFV EELEAVLQLT PEVQLAIEQV FPSQDPLDRA DFNAVEYINT
60 70 80 90 100
LFPTEQSLAN IDEVVNKIRL KIRRLDDNIR TVVRGQTNVG QDGRQALEEA
110 120 130 140 150
QKAIQQLFGK IKDIKDKAEK SEQMVKEITR DIKQLDHAKR HLTTSITTLN
160 170 180 190 200
HLHMLAGGVD SLEAMTRRRQ YGEVANLLQG VMNVLEHFHK YMGIPQIRQL
210 220 230 240 250
SERVKAAQTE LGQQILADFE EAFPSQGTKR PGGPSNVLRD ACLVANILDP
260 270 280 290 300
RIKQEIIKKF IKQHLSEYLV LFQENQDVAW LDKIDRRYAW IKRQLVDYEE
310 320 330 340 350
KYGRMFPREW CMAERIAVEF CHVTRAELAK IMRTRAKEIE VKLLLFAIQR
360 370 380 390 400
TTNFEGFLAK RFSGCTLTDG TLKKLESPPP STNPFLEDEP TPEMEELATE
410 420 430 440 450
KGDLDQPKKP KAPDNPFHGI VSKCFEPHLY VYIESQDKNL GELIDRFVAD
460 470 480 490 500
FKAQGPPKPN TDEGGAVLPS CADLFVYYKK CMVQCSQLST GEPMIALTTI
510 520 530 540 550
FQKYLREYAW KILSGNLPKT TTSSGGLTIS SLLKEKEGSE VAKFTLEELC
560 570 580 590 600
LICNILSTAE YCLATTQQLE EKLKEKVDVS LIERINLTGE MDTFSTVISS
610 620 630 640 650
SIQLLVQDLD AACDPALTAM SKMQWQNVEH VGDQSPYVTS VILHIKQNVP
660 670 680 690
IIRDNLASTR KYFTQFCVKF ANSFIPKFIT HLFKCKPISM VGAEQVRWT
Length:699
Mass (Da):79,653
Last modified:December 7, 2004 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i6C07EC07682BF4C6
GO
Isoform 2 (identifier: Q5VIR6-2) [UniParc]FASTAAdd to basket
Also known as: short

The sequence of this isoform differs from the canonical sequence as follows:
     96-124: Missing.

Show »
Length:670
Mass (Da):76,352
Checksum:i8057AAC082136EC7
GO
Isoform 3 (identifier: Q5VIR6-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     656-673: LASTRKYFTQFCVKFANS → PVASTRKYFTQLCVKFAK
     674-699: Missing.

Show »
Length:673
Mass (Da):76,569
Checksum:i82C41A7433B5EF79
GO
Isoform 4 (identifier: Q5VIR6-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     696-699: VRWT → LLLDTHSLKM...KLEKLIKKRL

Show »
Length:832
Mass (Da):94,405
Checksum:iEA71D35158E9419E
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There are 6 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F6VX93F6VX93_HUMAN
Vacuolar protein sorting-associated...
VPS53
547Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
E7EVT8E7EVT8_HUMAN
Vacuolar protein sorting-associated...
VPS53
422Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
I3L184I3L184_HUMAN
Vacuolar protein sorting-associated...
VPS53
237Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
I3L0S6I3L0S6_HUMAN
Vacuolar protein sorting-associated...
VPS53
216Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
I3L1W6I3L1W6_HUMAN
Vacuolar protein sorting-associated...
VPS53
145Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
I3L4P9I3L4P9_HUMAN
Vacuolar protein sorting-associated...
VPS53
68Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAL55842 differs from that shown. Reason: Frameshift.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti27I → V in ABW03005 (PubMed:18367545).Curated1
Sequence conflicti115K → N in ABW03005 (PubMed:18367545).Curated1
Sequence conflicti466A → T in AAK27973 (PubMed:12565177).Curated1
Sequence conflicti520T → P in AAK27973 (PubMed:12565177).Curated1
Sequence conflicti525G → E in AAK27973 (PubMed:12565177).Curated1
Sequence conflicti658 – 665STRKYFTQ → NMAKSHLY in AAL55842 (PubMed:15498874).Curated8

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_059959328L → I. Corresponds to variant dbSNP:rs16954056EnsemblClinVar.1
Natural variantiVAR_066561375L → R. Corresponds to variant dbSNP:rs61644407EnsemblClinVar.1
Natural variantiVAR_071803695Q → R in PCH2E. 1 PublicationCorresponds to variant dbSNP:rs587777465EnsemblClinVar.1
Isoform 4 (identifier: Q5VIR6-4)
Natural variantiVAR_082933695Q → R in PCH2E. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section describes the sequence of naturally occurring alternative protein isoform(s). The changes in the amino acid sequence may be due to alternative splicing, alternative promoter usage, alternative initiation, or ribosomal frameshifting.<p><a href='/help/var_seq' target='_top'>More...</a></p>Alternative sequenceiVSP_01623696 – 124Missing in isoform 2. 2 PublicationsAdd BLAST29
Alternative sequenceiVSP_016237656 – 673LASTR…KFANS → PVASTRKYFTQLCVKFAK in isoform 3. 1 PublicationAdd BLAST18
Alternative sequenceiVSP_016238674 – 699Missing in isoform 3. 1 PublicationAdd BLAST26
Alternative sequenceiVSP_042106696 – 699VRWT → LLLDTHSLKMVLLDLPSISS QVVRKAPASYTKIVVKGMTR AEMILKVVMAPHEPLVVFVD NYIKLLTDCNTETFQKILDM KGLKRSEQSSMLELLRQRLP APPSGAESSGSLSLTAPTPE QESSRIRKLEKLIKKRL in isoform 4. 1 Publication4

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

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DDBJi
Links Updated
AY444797 mRNA Translation: AAS20944.1
AF246287 mRNA Translation: AAK27973.1
EU021218 mRNA Translation: ABW03005.1
AK001841 mRNA Translation: BAA91935.1
AK290343 mRNA Translation: BAF83032.1
AC015853 Genomic DNA No translation available.
AC027455 Genomic DNA No translation available.
CH471108 Genomic DNA Translation: EAW90661.1
BC006116 mRNA Translation: AAH06116.1
AF318335 mRNA Translation: AAL55842.1 Frameshift.

The Consensus CDS (CCDS) project

More...
CCDSi
CCDS10995.1 [Q5VIR6-2]
CCDS45558.1 [Q5VIR6-4]

NCBI Reference Sequences

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RefSeqi
NP_001121631.1, NM_001128159.2 [Q5VIR6-4]
NP_060759.2, NM_018289.3 [Q5VIR6-2]

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENST00000291074; ENSP00000291074; ENSG00000141252 [Q5VIR6-2]
ENST00000437048; ENSP00000401435; ENSG00000141252 [Q5VIR6-4]
ENST00000571805; ENSP00000459312; ENSG00000141252 [Q5VIR6-1]
ENST00000638350; ENSP00000492070; ENSG00000283883 [Q5VIR6-2]
ENST00000639801; ENSP00000492761; ENSG00000283883 [Q5VIR6-4]
ENST00000639896; ENSP00000492119; ENSG00000283883 [Q5VIR6-1]

Database of genes from NCBI RefSeq genomes

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GeneIDi
55275

KEGG: Kyoto Encyclopedia of Genes and Genomes

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KEGGi
hsa:55275

UCSC genome browser

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UCSCi
uc002frm.3 human [Q5VIR6-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY444797 mRNA Translation: AAS20944.1
AF246287 mRNA Translation: AAK27973.1
EU021218 mRNA Translation: ABW03005.1
AK001841 mRNA Translation: BAA91935.1
AK290343 mRNA Translation: BAF83032.1
AC015853 Genomic DNA No translation available.
AC027455 Genomic DNA No translation available.
CH471108 Genomic DNA Translation: EAW90661.1
BC006116 mRNA Translation: AAH06116.1
AF318335 mRNA Translation: AAL55842.1 Frameshift.
CCDSiCCDS10995.1 [Q5VIR6-2]
CCDS45558.1 [Q5VIR6-4]
RefSeqiNP_001121631.1, NM_001128159.2 [Q5VIR6-4]
NP_060759.2, NM_018289.3 [Q5VIR6-2]

3D structure databases

SMRiQ5VIR6
ModBaseiSearch...

Protein-protein interaction databases

BioGridi120563, 101 interactors
CORUMiQ5VIR6
DIPiDIP-59352N
IntActiQ5VIR6, 19 interactors
STRINGi9606.ENSP00000401435

PTM databases

iPTMnetiQ5VIR6
PhosphoSitePlusiQ5VIR6

Polymorphism and mutation databases

BioMutaiVPS53
DMDMi74746777

Proteomic databases

jPOSTiQ5VIR6
MassIVEiQ5VIR6
MaxQBiQ5VIR6
PaxDbiQ5VIR6
PeptideAtlasiQ5VIR6
PRIDEiQ5VIR6
ProteomicsDBi65251 [Q5VIR6-1]
65252 [Q5VIR6-2]
65253 [Q5VIR6-3]
65254 [Q5VIR6-4]

Genome annotation databases

EnsembliENST00000291074; ENSP00000291074; ENSG00000141252 [Q5VIR6-2]
ENST00000437048; ENSP00000401435; ENSG00000141252 [Q5VIR6-4]
ENST00000571805; ENSP00000459312; ENSG00000141252 [Q5VIR6-1]
ENST00000638350; ENSP00000492070; ENSG00000283883 [Q5VIR6-2]
ENST00000639801; ENSP00000492761; ENSG00000283883 [Q5VIR6-4]
ENST00000639896; ENSP00000492119; ENSG00000283883 [Q5VIR6-1]
GeneIDi55275
KEGGihsa:55275
UCSCiuc002frm.3 human [Q5VIR6-1]

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
55275
DisGeNETi55275
EuPathDBiHostDB:ENSG00000141252.19

GeneCards: human genes, protein and diseases

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GeneCardsi
VPS53
HGNCiHGNC:25608 VPS53
HPAiHPA022988
HPA024446
MalaCardsiVPS53
MIMi615850 gene
615851 phenotype
neXtProtiNX_Q5VIR6
OpenTargetsiENSG00000141252
Orphaneti247198 Progressive cerebello-cerebral atrophy
PharmGKBiPA142670618

GenAtlas: human gene database

More...
GenAtlasi
Search...

Phylogenomic databases

eggNOGiKOG2180 Eukaryota
ENOG410XNMT LUCA
GeneTreeiENSGT00390000015165
HOGENOMiHOG000265899
InParanoidiQ5VIR6
KOiK20299
OMAiYRQVFRG
OrthoDBi1379600at2759
PhylomeDBiQ5VIR6
TreeFamiTF106150

Enzyme and pathway databases

ReactomeiR-HSA-6811440 Retrograde transport at the Trans-Golgi-Network

Miscellaneous databases

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data

More...
ChiTaRSi
VPS53 human

Database of phenotypes from RNA interference screens in Drosophila and Homo sapiens

More...
GenomeRNAii
55275
PharosiQ5VIR6 Tbio

Protein Ontology

More...
PROi
PR:Q5VIR6
RNActiQ5VIR6 protein

The Stanford Online Universal Resource for Clones and ESTs

More...
SOURCEi
Search...

Gene expression databases

BgeeiENSG00000141252 Expressed in 187 organ(s), highest expression level in frontal cortex
ExpressionAtlasiQ5VIR6 baseline and differential
GenevisibleiQ5VIR6 HS

Family and domain databases

InterProiView protein in InterPro
IPR039766 Vps53
IPR007234 Vps53_N
PANTHERiPTHR12820 PTHR12820, 1 hit
PfamiView protein in Pfam
PF04100 Vps53_N, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiVPS53_HUMAN
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q5VIR6
Secondary accession number(s): A8K2S8
, B3FH42, Q8WYW3, Q9BRR2, Q9BY02, Q9NV25
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: December 7, 2004
Last modified: December 11, 2019
This is version 133 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. Human chromosome 17
    Human chromosome 17: entries, gene names and cross-references to MIM
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