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VPS29 VPS29 retromer complex component [ Homo sapiens (human) ]

Gene ID: 51699, updated on 30-Jun-2019

Summary

Official Symbol
VPS29provided by HGNC
Official Full Name
VPS29 retromer complex componentprovided by HGNC
Primary source
HGNC:HGNC:14340
See related
Ensembl:ENSG00000111237 MIM:606932
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DC7; DC15; PEP11
Summary
This gene belongs to a group of vacuolar protein sorting (VPS) genes that, when functionally impaired, disrupt the efficient delivery of vacuolar hydrolases. The protein encoded by this gene is a component of a large multimeric complex, termed the retromer complex, which is involved in retrograde transport of proteins from endosomes to the trans-Golgi network. This VPS protein may be involved in the formation of the inner shell of the retromer coat for retrograde vesicles leaving the prevacuolar compartment. Alternative splice variants encoding different isoforms and representing non-protein coding transcripts have been found for this gene. [provided by RefSeq, Aug 2013]
Expression
Ubiquitous expression in fat (RPKM 31.1), esophagus (RPKM 28.7) and 25 other tissues See more
Orthologs

Genomic context

See VPS29 in Genome Data Viewer
Location:
12q24.11
Exon count:
8
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (110491083..110502140, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (110929330..110939916, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L31 pseudogene 49 Neighboring gene GPN-loop GTPase 3 Neighboring gene family with sequence similarity 216 member A Neighboring gene RAD9 checkpoint clamp component B Neighboring gene PTC7 protein phosphatase homolog Neighboring gene HNF4 motif-containing MPRA enhancer 250 Neighboring gene tectonic family member 1 Neighboring gene RNA, 7SL, cytoplasmic 387, pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Wnt, organism-specific biosystem (from REACTOME)
    Signaling by Wnt, organism-specific biosystemWNT signaling pathways control a wide range of developmental and adult process in metozoans including cell proliferation, cell fate decisions, cell polarity and stem cell maintenance (reviewed in Sai...
  • WNT ligand biogenesis and trafficking, organism-specific biosystem (from REACTOME)
    WNT ligand biogenesis and trafficking, organism-specific biosystem19 WNT proteins have been identified in human cells. The WNTs are members of a conserved metazoan family of secreted morphogens that activate several signaling pathways in the responding cell: the c...
  • serine and glycine biosynthesis, organism-specific biosystem (from BIOCYC)
    serine and glycine biosynthesis, organism-specific biosystemBackground : SER, is a nonessential amino acid, in that it is synthesized by at least two different pathways in vivo. It can also be derived from dietary intake, protein degradation and phospholipi...
  • serine biosynthesis (phosphorylated route), organism-specific biosystem (from BIOCYC)
    serine biosynthesis (phosphorylated route), organism-specific biosystemBackground : SER, is a nonessential amino acid, in that it is synthesized by at least two different pathways in vivo. It can also be derived from dietary intake, protein degradation and phospholipid...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20492, DKFZp564F0223

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Wnt signaling pathway TAS
Traceable Author Statement
more info
 
endocytic recycling IMP
Inferred from Mutant Phenotype
more info
PubMed 
intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
NOT regulation of autophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retrograde transport, endosome to Golgi NAS
Non-traceable Author Statement
more info
PubMed 
retrograde transport, endosome to plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
early endosome IEA
Inferred from Electronic Annotation
more info
 
endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endosome IDA
Inferred from Direct Assay
more info
 
endosome membrane IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
late endosome IEA
Inferred from Electronic Annotation
more info
 
retromer complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retromer complex IDA
Inferred from Direct Assay
more info
PubMed 
retromer, cargo-selective complex IDA
Inferred from Direct Assay
more info
PubMed 
retromer, cargo-selective complex NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
vacuolar protein sorting-associated protein 29
Names
PEP11 homolog
epididymis secretory sperm binding protein
hVPS29
retromer protein
vacuolar protein sorting 29 homolog
vacuolar sorting protein VPS29/PEP11
vesicle protein sorting 29
x 007 protein
NP_001269079.1
NP_001269080.1
NP_057310.1
NP_476528.1
XP_006719522.1
XP_006719523.1
XP_011536786.1
XP_016874946.1
XP_016874948.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001282150.1NP_001269079.1  vacuolar protein sorting-associated protein 29 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
    Source sequence(s)
    AB578892, AL832866, BM806646
    Consensus CDS
    CCDS73525.1
    UniProtKB/TrEMBL
    F8VXU5
    Related
    ENSP00000449044.1, ENST00000546588.1
    Conserved Domains (2) summary
    cd07394
    Location:34211
    MPP_Vps29; Homo sapiens Vps29 and related proteins, metallophosphatase domain
    pfam00149
    Location:35164
    Metallophos; Calcineurin-like phosphoesterase
  2. NM_001282151.1NP_001269080.1  vacuolar protein sorting-associated protein 29 isoform 4

    See identical proteins and their annotated locations for NP_001269080.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks several alternate exons compared to variant 3. The resulting isoform (4) has shorter and distinct N- and C-termini compared to isoform 3.
    Source sequence(s)
    AB578892, AL832866, CB158821
    Conserved Domains (1) summary
    cl13995
    Location:289
    MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain
  3. NM_016226.5NP_057310.1  vacuolar protein sorting-associated protein 29 isoform 1

    See identical proteins and their annotated locations for NP_057310.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks two alternate exons compared to variant 3. The resulting isoform (1) has a shorter and distinct N-terminus compared to isoform 3.
    Source sequence(s)
    AC002350, AL832866, BC095446
    Consensus CDS
    CCDS41832.1
    UniProtKB/Swiss-Prot
    Q9UBQ0
    Related
    ENSP00000447058.1, ENST00000549578.5
    Conserved Domains (1) summary
    cd07394
    Location:2179
    MPP_Vps29; Homo sapiens Vps29 and related proteins, metallophosphatase domain
  4. NM_057180.2NP_476528.1  vacuolar protein sorting-associated protein 29 isoform 2

    See identical proteins and their annotated locations for NP_476528.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon compared to variant 3. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 3.
    Source sequence(s)
    AB578892, AF168716, AL832866
    Consensus CDS
    CCDS53832.1
    UniProtKB/Swiss-Prot
    Q9UBQ0
    Related
    ENSP00000353786.7, ENST00000360579.11
    Conserved Domains (1) summary
    cd07394
    Location:6183
    MPP_Vps29; Homo sapiens Vps29 and related proteins, metallophosphatase domain

RNA

  1. NR_104099.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate exon and contains another alternate exon compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB578892, AL832866, BU568689
  2. NR_104100.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks two alternate exons and contains another alternate exon compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB578892, AC002350, AL832866, BC015095
    Related
    ENST00000447578.6
  3. NR_104101.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an alternate exon and uses an alternate splice junction at the 3' end of an exon compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB578892, AL832866, BC095446, BF030144
    Related
    ENST00000552130.6
  4. NR_104102.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) lacks two alternate exons and uses an alternate splice junction at the 5' end of an exon compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA148059, AB578892, AL832866

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    110491083..110502140 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538484.2XP_011536786.1  vacuolar protein sorting-associated protein 29 isoform X2

    See identical proteins and their annotated locations for XP_011536786.1

    Conserved Domains (2) summary
    cd07394
    Location:3180
    MPP_Vps29; Homo sapiens Vps29 and related proteins, metallophosphatase domain
    pfam00149
    Location:4133
    Metallophos; Calcineurin-like phosphoesterase
  2. XM_006719459.4XP_006719522.1  vacuolar protein sorting-associated protein 29 isoform X2

    See identical proteins and their annotated locations for XP_006719522.1

    Conserved Domains (2) summary
    cd07394
    Location:3180
    MPP_Vps29; Homo sapiens Vps29 and related proteins, metallophosphatase domain
    pfam00149
    Location:4133
    Metallophos; Calcineurin-like phosphoesterase
  3. XM_006719460.4XP_006719523.1  vacuolar protein sorting-associated protein 29 isoform X2

    See identical proteins and their annotated locations for XP_006719523.1

    Conserved Domains (2) summary
    cd07394
    Location:3180
    MPP_Vps29; Homo sapiens Vps29 and related proteins, metallophosphatase domain
    pfam00149
    Location:4133
    Metallophos; Calcineurin-like phosphoesterase
  4. XM_017019457.2XP_016874946.1  vacuolar protein sorting-associated protein 29 isoform X1

    UniProtKB/TrEMBL
    F8VXU5
    Related
    ENSP00000480853.1, ENST00000621131.4
    Conserved Domains (2) summary
    cd07394
    Location:34211
    MPP_Vps29; Homo sapiens Vps29 and related proteins, metallophosphatase domain
    pfam00149
    Location:35164
    Metallophos; Calcineurin-like phosphoesterase
  5. XM_017019459.2XP_016874948.1  vacuolar protein sorting-associated protein 29 isoform X3

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