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VAMP7 vesicle associated membrane protein 7 [ Homo sapiens (human) ]

Gene ID: 6845, updated on 15-Apr-2019

Summary

Official Symbol
VAMP7provided by HGNC
Official Full Name
vesicle associated membrane protein 7provided by HGNC
Primary source
HGNC:HGNC:11486
See related
Ensembl:ENSG00000124333 MIM:300053
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
SYBL1; TIVAMP; VAMP-7; TI-VAMP
Summary
This gene encodes a transmembrane protein that is a member of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) family. The encoded protein localizes to late endosomes and lysosomes and is involved in the fusion of transport vesicles to their target membranes. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jun 2010]
Expression
Ubiquitous expression in placenta (RPKM 18.0), kidney (RPKM 17.3) and 25 other tissues See more
Orthologs

Genomic context

See VAMP7 in Genome Data Viewer
Location:
Xq28 and Yq12
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) X NC_000023.11 (155881280..155943769)
109 current GRCh38.p12 (GCF_000001405.38) Y NC_000024.10 (57067800..57130289)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (155110943..155173433)
105 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (59213949..59276439)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene adenosylmethionine decarboxylase 1 pseudogene 2 Neighboring gene diphthamide biosynthesis 3 pseudogene 2 Neighboring gene elongin C pseudogene 24 Neighboring gene transient receptor potential cation channel subfamily C member 6, pseudogene

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene adenosylmethionine decarboxylase 1 pseudogene 2 Neighboring gene diphthamide biosynthesis 3 pseudogene 2 Neighboring gene elongin C pseudogene 24 Neighboring gene transient receptor potential cation channel subfamily C member 6, 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?

Phenotypes

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated (2012-09-06)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated (2012-09-06)

ClinGen Genome Curation Page

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag Inhibition of endocytosis by siRNA-mediated depletion of EPS15, STX7, RAB7, and VAMP7 restores Gag/p24 expression in the presence of APOL1 PubMed
gag HIV-1 Gag accumulates in late endosome and co-localizes with TiVamp as a result of disruption of endosomal pathways PubMed
gag HIV-1 Gag and genomic RNA are transported on endosomal vesicles, in which endosomal protein TiVamp is co-localized and involved in fusion events with the plasma membrane PubMed
capsid gag Inhibition of endocytosis by siRNA-mediated depletion of EPS15, STX7, RAB7, and VAMP7 restores Gag/p24 expression in the presence of APOL1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
    Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystemRecruitment of plasma membrane-localized cargo into clathrin-coated endocytic vesicles is mediated by interaction with a variety of clathrin-interacting proteins collectively called CLASPs (clathrin-...
  • Clathrin derived vesicle budding, organism-specific biosystem (from REACTOME)
    Clathrin derived vesicle budding, organism-specific biosystemThere at least two classes of clathrin coated vesicles in cells, one predominantly Golgi-associated, involved in budding from the trans-Golgi network and the other at the plasma membrane. Here the cl...
  • Clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
    Clathrin-mediated endocytosis, organism-specific biosystemClathrin-mediated endocytosis (CME) is one of a number of process that control the uptake of material from the plasma membrane, and leads to the formation of clathrin-coated vesicles (Pearse et al, 1...
  • Golgi Associated Vesicle Biogenesis, organism-specific biosystem (from REACTOME)
    Golgi Associated Vesicle Biogenesis, organism-specific biosystemProteins that have been synthesized, processed and sorted eventually reach the final steps of the secretory pathway. This pathway is responsible not only for proteins that are secreted from the cell ...
  • Lysosome Vesicle Biogenesis, organism-specific biosystem (from REACTOME)
    Lysosome Vesicle Biogenesis, organism-specific biosystemProteins that have been synthesized, processed and sorted eventually reach the final steps of the secretory pathway. This pathway is responsible not only for proteins that are secreted from the cell ...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • SNARE interactions in vesicular transport, organism-specific biosystem (from KEGG)
    SNARE interactions in vesicular transport, organism-specific biosystem
    SNARE interactions in vesicular transport
  • SNARE interactions in vesicular transport, conserved biosystem (from KEGG)
    SNARE interactions in vesicular transport, conserved biosystem
    SNARE interactions in vesicular transport
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...
  • trans-Golgi Network Vesicle Budding, organism-specific biosystem (from REACTOME)
    trans-Golgi Network Vesicle Budding, organism-specific biosystemAfter passing through the Golgi complex, secretory cargo is packaged into post-Golgi transport intermediates (post-Golgi), which translocate plus-end directed along microtubules to the plasma membran...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ53045, FLJ53762, FLJ54296

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SNAP receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
SNARE binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
syntaxin binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
ER to Golgi vesicle-mediated transport ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
Golgi to plasma membrane protein transport IEA
Inferred from Electronic Annotation
more info
 
SNARE complex assembly IEA
Inferred from Electronic Annotation
more info
 
NOT autophagosome maturation IMP
Inferred from Mutant Phenotype
more info
PubMed 
calcium ion regulated exocytosis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
endosome to lysosome transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endosome to lysosome transport IDA
Inferred from Direct Assay
more info
PubMed 
eosinophil degranulation IMP
Inferred from Mutant Phenotype
more info
PubMed 
eosinophil degranulation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
membrane organization TAS
Traceable Author Statement
more info
 
natural killer cell degranulation IMP
Inferred from Mutant Phenotype
more info
PubMed 
neutrophil degranulation IMP
Inferred from Mutant Phenotype
more info
PubMed 
neutrophil degranulation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
phagocytosis, engulfment ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of dendrite morphogenesis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of histamine secretion by mast cell IMP
Inferred from Mutant Phenotype
more info
PubMed 
post-Golgi vesicle-mediated transport TAS
Traceable Author Statement
more info
 
regulation of protein targeting to vacuolar membrane IEA
Inferred from Electronic Annotation
more info
 
triglyceride transport IEA
Inferred from Electronic Annotation
more info
 
vesicle fusion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
vesicle fusion IDA
Inferred from Direct Assay
more info
PubMed 
vesicle fusion with Golgi apparatus IEA
Inferred from Electronic Annotation
more info
 
vesicle transport along microtubule IEA
Inferred from Electronic Annotation
more info
 
vesicle-mediated transport IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
SNARE complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
SNARE complex IDA
Inferred from Direct Assay
more info
PubMed 
SNARE complex ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
apical part of cell IEA
Inferred from Electronic Annotation
more info
 
azurophil granule membrane IDA
Inferred from Direct Assay
more info
PubMed 
cell junction IEA
Inferred from Electronic Annotation
more info
 
cell surface IEA
Inferred from Electronic Annotation
more info
 
clathrin-coated vesicle membrane TAS
Traceable Author Statement
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
extracellular exosome HDA PubMed 
hippocampal mossy fiber to CA3 synapse IEA
Inferred from Electronic Annotation
more info
 
integral component of synaptic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
lamellipodium IDA
Inferred from Direct Assay
more info
PubMed 
late endosome membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
lysosomal membrane HDA PubMed 
lysosomal membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
lysosomal membrane TAS
Traceable Author Statement
more info
 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
neuron projection ISS
Inferred from Sequence or Structural Similarity
more info
 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 
phagocytic vesicle ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
phagocytic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
platelet alpha granule IDA
Inferred from Direct Assay
more info
PubMed 
pseudopodium IDA
Inferred from Direct Assay
more info
PubMed 
secretory granule IDA
Inferred from Direct Assay
more info
PubMed 
secretory granule membrane IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
vesicle-associated membrane protein 7
Names
synaptobrevin-like 1
synaptobrevin-like protein 1
tetanus neurotoxin-insensitive VAMP
tetanus-insensitive VAMP

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.

Genomic

  1. NG_021435.1 RefSeqGene

    Range
    5001..67491
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145149.2NP_001138621.1  vesicle-associated membrane protein 7 isoform 2

    See identical proteins and their annotated locations for NP_001138621.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame segment compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AI522002, AJ271736, AJ549301, X92396
    Consensus CDS
    CCDS48199.1
    UniProtKB/Swiss-Prot
    P51809
    Related
    ENSP00000427822.1, ENST00000460621.6
    Conserved Domains (2) summary
    cd15871
    Location:83147
    R-SNARE_VAMP7; SNARE motif of VAMP7
    cl26083
    Location:31131
    Synaptobrevin; Synaptobrevin
  2. NM_001185183.1NP_001172112.1  vesicle-associated membrane protein 7 isoform 3

    See identical proteins and their annotated locations for NP_001172112.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (3) is longer and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AI522002, AJ271736, AJ295938
    Consensus CDS
    CCDS55548.1
    UniProtKB/Swiss-Prot
    P51809
    UniProtKB/TrEMBL
    A0A024R074
    Related
    ENSP00000262640.6, ENST00000262640.11
    Conserved Domains (2) summary
    pfam13774
    Location:29104
    Longin; Regulated-SNARE-like domain
    cl22856
    Location:124144
    SNARE; SNARE motif
  3. NM_005638.6NP_005629.1  vesicle-associated membrane protein 7 isoform 1

    See identical proteins and their annotated locations for NP_005629.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform (1).
    Source sequence(s)
    AI522002, BC056141
    Consensus CDS
    CCDS14770.4
    UniProtKB/Swiss-Prot
    P51809
    UniProtKB/TrEMBL
    A0A024R061
    Related
    ENSP00000286448.6, ENST00000286448.12
    Conserved Domains (2) summary
    cd15871
    Location:124188
    R-SNARE_VAMP7; SNARE motif of VAMP7
    pfam13774
    Location:29104
    Longin; Regulated-SNARE-like domain

RNA

  1. NR_033714.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI522002, AJ271736, AK297385, X92396
  2. NR_033715.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI522002, AJ271736, AK295605, X92396

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p12 Primary Assembly

    Range
    155881280..155943769
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029760.1XP_016885249.1  vesicle-associated membrane protein 7 isoform X2

    Conserved Domains (2) summary
    cd15871
    Location:77141
    R-SNARE_VAMP7; SNARE motif of VAMP7
    pfam13774
    Location:357
    Longin; Regulated-SNARE-like domain
  2. XM_011531188.1XP_011529490.1  vesicle-associated membrane protein 7 isoform X1

    See identical proteins and their annotated locations for XP_011529490.1

    Conserved Domains (2) summary
    pfam13774
    Location:351
    Longin; Regulated-SNARE-like domain
    cl22856
    Location:7797
    SNARE; SNARE motif

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p12 Primary Assembly

    Range
    57067800..57130289
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017030063.1XP_016885552.1  vesicle-associated membrane protein 7 isoform X2

    Conserved Domains (2) summary
    cd15871
    Location:77141
    R-SNARE_VAMP7; SNARE motif of VAMP7
    pfam13774
    Location:357
    Longin; Regulated-SNARE-like domain
  2. XM_011545653.1XP_011543955.1  vesicle-associated membrane protein 7 isoform X1

    See identical proteins and their annotated locations for XP_011543955.1

    Conserved Domains (2) summary
    pfam13774
    Location:351
    Longin; Regulated-SNARE-like domain
    cl22856
    Location:7797
    SNARE; SNARE motif
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