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STX5 syntaxin 5 [ Homo sapiens (human) ]

Gene ID: 6811, updated on 11-Apr-2024

Summary

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Official Symbol
STX5provided by HGNC
Official Full Name
syntaxin 5provided by HGNC
Primary source
HGNC:HGNC:11440
See related
Ensembl:ENSG00000162236 MIM:603189; AllianceGenome:HGNC:11440
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
SED5; STX5A; CDG2AA
Summary
This gene encodes a member of the syntaxin or t-SNARE (target-SNAP receptor) family. These proteins are found on cell membranes and serve as the targets for v-SNAREs (vesicle-SNAP receptors), permitting specific synaptic vesicle docking and fusion. The encoded protein regulates endoplasmic reticulum to Golgi transport and plays a critical role in autophagy. Autoantibodies targeting the encoded protein may be a diagnostic marker for endometriosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]
Expression
Ubiquitous expression in thyroid (RPKM 22.3), ovary (RPKM 17.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
11q12.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (62806860..62832051, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (62796253..62821448, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (62574332..62599523, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene transmembrane protein 223 Neighboring gene transmembrane protein 179B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4849 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3431 Neighboring gene microRNA 6748 Neighboring gene microRNA 6514 Neighboring gene nuclear RNA export factor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:62572705-62573204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4851 Neighboring gene RNA, U6 small nuclear 118, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4854 Neighboring gene STX5 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4855 Neighboring gene testis expressed 54 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4857 Neighboring gene WD repeat domain 74 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3432 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:62608631-62609244 Neighboring gene RNA, U2 small nuclear 2, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Syntaxin 5 determines Weibel-Palade body size and von Willebrand factor secretion by controlling Golgi architecture. Kat M, et al. Haematologica, 2022 Aug 1. PMID 35081689, Free PMC Article
  2. Congenital disorder of glycosylation caused by starting site-specific variant in syntaxin-5. Linders PTA, et al. Nat Commun, 2021 Oct 28. PMID 34711829, Free PMC Article
  3. Syntaxin 5-dependent retrograde transport to the trans-Golgi network is required for adeno-associated virus transduction. Nonnenmacher ME, et al. J Virol, 2015 Feb. PMID 25410859, Free PMC Article
  4. Identification of anti-syntaxin 5 autoantibody as a novel serum marker of endometriosis. Nabeta M, et al. J Reprod Immunol, 2011 Sep. PMID 21715015
  5. Cloning and identification of human syntaxin 5 as a synaptobrevin/VAMP binding protein. Ravichandran V, et al. J Mol Neurosci, 1997 Apr. PMID 9188044

See all (93) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Syntaxin 5 determines Weibel-Palade body size and von Willebrand factor secretion by controlling Golgi architecture.
    Title: Syntaxin 5 determines Weibel-Palade body size and von Willebrand factor secretion by controlling Golgi architecture.
  2. Congenital disorder of glycosylation caused by starting site-specific variant in syntaxin-5.
    Title: Congenital disorder of glycosylation caused by starting site-specific variant in syntaxin-5.
  3. Golgin45-Syntaxin5 Interaction Contributes to Structural Integrity of the Golgi Stack.
    Title: Golgin45-Syntaxin5 Interaction Contributes to Structural Integrity of the Golgi Stack.
  4. Expression of the Syn5 K270R mutant in cells impairs post-mitotic Golgi reassembly
    Title: Monoubiquitination of Syntaxin 5 Regulates Golgi Membrane Dynamics during the Cell Cycle.
  5. Together, these data strongly suggest that syntaxin 5-mediated retrograde transport to the Golgi apparatus is a broadly conserved feature of adeno-associated virus trafficking.
    Title: Syntaxin 5-dependent retrograde transport to the trans-Golgi network is required for adeno-associated virus transduction.
  6. Stx5 might play a role in modulating VLDL-R physiology by participating in an abrasively described or completely novel Golgi-bypass pathway.
    Title: Stx5 is a novel interactor of VLDL-R to affect its intracellular trafficking and processing.
  7. serum anti-STX5 autoantibody, which was discovered by a proteomic approach, is a potential new serum marker for the diagnosis of endometriosis.
    Title: Identification of anti-syntaxin 5 autoantibody as a novel serum marker of endometriosis.
  8. Depletion of syntaxin-5 complex components results in the accumulation of autophagosomes as a result of lysosomal dysfunction, leading to decreased degradation of autophagic substrates.
    Title: Autophagic substrate clearance requires activity of the syntaxin-5 SNARE complex.
  9. Study shows that the SM protein, Sly1, interacts directly with the conserved oligomeric Golgi (COG) tethering complex; Sly1-COG interaction is mediated by the Cog4 subunit, which also interacts with Syntaxin 5 through a different binding site.
    Title: Direct interaction between the COG complex and the SM protein, Sly1, is required for Golgi SNARE pairing.
  10. depletion of GM130 by RNA interference slows the rate of ER to Golgi trafficking in vivo; interactions of GM130 with syntaxin 5 and Rab1 are regulated by mitotic phosphorylation
    Title: Coordination of golgin tethering and SNARE assembly: GM130 binds syntaxin 5 in a p115-regulated manner.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Congenital disorder of glycosylation, type IIaa
MedGen: C5830651 OMIM: 620454 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of syntaxin 5 (STX5) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SNAP receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables SNAP receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables SNARE binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cadherin binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Golgi disassembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in early endosome to Golgi transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of protein catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of Golgi organization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in retrograde transport, endosome to Golgi IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in vesicle docking IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in vesicle fusion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in vesicle fusion with Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in ER to Golgi transport vesicle membrane TAS
Traceable Author Statement
more info
  
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in Golgi membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi membrane TAS
Traceable Author Statement
more info
  
part_of SNARE complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of SNARE complex TAS
Traceable Author Statement
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in endomembrane system IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum-Golgi intermediate compartment membrane TAS
Traceable Author Statement
more info
  
located_in vesicle IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
syntaxin-5
Names
syntaxin 5A

NCBI Reference Sequences (RefSeq)

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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_030034.1 RefSeqGene

    Range
    5041..30232
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001244666.3 → NP_001231595.1  syntaxin-5 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift and early stop codon compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC002645, CB155395
    Consensus CDS
    CCDS58140.1
    UniProtKB/Swiss-Prot
    Q13190
    Related
    ENSP00000367129.4, ENST00000377897.8
    Conserved Domains (3) summary
    COG5325
    Location:94 → 301
    COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
    pfam11416
    Location:53 → 74
    Syntaxin-5_N; Syntaxin-5 N-terminal, Sly1p-binding domain
    cl22856
    Location:266 → 304
    SNARE; SNARE motif

  2. NM_001330294.2 → NP_001317223.1  syntaxin-5 isoform 3

    Status: REVIEWED

    Source sequence(s)
    BE409085, BI820950, BT019647, BX537426
    Consensus CDS
    CCDS81578.1
    UniProtKB/Swiss-Prot
    Q13190
    Related
    ENSP00000378182.1, ENST00000394690.5
    Conserved Domains (3) summary
    COG5325
    Location:128 → 270
    COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
    cd15844
    Location:212 → 284
    SNARE_syntaxin5; SNARE motif of syntaxin 5
    pfam11416
    Location:1 → 18
    Syntaxin-5_N; Syntaxin-5 N-terminal, Sly1p-binding domain

  3. NM_003164.5 → NP_003155.2  syntaxin-5 isoform 1

    See identical proteins and their annotated locations for NP_003155.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the longer isoform (1).
    Source sequence(s)
    BE409085, CB155395, U26648
    Consensus CDS
    CCDS8038.2
    UniProtKB/Swiss-Prot
    B2R8T2, F8W8Q9, Q13190, Q5U0D4, Q7Z3T6, Q9BUG1
    Related
    ENSP00000294179.3, ENST00000294179.8
    Conserved Domains (3) summary
    COG5325
    Location:182 → 324
    COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
    cd15844
    Location:266 → 338
    SNARE_syntaxin5; SNARE motif of syntaxin 5
    pfam11416
    Location:53 → 74
    Syntaxin-5_N; Syntaxin-5 N-terminal, Sly1p-binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    62806860..62832051 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545224.4 → XP_011543526.1  syntaxin-5 isoform X2

    See identical proteins and their annotated locations for XP_011543526.1

    UniProtKB/TrEMBL
    B4DKR0
    Conserved Domains (2) summary
    cd15844
    Location:170 → 242
    SNARE_syntaxin5; SNARE motif of syntaxin 5
    cl26014
    Location:86 → 228
    SynN; Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may ...

  2. XM_047427505.1 → XP_047283461.1  syntaxin-5 isoform X1

    UniProtKB/Swiss-Prot
    B2R8T2, F8W8Q9, Q13190, Q5U0D4, Q7Z3T6, Q9BUG1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    62796253..62821448 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369769.1 → XP_054225744.1  syntaxin-5 isoform X2

    UniProtKB/TrEMBL
    B4DKR0

  2. XM_054369768.1 → XP_054225743.1  syntaxin-5 isoform X1

    UniProtKB/Swiss-Prot
    B2R8T2, F8W8Q9, Q13190, Q5U0D4, Q7Z3T6, Q9BUG1
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13190.2 GenPept UniProtKB/Swiss-Prot:Q13190

Gene LinkOut

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