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Human Gene STX6 (ENST00000258301.6) from GENCODE V50
  Description: syntaxin 6, transcript variant 1 (from RefSeq NM_005819.6)
Gencode Transcript: ENST00000258301.6
Gencode Gene: ENSG00000135823.15
Transcript (Including UTRs)
   Position: hg38 chr1:180,972,725-181,022,870 Size: 50,146 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg38 chr1:180,976,570-181,022,673 Size: 46,104 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2026-07-12 09:30:09

-  Comments and Description Text from UniProtKB
  ID: STX6_HUMAN
DESCRIPTION: RecName: Full=Syntaxin-6;
FUNCTION: Involved in intracellular vesicle trafficking.
SUBUNIT: Binds EEA1. Interacts with VPS45A. Interacts with MARCH2 and MARCH3 (By similarity). Interacts with GOPC. Identified in a complex containing STX6, STX12, VAMP4 and VTI1A.
SUBCELLULAR LOCATION: Golgi apparatus membrane; Single-pass type IV membrane protein (Potential).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the syntaxin family.
SIMILARITY: Contains 1 t-SNARE coiled-coil homology domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.09 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 336.90 RPKM



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

+  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -98.50197-0.500 Picture PostScript Text
3' UTR -1068.503845-0.278 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
IPR015260 - Syntaxin-6_N
IPR006012 - Syntaxin/epimorphin_CS
IPR010989 - t-SNARE
IPR000727 - T_SNARE_dom

Pfam Domains:
PF05739 - SNARE domain
PF09177 - Syntaxin 6, N-terminal

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2NPS - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O43752
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGI     
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005484 SNAP receptor activity
GO:0005515 protein binding
GO:0019905 syntaxin binding

Biological Process:
GO:0006886 intracellular protein transport
GO:0006906 vesicle fusion
GO:0007032 endosome organization
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0032456 endocytic recycling
GO:0032880 regulation of protein localization
GO:0042147 retrograde transport, endosome to Golgi
GO:0048193 Golgi vesicle transport
GO:0048278 vesicle docking
GO:0090161 Golgi ribbon formation
GO:1903827 regulation of cellular protein localization

Cellular Component:
GO:0000139 Golgi membrane
GO:0005654 nucleoplasm
GO:0005769 early endosome
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030136 clathrin-coated vesicle
GO:0030285 integral component of synaptic vesicle membrane
GO:0031201 SNARE complex
GO:0032588 trans-Golgi network membrane
GO:0045335 phagocytic vesicle
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC009944 - Homo sapiens syntaxin 6, mRNA (cDNA clone MGC:12919 IMAGE:4122224), complete cds.
AK299063 - Homo sapiens cDNA FLJ57566 complete cds, highly similar to Syntaxin-6.
AJ002078 - Homo sapiens mRNA for syntaxin 6, complete CDS.
CR541856 - Homo sapiens full open reading frame cDNA clone RZPDo834F0632D for gene STX6, syntaxin 6; complete cds, incl. stopcodon.
AK312440 - Homo sapiens cDNA, FLJ92788, Homo sapiens syntaxin 6 (STX6), mRNA.
KJ892968 - Synthetic construct Homo sapiens clone ccsbBroadEn_02362 STX6 gene, encodes complete protein.
DQ891932 - Synthetic construct clone IMAGE:100004562; FLH181536.01X; RZPDo839E06136D syntaxin 6 (STX6) gene, encodes complete protein.
DQ895119 - Synthetic construct Homo sapiens clone IMAGE:100009579; FLH181532.01L; RZPDo839E06135D syntaxin 6 (STX6) gene, encodes complete protein.
CR541873 - Homo sapiens full open reading frame cDNA clone RZPDo834D0133D for gene STX6, syntaxin 6; complete cds, without stopcodon.
AB590197 - Synthetic construct DNA, clone: pFN21AE0897, Homo sapiens STX6 gene for syntaxin 6, without stop codon, in Flexi system.
AK056657 - Homo sapiens cDNA FLJ32095 fis, clone OCBBF2000998.
AF038202 - Homo sapiens clone 23570 mRNA sequence.
BC039118 - Homo sapiens syntaxin 6, mRNA (cDNA clone IMAGE:4831269), with apparent retained intron.
JD280639 - Sequence 261663 from Patent EP1572962.
JD527161 - Sequence 508185 from Patent EP1572962.
JD087291 - Sequence 68315 from Patent EP1572962.
JD508761 - Sequence 489785 from Patent EP1572962.
JD406487 - Sequence 387511 from Patent EP1572962.
JD371926 - Sequence 352950 from Patent EP1572962.
JD156293 - Sequence 137317 from Patent EP1572962.
JD465755 - Sequence 446779 from Patent EP1572962.
JD255631 - Sequence 236655 from Patent EP1572962.
JD183044 - Sequence 164068 from Patent EP1572962.
JD333448 - Sequence 314472 from Patent EP1572962.
JD073492 - Sequence 54516 from Patent EP1572962.
JD251444 - Sequence 232468 from Patent EP1572962.
JD471305 - Sequence 452329 from Patent EP1572962.
JD460935 - Sequence 441959 from Patent EP1572962.
JD271528 - Sequence 252552 from Patent EP1572962.
JD215236 - Sequence 196260 from Patent EP1572962.
JD498530 - Sequence 479554 from Patent EP1572962.
JD223148 - Sequence 204172 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04130 - SNARE interactions in vesicular transport

Reactome (by CSHL, EBI, and GO)

Protein O43752 (Reactome details) participates in the following event(s):

R-HSA-6814683 NSF-dependent ATP hydrolysis disassembles the cis-SNARE at the TGN
R-HSA-6811433 The COG tethering complex interacts with numerous SNAREs at the Golgi membrane
R-HSA-6811431 RAB6:GTP binds the GARP and COG complexes, t-SNAREs and endosome-derived vesicles
R-HSA-6814684 cis-SNARE binds SNAPs and NSF hexamer at the TGN
R-HSA-6811440 Retrograde transport at the Trans-Golgi-Network
R-HSA-6811438 Intra-Golgi traffic
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: B2R652, B4DR17, ENST00000258301.1, ENST00000258301.2, ENST00000258301.3, ENST00000258301.4, ENST00000258301.5, NM_005819, O43752, Q5VY08, Q6FH83, STX6_HUMAN, uc021pfr.1, uc021pfr.2, uc021pfr.3, uc021pfr.4
UCSC ID: ENST00000258301.6
RefSeq Accession: NM_005819.6
Protein: O43752 (aka STX6_HUMAN)
CCDS: CCDS1341.1

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