Human Gene SNAP23 (ENST00000249647.8_4) from GENCODE V47lift37
  Description: synaptosome associated protein 23, transcript variant 1 (from RefSeq NM_003825.4)
Gencode Transcript: ENST00000249647.8_4
Gencode Gene: ENSG00000092531.10_11
Transcript (Including UTRs)
   Position: hg19 chr15:42,787,832-42,825,256 Size: 37,425 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr15:42,804,045-42,823,676 Size: 19,632 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:42,787,832-42,825,256)mRNA (may differ from genome)Protein (211 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SNP23_HUMAN
DESCRIPTION: RecName: Full=Synaptosomal-associated protein 23; Short=SNAP-23; AltName: Full=Vesicle-membrane fusion protein SNAP-23;
FUNCTION: Essential component of the high affinity receptor for the general membrane fusion machinery and an important regulator of transport vesicle docking and fusion.
SUBUNIT: Binds simultaneously to SNAPIN and SYN4. Found in a complex with VAMP8 and STX4 in pancreas. Interacts with STX1A and STX12 (By similarity). Binds tightly to multiple syntaxins and synaptobrevins/VAMPs. Found in a complex with VAMP8 and STX1A.
INTERACTION: P54920:NAPA; NbExp=2; IntAct=EBI-745000, EBI-749652;
SUBCELLULAR LOCATION: Cell membrane; Peripheral membrane protein. Cell membrane; Lipid-anchor. Cell junction, synapse, synaptosome. Note=Mainly localized to the plasma membrane.
TISSUE SPECIFICITY: Ubiquitous. Highest levels where found in placenta.
SIMILARITY: Belongs to the SNAP-25 family.
SIMILARITY: Contains 2 t-SNARE coiled-coil homology domains.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: SNAP23
Diseases sorted by gene-association score: tetanus (4), hemophagocytic lymphohistiocytosis (3), chief cell adenoma (2)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 28.35 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 642.82 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -35.7094-0.380 Picture PostScript Text
3' UTR -409.501580-0.259 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
IPR000928 - SNAP-25
IPR000727 - T_SNARE_dom

Pfam Domains:
PF00835 - SNAP-25 family

SCOP Domains:
58038 - SNARE fusion complex

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1NHL - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O00161
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  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:0002479 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent
GO:0002553 histamine secretion by mast cell
GO:0006892 post-Golgi vesicle-mediated transport
GO:0006903 vesicle targeting
GO:0015031 protein transport
GO:0016082 synaptic vesicle priming
GO:0031629 synaptic vesicle fusion to presynaptic active zone membrane
GO:0043312 neutrophil degranulation
GO:0061025 membrane fusion

Cellular Component:
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0005913 cell-cell adherens junction
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0030054 cell junction
GO:0030670 phagocytic vesicle membrane
GO:0031201 SNARE complex
GO:0035579 specific granule membrane
GO:0042581 specific granule
GO:0042582 azurophil granule
GO:0042629 mast cell granule
GO:0043005 neuron projection
GO:0045202 synapse
GO:0070062 extracellular exosome
GO:0070821 tertiary granule membrane
GO:0098793 presynapse


-  Descriptions from all associated GenBank mRNAs
  AK290152 - Homo sapiens cDNA FLJ77854 complete cds, highly similar to Homo sapiens synaptosomal-associated protein, 23kDa (SNAP23), transcript variant 1, mRNA.
AK315279 - Homo sapiens cDNA, FLJ96291.
U55936 - Human SNAP-23 mRNA, complete cds.
BC022890 - Homo sapiens synaptosomal-associated protein, 23kDa, mRNA (cDNA clone MGC:27295 IMAGE:4658930), complete cds.
BC003686 - Homo sapiens synaptosomal-associated protein, 23kDa, mRNA (cDNA clone MGC:5155 IMAGE:3461227), complete cds.
AK313161 - Homo sapiens cDNA, FLJ93656, Homo sapiens synaptosomal-associated protein, 23kDa (SNAP23),transcript variant 1, mRNA.
JD220711 - Sequence 201735 from Patent EP1572962.
BC000148 - Homo sapiens synaptosomal-associated protein, 23kDa, mRNA (cDNA clone MGC:5325 IMAGE:2900640), complete cds.
AJ011915 - Homo sapiens mRNA for synaptosome associated protein of 23 kilodaltons, isoform A.
AB528483 - Synthetic construct DNA, clone: pF1KB3484, Homo sapiens SNAP23 gene for synaptosomal-associated protein, 23kDa, without stop codon, in Flexi system.
DQ894086 - Synthetic construct Homo sapiens clone IMAGE:100008546; FLH167556.01L; RZPDo839C0489D synaptosomal-associated protein, 23kDa (SNAP23) gene, encodes complete protein.
CU674062 - Synthetic construct Homo sapiens gateway clone IMAGE:100018588 5' read SNAP23 mRNA.
KJ892619 - Synthetic construct Homo sapiens clone ccsbBroadEn_02013 SNAP23 gene, encodes complete protein.
BT006916 - Homo sapiens synaptosomal-associated protein, 23kDa mRNA, complete cds.
CR457212 - Homo sapiens full open reading frame cDNA clone RZPDo834E098D for gene SNAP23, synaptosomal-associated protein, 23kDa; complete cds, incl. stopcodon.
Y09567 - Homo sapiens mRNA for SNAP23A protein, complete CDS.
Y09568 - Homo sapiens mRNA for SNAP23B protein, complete CDS.
JD337116 - Sequence 318140 from Patent EP1572962.
JD550154 - Sequence 531178 from Patent EP1572962.
JD533492 - Sequence 514516 from Patent EP1572962.
JD438106 - Sequence 419130 from Patent EP1572962.
JD561673 - Sequence 542697 from Patent EP1572962.
JD036443 - Sequence 17467 from Patent EP1572962.
JD454503 - Sequence 435527 from Patent EP1572962.
JD051952 - Sequence 32976 from Patent EP1572962.
JD066501 - Sequence 47525 from Patent EP1572962.
JD140544 - Sequence 121568 from Patent EP1572962.
JD465343 - Sequence 446367 from Patent EP1572962.
JD419012 - Sequence 400036 from Patent EP1572962.
JD154248 - Sequence 135272 from Patent EP1572962.
JD295874 - Sequence 276898 from Patent EP1572962.
JD461766 - Sequence 442790 from Patent EP1572962.
JD527063 - Sequence 508087 from Patent EP1572962.
JD425932 - Sequence 406956 from Patent EP1572962.
JD358366 - Sequence 339390 from Patent EP1572962.
JD345680 - Sequence 326704 from Patent EP1572962.
JD225363 - Sequence 206387 from Patent EP1572962.
JD506063 - Sequence 487087 from Patent EP1572962.
JD364406 - Sequence 345430 from Patent EP1572962.
JD488520 - Sequence 469544 from Patent EP1572962.
JD494569 - Sequence 475593 from Patent EP1572962.
JD254797 - Sequence 235821 from Patent EP1572962.
JD442588 - Sequence 423612 from Patent EP1572962.
JD285524 - Sequence 266548 from Patent EP1572962.
JD075972 - Sequence 56996 from Patent EP1572962.
JD063425 - Sequence 44449 from Patent EP1572962.
JD362846 - Sequence 343870 from Patent EP1572962.
JD312482 - Sequence 293506 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O00161 (Reactome details) participates in the following event(s):

R-HSA-376357 Vamp7 associated Lysosome to Plasma membrane transport
R-HSA-376364 Vamp8 associated secretory vesicle to plasma membrane transport
R-HSA-376369 Vamp2 associated secretory vesicle to plasma membrane transport
R-HSA-8863895 IKKB phosphorylates SNAP23
R-HSA-6799350 Exocytosis of specific granule membrane proteins
R-HSA-6798747 Exocytosis of tertiary granule membrane proteins
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-1445148 Translocation of GLUT4 to the plasma membrane
R-HSA-1236974 ER-Phagosome pathway
R-HSA-6798695 Neutrophil degranulation
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-199991 Membrane Trafficking
R-HSA-1236975 Antigen processing-Cross presentation
R-HSA-168249 Innate Immune System
R-HSA-5653656 Vesicle-mediated transport
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-168256 Immune System
R-HSA-1280218 Adaptive Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000249647.1, ENST00000249647.2, ENST00000249647.3, ENST00000249647.4, ENST00000249647.5, ENST00000249647.6, ENST00000249647.7, NM_003825, O00161, O00162, Q13602, Q6IAE3, SNP23_HUMAN, uc317ezx.1, uc317ezx.2
UCSC ID: ENST00000249647.8_4
RefSeq Accession: NM_003825.4
Protein: O00161 (aka SNP23_HUMAN or SN23_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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