Human Gene STX1A (uc003tyy.3)
  Description: Homo sapiens syntaxin 1A (brain) (STX1A), transcript variant 2, mRNA.
RefSeq Summary (NM_001165903): This gene encodes a member of the syntaxin superfamily. Syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins possess a single C-terminal transmembrane domain, a SNARE [Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein REceptor] domain (known as H3), and an N-terminal regulatory domain (Habc). Syntaxins bind synaptotagmin in a calcium-dependent fashion and interact with voltage dependent calcium and potassium channels via the C-terminal H3 domain. This gene product is a key molecule in ion channel regulation and synaptic exocytosis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009].
Transcript (Including UTRs)
   Position: hg19 chr7:73,113,535-73,134,017 Size: 20,483 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr7:73,114,802-73,133,961 Size: 19,160 Coding Exon Count: 10 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:73,113,535-73,134,017)mRNA (may differ from genome)Protein (251 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCLynxMalacardsMGIOMIMPubMed
ReactomeTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): STX1A
CDC HuGE Published Literature: STX1A
Positive Disease Associations: diabetes, type 2
Related Studies:
  1. diabetes, type 2
    Tsunoda, K. et al. 2001, Single nucleotide polymorphism (D68D, T to C) in the syntaxin 1A gene correlates to age at onset and insulin requirement in Type II diabetic patients, Diabetologia. 2001 Nov;44(11):2092-7. [PubMed 11719842]
    These data indicate that the SNP in the syntaxin 1A gene (D68D, T to C) correlates to the age of onset and insulin requirements of Type II diabetic

-  MalaCards Disease Associations
  MalaCards Gene Search: STX1A
Diseases sorted by gene-association score: cystic fibrosis* (15), osteogenesis imperfecta, type xv (11), benign familial neonatal epilepsy (6), acute diarrhea (6), williams-beuren syndrome (3), attention deficit-hyperactivity disorder (1)
* = Manually curated disease association

-  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: 89.65 RPKM in Brain - Cortex
Total median expression: 597.32 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -23.0056-0.411 Picture PostScript Text
3' UTR -547.921267-0.432 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
  Pfam Domains:
PF00804 - Syntaxin
PF14523 - Syntaxin-like protein

SCOP Domains:
47661 - t-snare proteins

ModBase Predicted Comparative 3D Structure on Q16623-3
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  D37932 - Homo sapiens mRNA for HPC-1, partial cds.
L37792 - Homo sapiens syntaxin 1A mRNA, complete cds.
BC064644 - Homo sapiens syntaxin 1A (brain), mRNA (cDNA clone MGC:70785 IMAGE:5769528), complete cds.
BC000444 - Homo sapiens syntaxin 1A (brain), mRNA (cDNA clone IMAGE:2820851), partial cds.
BC003011 - Homo sapiens syntaxin 1A (brain), mRNA (cDNA clone MGC:4038 IMAGE:2820851), complete cds.
U12918 - Human syntaxin mRNA, complete cds.
JD127129 - Sequence 108153 from Patent EP1572962.
JD282540 - Sequence 263564 from Patent EP1572962.
JD416911 - Sequence 397935 from Patent EP1572962.
JD411646 - Sequence 392670 from Patent EP1572962.
JD271189 - Sequence 252213 from Patent EP1572962.
JD376269 - Sequence 357293 from Patent EP1572962.
JD193808 - Sequence 174832 from Patent EP1572962.
JD337333 - Sequence 318357 from Patent EP1572962.
JD371164 - Sequence 352188 from Patent EP1572962.
JD245187 - Sequence 226211 from Patent EP1572962.
JD466816 - Sequence 447840 from Patent EP1572962.
JD079404 - Sequence 60428 from Patent EP1572962.
JD247571 - Sequence 228595 from Patent EP1572962.
AK299959 - Homo sapiens cDNA FLJ58938 complete cds, moderately similar to Syntaxin-1A.
JD317454 - Sequence 298478 from Patent EP1572962.
JD488917 - Sequence 469941 from Patent EP1572962.
JD433113 - Sequence 414137 from Patent EP1572962.
JD498617 - Sequence 479641 from Patent EP1572962.
JD220593 - Sequence 201617 from Patent EP1572962.
JD371740 - Sequence 352764 from Patent EP1572962.
JD098348 - Sequence 79372 from Patent EP1572962.
JD481145 - Sequence 462169 from Patent EP1572962.
JD043830 - Sequence 24854 from Patent EP1572962.
JD407996 - Sequence 389020 from Patent EP1572962.
JD280401 - Sequence 261425 from Patent EP1572962.
JD196368 - Sequence 177392 from Patent EP1572962.
JD397935 - Sequence 378959 from Patent EP1572962.
JD210295 - Sequence 191319 from Patent EP1572962.
JD152666 - Sequence 133690 from Patent EP1572962.
JD156861 - Sequence 137885 from Patent EP1572962.
JD059968 - Sequence 40992 from Patent EP1572962.
JD360682 - Sequence 341706 from Patent EP1572962.
JD379379 - Sequence 360403 from Patent EP1572962.
GQ129291 - Synthetic construct Homo sapiens clone HAIB:100068675; DKFZo004D0136 syntaxin 1A (brain) protein (STX1A) gene, partial cds.
GQ129292 - Synthetic construct Homo sapiens clone HAIB:100068578; DKFZo008D0135 syntaxin 1A (brain) protein (STX1A) gene, complete cds.
AK313980 - Homo sapiens cDNA, FLJ94630, Homo sapiens syntaxin 1A (brain) (STX1A), mRNA.
KJ897619 - Synthetic construct Homo sapiens clone ccsbBroadEn_07013 STX1A gene, encodes complete protein.
KJ534952 - Homo sapiens clone STX1A_iso-A_adult-A01 syntaxin 1A isoform A (STX1A) mRNA, partial cds, alternatively spliced.
KJ534980 - Homo sapiens clone STX1A_iso-B_fetal-F01 syntaxin 1A isoform B (STX1A) mRNA, partial cds, alternatively spliced.
AB464271 - Synthetic construct DNA, clone: pF1KB5463, Homo sapiens STX1A gene for syntaxin 1A, without stop codon, in Flexi system.
CR457018 - Homo sapiens full open reading frame cDNA clone RZPDo834H065D for gene STX1A, syntaxin 1A (brain); complete cds, incl. stopcodon.
AB086954 - Homo sapiens stx1c mRNA for syntaxin 1C, complete cds.

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

BioCarta from NCI Cancer Genome Anatomy Project
h_botulinPathway - Blockade of Neurotransmitter Relase by Botulinum Toxin

Reactome (by CSHL, EBI, and GO)

Protein Q16623 (Reactome details) participates in the following event(s):

R-HSA-210426 Glutamate synaptic vesicle docking and priming
R-HSA-372505 Acetylcholine synaptic vesicle docking and priming
R-HSA-374922 Noradrenalin synaptic vesicle docking and priming
R-HSA-380574 Dopamine synaptic vesicle docking and priming
R-HSA-380905 Serotonin loaded synaptic vesicle docking and priming
R-HSA-449117 TXLNA (IL14) binds syntaxin1A
R-HSA-917744 GABA loaded synaptic vesicle Docking and Priming
R-HSA-210430 release of L-Glutamate at the synapse
R-HSA-372529 Release of acetylcholine at the synapse
R-HSA-374899 Release of noradrenaline at the synapse
R-HSA-380869 Release of docked dopamine loaded synaptic vesicle
R-HSA-380901 Release of docked serotonin loaded synaptic vesicle
R-HSA-888589 Release of GABA at the synapse
R-HSA-181567 BoNT/C LC cleaves target cell STX1
R-HSA-5682802 LGI3 binds ADAM22,23,synatxin1
R-HSA-6794353 NRXNs binds MUNC18
R-HSA-210500 Glutamate Neurotransmitter Release Cycle
R-HSA-264642 Acetylcholine Neurotransmitter Release Cycle
R-HSA-181430 Norepinephrine Neurotransmitter Release Cycle
R-HSA-212676 Dopamine Neurotransmitter Release Cycle
R-HSA-181429 Serotonin Neurotransmitter Release Cycle
R-HSA-449836 Other interleukin signaling
R-HSA-888590 GABA synthesis, release, reuptake and degradation
R-HSA-422356 Regulation of insulin secretion
R-HSA-5250971 Toxicity of botulinum toxin type C (BoNT/C)
R-HSA-112310 Neurotransmitter release cycle
R-HSA-449147 Signaling by Interleukins
R-HSA-163685 Energy Metabolism
R-HSA-264876 Insulin processing
R-HSA-5682910 LGI-ADAM interactions
R-HSA-168799 Neurotoxicity of clostridium toxins
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-6794361 Neurexins and neuroligins
R-HSA-1430728 Metabolism
R-HSA-2980736 Peptide hormone metabolism
R-HSA-1266738 Developmental Biology
R-HSA-5339562 Uptake and actions of bacterial toxins
R-HSA-112316 Neuronal System
R-HSA-168256 Immune System
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-392499 Metabolism of proteins
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001165903, NP_001159375, Q16623-3, STX1
UCSC ID: uc003tyy.3
RefSeq Accession: NM_001165903
Protein: Q16623-3, splice isoform of Q16623 CCDS: CCDS55120.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001165903.1
exon count: 10CDS single in 3' UTR: no RNA size: 2092
ORF size: 756CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1687.50frame shift in genome: no % Coverage: 99.38
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.