Human Gene SYN3 (ENST00000358763.7_6) from GENCODE V47lift37
  Description: synapsin III, transcript variant IIIc (from RefSeq NM_133633.3)
Gencode Transcript: ENST00000358763.7_6
Gencode Gene: ENSG00000185666.16_12
Transcript (Including UTRs)
   Position: hg19 chr22:32,903,807-33,454,367 Size: 550,561 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr22:32,909,679-33,402,647 Size: 492,969 Coding Exon Count: 13 

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 (chr22:32,903,807-33,454,367)mRNA (may differ from genome)Protein (580 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMalacardsMGIOMIMPubMed
ReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SYN3_HUMAN
DESCRIPTION: RecName: Full=Synapsin-3; AltName: Full=Synapsin III;
FUNCTION: May be involved in the regulation of neurotransmitter release and synaptogenesis.
SUBUNIT: Interacts with CAPON (By similarity).
SUBCELLULAR LOCATION: Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Peripheral membrane protein; Cytoplasmic side. Note=Peripheral membrane protein localized to the cytoplasmic surface of synaptic vesicles.
TISSUE SPECIFICITY: Neuron specific. Detected predominantly in brain.
MISCELLANEOUS: Regulated by calcium. Calcium inhibits ATP binding to the C-domain.
SIMILARITY: Belongs to the synapsin family.

-  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: SYN3
Diseases sorted by gene-association score: visual epilepsy* (94), seizure disorder* (89), schizophrenia (3), attention deficit-hyperactivity disorder (2)
* = 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: 2.38 RPKM in Testis
Total median expression: 19.71 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 -91.80252-0.364 Picture PostScript Text
3' UTR -1844.205872-0.314 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
IPR013815 - ATP_grasp_subdomain_1
IPR013816 - ATP_grasp_subdomain_2
IPR016185 - PreATP-grasp_fold
IPR001359 - Synapsin
IPR020898 - Synapsin_ATP-bd_dom
IPR019735 - Synapsin_CS
IPR019736 - Synapsin_P_site
IPR020897 - Synapsin_pre-ATP-grasp_dom

Pfam Domains:
PF02078 - Synapsin, N-terminal domain
PF02750 - Synapsin, ATP binding domain
PF10581 - Synapsin N-terminal

SCOP Domains:
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2P0A - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O14994
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005524 ATP binding

Biological Process:
GO:0007269 neurotransmitter secretion
GO:0032228 regulation of synaptic transmission, GABAergic

Cellular Component:
GO:0008021 synaptic vesicle
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0030054 cell junction
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  AL049348 - Homo sapiens mRNA; cDNA DKFZp566B233 (from clone DKFZp566B233).
AK123891 - Homo sapiens cDNA FLJ41897 fis, clone OCBBF2035658.
AF046873 - Homo sapiens synapsin IIIa mRNA, complete cds.
AB209684 - Homo sapiens mRNA for Synapsin-3 variant protein.
BC117460 - Homo sapiens synapsin III, mRNA (cDNA clone MGC:151069 IMAGE:40126011), complete cds.
BC143874 - Homo sapiens synapsin III, mRNA (cDNA clone MGC:177407 IMAGE:9052390), complete cds.
CR456589 - Homo sapiens SYN3 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.SYN3.V3).
BC075065 - Homo sapiens synapsin III, transcript variant IIIa, mRNA (cDNA clone MGC:104132 IMAGE:30915588), complete cds.
BC075066 - Homo sapiens synapsin III, mRNA (cDNA clone MGC:103970 IMAGE:30915375), complete cds.
CU013189 - Homo sapiens SYN3, mRNA (cDNA clone IMAGE:100000542), complete cds, with stop codon, in Gateway system.
CU013477 - Homo sapiens SYN3, mRNA (cDNA clone IMAGE:100000446), complete cds, without stop codon, in Gateway system.
HQ258468 - Synthetic construct Homo sapiens clone IMAGE:100072897 synapsin III (SYN3), transcript variant IIIa (SYN3) gene, encodes complete protein.
KJ892479 - Synthetic construct Homo sapiens clone ccsbBroadEn_01873 SYN3 gene, encodes complete protein.
KR711640 - Synthetic construct Homo sapiens clone CCSBHm_00027917 SYN3 (SYN3) mRNA, encodes complete protein.
AB463296 - Synthetic construct DNA, clone: pF1KB4948, Homo sapiens SYN3 gene for synapsin III, without stop codon, in Flexi system.
DQ655947 - Homo sapiens clone UGL3c10, mRNA sequence.
JD027972 - Sequence 8996 from Patent EP1572962.
JD173393 - Sequence 154417 from Patent EP1572962.
JD204763 - Sequence 185787 from Patent EP1572962.
JD350695 - Sequence 331719 from Patent EP1572962.
JD292025 - Sequence 273049 from Patent EP1572962.
JD565388 - Sequence 546412 from Patent EP1572962.
JD152090 - Sequence 133114 from Patent EP1572962.
JD152089 - Sequence 133113 from Patent EP1572962.
JD124622 - Sequence 105646 from Patent EP1572962.
JD384286 - Sequence 365310 from Patent EP1572962.
JD432667 - Sequence 413691 from Patent EP1572962.
JD392228 - Sequence 373252 from Patent EP1572962.
JD355968 - Sequence 336992 from Patent EP1572962.
AK300171 - Homo sapiens cDNA FLJ57587 complete cds, highly similar to Synapsin-3.
JD137477 - Sequence 118501 from Patent EP1572962.
JD132018 - Sequence 113042 from Patent EP1572962.
JD367015 - Sequence 348039 from Patent EP1572962.
JD325490 - Sequence 306514 from Patent EP1572962.
JD538581 - Sequence 519605 from Patent EP1572962.
JD423395 - Sequence 404419 from Patent EP1572962.
JD261166 - Sequence 242190 from Patent EP1572962.
JD240346 - Sequence 221370 from Patent EP1572962.
JD307448 - Sequence 288472 from Patent EP1572962.
JD190352 - Sequence 171376 from Patent EP1572962.
JD190351 - Sequence 171375 from Patent EP1572962.
JD434374 - Sequence 415398 from Patent EP1572962.
JD387721 - Sequence 368745 from Patent EP1572962.
JD437769 - Sequence 418793 from Patent EP1572962.
JD043963 - Sequence 24987 from Patent EP1572962.
JD530185 - Sequence 511209 from Patent EP1572962.
JD221957 - Sequence 202981 from Patent EP1572962.
JD334879 - Sequence 315903 from Patent EP1572962.
JD455637 - Sequence 436661 from Patent EP1572962.
JD476620 - Sequence 457644 from Patent EP1572962.
JD483508 - Sequence 464532 from Patent EP1572962.
JD385862 - Sequence 366886 from Patent EP1572962.
JD442708 - Sequence 423732 from Patent EP1572962.

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

Protein O14994 (Reactome details) participates in the following event(s):

R-HSA-380574 Dopamine synaptic vesicle docking and priming
R-HSA-380905 Serotonin loaded synaptic vesicle docking and priming
R-HSA-380869 Release of docked dopamine loaded synaptic vesicle
R-HSA-380901 Release of docked serotonin loaded synaptic vesicle
R-HSA-212676 Dopamine Neurotransmitter Release Cycle
R-HSA-181429 Serotonin Neurotransmitter Release Cycle
R-HSA-112310 Neurotransmitter release cycle
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: B1B1F9, ENST00000358763.1, ENST00000358763.2, ENST00000358763.3, ENST00000358763.4, ENST00000358763.5, ENST00000358763.6, NM_133633, O14994, SYN3_HUMAN, uc318asr.1, uc318asr.2
UCSC ID: ENST00000358763.7_6
RefSeq Accession: NM_003490.4
Protein: O14994 (aka SYN3_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.