Human Gene SYNGR3 (ENST00000248121.7_4) from GENCODE V47lift37
  Description: synaptogyrin 3 (from RefSeq NM_004209.6)
Gencode Transcript: ENST00000248121.7_4
Gencode Gene: ENSG00000127561.16_8
Transcript (Including UTRs)
   Position: hg19 chr16:2,039,971-2,044,276 Size: 4,306 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr16:2,040,104-2,043,073 Size: 2,970 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:2,039,971-2,044,276)mRNA (may differ from genome)Protein (229 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SNG3_HUMAN
DESCRIPTION: RecName: Full=Synaptogyrin-3;
FUNCTION: Involved in the positive regulation of dopamine transporter activity. Probably facilitates the physical and functional interactions of the transporter with the dopamine vesicular storage system, allowing a more efficient loading of the vesicles with extracellular dopamine after release (By similarity).
SUBUNIT: Interacts (via N-terminus) with SLC6A3 (via N-terminus) (By similarity).
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein. Cytoplasmic vesicle, secretory vesicle, synaptic vesicle (By similarity). Cell junction, synapse. Note=Found at the neuromuscular synapses (By similarity).
TISSUE SPECIFICITY: Expressed in brain and placenta.
SIMILARITY: Belongs to the synaptogyrin family.
SIMILARITY: Contains 1 MARVEL 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

+  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: 56.89 RPKM in Brain - Hypothalamus
Total median expression: 436.89 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 -74.20133-0.558 Picture PostScript Text
3' UTR -473.401203-0.394 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
IPR008253 - Marvel
IPR021128 - MARVEL-like_dom
IPR016579 - Synaptogyrin

Pfam Domains:
PF01284 - Membrane-associating domain

SCOP Domains:
54358 - Immunoglobulin-binding domains

ModBase Predicted Comparative 3D Structure on O43761
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    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0042169 SH2 domain binding
GO:0047485 protein N-terminus binding

Biological Process:
GO:0021762 substantia nigra development
GO:0032411 positive regulation of transporter activity
GO:0045055 regulated exocytosis

Cellular Component:
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0031594 neuromuscular junction
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  KJ892698 - Synthetic construct Homo sapiens clone ccsbBroadEn_02092 SYNGR3 gene, encodes complete protein.
KJ905988 - Synthetic construct Homo sapiens clone ccsbBroadEn_15658 SYNGR3 gene, encodes complete protein.
LF210731 - JP 2014500723-A/18234: Polycomb-Associated Non-Coding RNAs.
JD408193 - Sequence 389217 from Patent EP1572962.
JD336786 - Sequence 317810 from Patent EP1572962.
AK313894 - Homo sapiens cDNA, FLJ94530, Homo sapiens synaptogyrin 3 (SYNGR3), mRNA.
BC009568 - Homo sapiens synaptogyrin 3, mRNA (cDNA clone MGC:12440 IMAGE:3932502), complete cds.
BC014087 - Homo sapiens synaptogyrin 3, mRNA (cDNA clone MGC:20003 IMAGE:4334996), complete cds.
AJ002309 - Homo sapiens mRNA for synaptogyrin 3.
DQ895555 - Synthetic construct Homo sapiens clone IMAGE:100010015; FLH187835.01L; RZPDo839D08149D synaptogyrin 3 (SYNGR3) gene, encodes complete protein.
DQ892351 - Synthetic construct clone IMAGE:100004981; FLH187839.01X; RZPDo839D08150D synaptogyrin 3 (SYNGR3) gene, encodes complete protein.
CU680772 - Synthetic construct Homo sapiens gateway clone IMAGE:100023286 5' read SYNGR3 mRNA.
LF340755 - JP 2014500723-A/148258: Polycomb-Associated Non-Coding RNAs.
LF340754 - JP 2014500723-A/148257: Polycomb-Associated Non-Coding RNAs.
JD373650 - Sequence 354674 from Patent EP1572962.
JD074470 - Sequence 55494 from Patent EP1572962.
JD403437 - Sequence 384461 from Patent EP1572962.
JD269326 - Sequence 250350 from Patent EP1572962.
JD067759 - Sequence 48783 from Patent EP1572962.
JD130657 - Sequence 111681 from Patent EP1572962.
JD214664 - Sequence 195688 from Patent EP1572962.
JD174791 - Sequence 155815 from Patent EP1572962.
JD141579 - Sequence 122603 from Patent EP1572962.
JD442526 - Sequence 423550 from Patent EP1572962.
JD418302 - Sequence 399326 from Patent EP1572962.
JD327573 - Sequence 308597 from Patent EP1572962.
JD085227 - Sequence 66251 from Patent EP1572962.
JD398371 - Sequence 379395 from Patent EP1572962.
JD159152 - Sequence 140176 from Patent EP1572962.
JD275953 - Sequence 256977 from Patent EP1572962.
JD437685 - Sequence 418709 from Patent EP1572962.
JD521054 - Sequence 502078 from Patent EP1572962.
JD065548 - Sequence 46572 from Patent EP1572962.
JD170253 - Sequence 151277 from Patent EP1572962.
JD207192 - Sequence 188216 from Patent EP1572962.
JD248593 - Sequence 229617 from Patent EP1572962.
JD403340 - Sequence 384364 from Patent EP1572962.
JD164170 - Sequence 145194 from Patent EP1572962.
JD122281 - Sequence 103305 from Patent EP1572962.
LF340753 - JP 2014500723-A/148256: Polycomb-Associated Non-Coding RNAs.
JD534561 - Sequence 515585 from Patent EP1572962.
JD377927 - Sequence 358951 from Patent EP1572962.
JD084473 - Sequence 65497 from Patent EP1572962.
MA446308 - JP 2018138019-A/18234: Polycomb-Associated Non-Coding RNAs.
MA576332 - JP 2018138019-A/148258: Polycomb-Associated Non-Coding RNAs.
MA576331 - JP 2018138019-A/148257: Polycomb-Associated Non-Coding RNAs.
MA576330 - JP 2018138019-A/148256: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B2R9S0, ENST00000248121.1, ENST00000248121.2, ENST00000248121.3, ENST00000248121.4, ENST00000248121.5, ENST00000248121.6, NM_004209, O43761, SNG3_HUMAN, SYNGR3 , uc317ewx.1, uc317ewx.2
UCSC ID: ENST00000248121.7_4
RefSeq Accession: NM_004209.6
Protein: O43761 (aka SNG3_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.