Human Gene ESYT3 (ENST00000389567.9_4) from GENCODE V47lift37
  Description: extended synaptotagmin 3, transcript variant 4 (from RefSeq NR_136409.2)
Gencode Transcript: ENST00000389567.9_4
Gencode Gene: ENSG00000158220.14_7
Transcript (Including UTRs)
   Position: hg19 chr3:138,153,458-138,198,767 Size: 45,310 Total Exon Count: 23 Strand: +
Coding Region
   Position: hg19 chr3:138,153,641-138,195,696 Size: 42,056 Coding Exon Count: 23 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:138,153,458-138,198,767)mRNA (may differ from genome)Protein (886 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ESYT3_HUMAN
DESCRIPTION: RecName: Full=Extended synaptotagmin-3; Short=E-Syt3; AltName: Full=Chr3Syt;
FUNCTION: May play a role as calcium-regulated intrinsic membrane protein (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Single-pass membrane protein.
TISSUE SPECIFICITY: Widely expressed with high level in cerebellum and skin.
SIMILARITY: Belongs to the extended synaptotagmin family.
SIMILARITY: Contains 3 C2 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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 5.69 RPKM in Brain - Cerebellum
Total median expression: 55.68 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 -76.40183-0.417 Picture PostScript Text
3' UTR -792.913071-0.258 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
IPR000008 - C2_Ca-dep
IPR008973 - C2_Ca/lipid-bd_dom_CaLB
IPR020477 - C2_dom
IPR018029 - C2_membr_targeting

Pfam Domains:
PF00168 - C2 domain
PF17047 - Synaptotagmin-like mitochondrial-lipid-binding domain

SCOP Domains:
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)

ModBase Predicted Comparative 3D Structure on A0FGR9
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    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008289 lipid binding
GO:0046872 metal ion binding

Biological Process:
GO:0006869 lipid transport
GO:0061817 endoplasmic reticulum-plasma membrane tethering

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031227 intrinsic component of endoplasmic reticulum membrane
GO:0031234 extrinsic component of cytoplasmic side of plasma membrane
GO:0044232 organelle membrane contact site


-  Descriptions from all associated GenBank mRNAs
  BC037292 - Homo sapiens family with sequence similarity 62 (C2 domain containing), member C, mRNA (cDNA clone MGC:33352 IMAGE:4837811), complete cds.
AK125080 - Homo sapiens cDNA FLJ43090 fis, clone COLON2001721.
AK289530 - Homo sapiens cDNA FLJ76329 complete cds.
JD343523 - Sequence 324547 from Patent EP1572962.
JD465015 - Sequence 446039 from Patent EP1572962.
JD256939 - Sequence 237963 from Patent EP1572962.
JD538158 - Sequence 519182 from Patent EP1572962.
DQ993202 - Homo sapiens extended-synaptotagmin 3 (ESYT3) mRNA, complete cds.
JD541069 - Sequence 522093 from Patent EP1572962.
JD253352 - Sequence 234376 from Patent EP1572962.
JD389609 - Sequence 370633 from Patent EP1572962.
JD172849 - Sequence 153873 from Patent EP1572962.
JD336680 - Sequence 317704 from Patent EP1572962.
JD251586 - Sequence 232610 from Patent EP1572962.
JD497618 - Sequence 478642 from Patent EP1572962.
JD066911 - Sequence 47935 from Patent EP1572962.
JD510286 - Sequence 491310 from Patent EP1572962.
JD447470 - Sequence 428494 from Patent EP1572962.
JD114616 - Sequence 95640 from Patent EP1572962.
JD456601 - Sequence 437625 from Patent EP1572962.
JD120855 - Sequence 101879 from Patent EP1572962.
JD074417 - Sequence 55441 from Patent EP1572962.
JD489694 - Sequence 470718 from Patent EP1572962.
JD204464 - Sequence 185488 from Patent EP1572962.
JD066452 - Sequence 47476 from Patent EP1572962.
AJ697972 - Homo sapiens chromosome 3 cDNA.
JD232714 - Sequence 213738 from Patent EP1572962.
JD200404 - Sequence 181428 from Patent EP1572962.
JD230964 - Sequence 211988 from Patent EP1572962.
AJ303366 - Homo sapiens partial mRNA for FAM62C.
JD500253 - Sequence 481277 from Patent EP1572962.
JD037777 - Sequence 18801 from Patent EP1572962.
JD042662 - Sequence 23686 from Patent EP1572962.
JD062303 - Sequence 43327 from Patent EP1572962.
JD302690 - Sequence 283714 from Patent EP1572962.
JD436519 - Sequence 417543 from Patent EP1572962.

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

Protein A0FGR9 (Reactome details) participates in the following event(s):

R-HSA-8857662 ESYT1:ESYT2:ESYT3 transport GPL from plasma membrane to ER membrane
R-HSA-1660662 Glycosphingolipid metabolism
R-HSA-428157 Sphingolipid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: A0FGR9, A8K0G5, ENST00000389567.1, ENST00000389567.2, ENST00000389567.3, ENST00000389567.4, ENST00000389567.5, ENST00000389567.6, ENST00000389567.7, ENST00000389567.8, ESYT3 , ESYT3_HUMAN, FAM62C, NR_136409, Q6ZV21, Q8NDZ5, Q9BQR9, uc318tfw.1, uc318tfw.2
UCSC ID: ENST00000389567.9_4
RefSeq Accession: NM_031913.5
Protein: A0FGR9 (aka ESYT3_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.