Human Gene SYT8 (ENST00000341958.4_7) from GENCODE V47lift37
  Description: synaptotagmin 8, transcript variant 5 (from RefSeq NM_001394072.1)
Gencode Transcript: ENST00000341958.4_7
Gencode Gene: ENSG00000149043.17_13
Transcript (Including UTRs)
   Position: hg19 chr11:1,856,220-1,858,751 Size: 2,532 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr11:1,856,336-1,858,661 Size: 2,326 Coding Exon Count: 8 

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 (chr11:1,856,220-1,858,751)mRNA (may differ from genome)Protein (387 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsHGNC
MGIPubMedReactomeUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SYT8_HUMAN
DESCRIPTION: RecName: Full=Synaptotagmin-8; AltName: Full=Synaptotagmin VIII; Short=SytVIII;
FUNCTION: Isoform 4 may play a role in the trafficking and exocytosis of secretory vesicles in non-neuronal tissues. Mediates Ca(2+)-regulation of exocytosis acrosomal reaction in sperm. May mediate Ca(2+)-regulation of exocytosis in insulin secreted cells (By similarity).
SUBUNIT: Homodimer or homooligomer. Homodimerization and homooligomerization do not depend on Ca(2+). Interacts with SYNCRIP isoform 2 C-terminus. Binds inositol 1,3,4,5- tetrakisphosphate (IP4). Binds to AP2 in a Ca(2+)-independent manner. Interacts with STX1A, STX1B and STX2; the interaction is Ca(2+)-dependent (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Single-pass type III membrane protein (By similarity). Cytoplasmic vesicle, secretory vesicle, acrosome (By similarity).
DOMAIN: The first C2 domain/C2A does not mediate Ca(2+)-dependent phospholipid binding (By similarity).
DOMAIN: The second C2 domain/C2B is responsible for SYNCRIP and inositol 1,3,4,5-tetrakisphosphate (IP4)-binding (By similarity).
SIMILARITY: Belongs to the synaptotagmin family.
SIMILARITY: Contains 2 C2 domains.
SEQUENCE CAUTION: Sequence=AAQ57209.1; Type=Miscellaneous discrepancy; Note=May be due to an intron retention; Sequence=CAB70885.2; Type=Miscellaneous discrepancy; Note=The sequence differs from that shown because it is a pre-mRNA;

-  Primer design for this transcript
 

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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: 40.26 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 133.97 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 -49.80116-0.429 Picture PostScript Text
3' UTR -20.8090-0.231 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
IPR018029 - C2_membr_targeting
IPR001565 - Synaptotagmin

Pfam Domains:
PF00168 - C2 domain

SCOP Domains:
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
58069 - Virus ectodomain

ModBase Predicted Comparative 3D Structure on Q8NBV8
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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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0005544 calcium-dependent phospholipid binding
GO:0019905 syntaxin binding
GO:0030276 clathrin binding
GO:0048306 calcium-dependent protein binding

Biological Process:
GO:0006887 exocytosis
GO:0006906 vesicle fusion
GO:0007340 acrosome reaction
GO:0017158 regulation of calcium ion-dependent exocytosis
GO:0048488 synaptic vesicle endocytosis
GO:0048791 calcium ion-regulated exocytosis of neurotransmitter

Cellular Component:
GO:0001669 acrosomal vesicle
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0031982 vesicle


-  Descriptions from all associated GenBank mRNAs
  BC160127 - Synthetic construct Homo sapiens clone IMAGE:100064159, MGC:193242 synaptotagmin VIII (SYT8) mRNA, encodes complete protein.
AK293395 - Homo sapiens cDNA FLJ57703 complete cds, highly similar to Synaptotagmin-8.
AK131292 - Homo sapiens cDNA FLJ16250 fis, clone HLUNG2013350, moderately similar to Mus musculus mRNA for synaptotagmin VIII.
BC038591 - Homo sapiens synaptotagmin VIII, mRNA (cDNA clone IMAGE:5735067), with apparent retained intron.
AL137708 - Homo sapiens mRNA; cDNA DKFZp434K0322 (from clone DKFZp434K0322).
AK075202 - Homo sapiens cDNA FLJ90721 fis, clone PLACE1008985, moderately similar to Mus musculus synaptotagmin VIII mRNA.
BC144657 - Homo sapiens cDNA clone IMAGE:9053188.
BC144659 - Homo sapiens cDNA clone IMAGE:9053190.
BC144660 - Homo sapiens cDNA clone IMAGE:9053191.
BC144661 - Homo sapiens cDNA clone IMAGE:9053192.
JD126994 - Sequence 108018 from Patent EP1572962.
JD397421 - Sequence 378445 from Patent EP1572962.
AY353087 - Homo sapiens synaptotagmin VIII (SYT8) mRNA, complete cds; alternatively spliced.
JD484878 - Sequence 465902 from Patent EP1572962.
JD478224 - Sequence 459248 from Patent EP1572962.
JD452959 - Sequence 433983 from Patent EP1572962.
JD147015 - Sequence 128039 from Patent EP1572962.
JD311535 - Sequence 292559 from Patent EP1572962.
JD322706 - Sequence 303730 from Patent EP1572962.
JD484519 - Sequence 465543 from Patent EP1572962.
JD156144 - Sequence 137168 from Patent EP1572962.
JD205451 - Sequence 186475 from Patent EP1572962.
JD282446 - Sequence 263470 from Patent EP1572962.
JD418512 - Sequence 399536 from Patent EP1572962.
JD264461 - Sequence 245485 from Patent EP1572962.
JD204274 - Sequence 185298 from Patent EP1572962.
JD162788 - Sequence 143812 from Patent EP1572962.
JD100069 - Sequence 81093 from Patent EP1572962.
JD402523 - Sequence 383547 from Patent EP1572962.
JD422390 - Sequence 403414 from Patent EP1572962.
JD104591 - Sequence 85615 from Patent EP1572962.
JD335936 - Sequence 316960 from Patent EP1572962.
JD392888 - Sequence 373912 from Patent EP1572962.
JD392629 - Sequence 373653 from Patent EP1572962.
JD190628 - Sequence 171652 from Patent EP1572962.
JD187858 - Sequence 168882 from Patent EP1572962.

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

Protein Q8NBV8 (Reactome details) participates in the following event(s):

R-HSA-8863463 STON2 binds SYT proteins
R-HSA-8867756 CLASP proteins and cargo are recruited to the nascent clathrin-coated pit
R-HSA-8868071 Clathrin recruits PIK3C2A
R-HSA-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission
R-HSA-8868648 SYNJ hydrolyze PI(4,5)P2 to PI(4)P
R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-8868658 HSPA8-mediated ATP hydrolysis promotes vesicle uncoating
R-HSA-8868659 Clathrin recruits auxilins to the clathrin-coated vesicle
R-HSA-8868660 Auxilin recruits HSPA8:ATP to the clathrin-coated vesicle
R-HSA-8867754 F- and N- BAR domain proteins bind the clathrin-coated pit
R-HSA-8868230 SNX9 recruits components of the actin polymerizing machinery
R-HSA-8868072 Clathrin-associated PIK3C2A phosphorylates PI(4)P to PI(3,4)P2
R-HSA-8868236 BAR domain proteins recruit dynamin
R-HSA-8868651 Endophilins recruit synaptojanins to the clathrin-coated pit
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: A6NCR4, A6NFJ4, ENST00000341958.1, ENST00000341958.2, ENST00000341958.3, NM_001394072, Q8NBV8, Q9NSV9, SYT8_HUMAN, uc317weq.1, uc317weq.2
UCSC ID: ENST00000341958.4_7
RefSeq Accession: NM_001394072.1
Protein: Q8NBV8 (aka SYT8_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.