Human Gene ESYT1 (ENST00000394048.10_4) from GENCODE V47lift37
  Description: extended synaptotagmin 1, transcript variant 2 (from RefSeq NM_015292.3)
Gencode Transcript: ENST00000394048.10_4
Gencode Gene: ENSG00000139641.13_8
Transcript (Including UTRs)
   Position: hg19 chr12:56,522,051-56,538,458 Size: 16,408 Total Exon Count: 31 Strand: +
Coding Region
   Position: hg19 chr12:56,522,104-56,537,646 Size: 15,543 Coding Exon Count: 31 

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 (chr12:56,522,051-56,538,458)mRNA (may differ from genome)Protein (1104 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ESYT1_HUMAN
DESCRIPTION: RecName: Full=Extended synaptotagmin-1; Short=E-Syt1; AltName: Full=Membrane-bound C2 domain-containing protein;
FUNCTION: May play a role as calcium-regulated intrinsic membrane protein (By similarity).
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein. Note=Localizes to intracellular membranes.
TISSUE SPECIFICITY: Widely expressed.
SIMILARITY: Belongs to the extended synaptotagmin family.
SIMILARITY: Contains 5 C2 domains.
SEQUENCE CAUTION: Sequence=BAB15139.1; Type=Erroneous initiation; Sequence=BAB15268.1; Type=Erroneous initiation;

-  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: 54.38 RPKM in Adipose - Subcutaneous
Total median expression: 1273.52 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 -18.3053-0.345 Picture PostScript Text
3' UTR -267.60812-0.330 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:
50249 - Nucleic acid-binding proteins
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)

ModBase Predicted Comparative 3D Structure on Q9BSJ8
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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:0005515 protein binding
GO:0008289 lipid binding
GO:0042802 identical protein 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:0016020 membrane
GO:0016021 integral component of membrane
GO:0030176 integral component of endoplasmic reticulum membrane
GO:0044232 organelle membrane contact site


-  Descriptions from all associated GenBank mRNAs
  AK022790 - Homo sapiens cDNA FLJ12728 fis, clone NT2RP2000040, highly similar to Protein FAM62A.
AK128730 - Homo sapiens cDNA FLJ46898 fis, clone UTERU3022168, highly similar to Protein FAM62A.
AK225035 - Homo sapiens mRNA for family with sequence similarity 62, member A variant, clone: adKA02733.
AK290337 - Homo sapiens cDNA FLJ78376 complete cds.
BC004998 - Homo sapiens family with sequence similarity 62 (C2 domain containing), member A, mRNA (cDNA clone MGC:4422 IMAGE:2958094), complete cds.
BC013880 - Homo sapiens cDNA clone IMAGE:3832326, containing frame-shift errors.
JD375238 - Sequence 356262 from Patent EP1572962.
JD382642 - Sequence 363666 from Patent EP1572962.
EU832620 - Synthetic construct Homo sapiens clone HAIB:100067649; DKFZo008B0531 family with sequence similarity 62 (C2 domain containing), member A protein (FAM62A) gene, encodes complete protein.
EU832692 - Synthetic construct Homo sapiens clone HAIB:100067721; DKFZo004B0532 family with sequence similarity 62 (C2 domain containing), member A protein (FAM62A) gene, encodes complete protein.
DQ993200 - Homo sapiens extended-synaptotagmin 1 (ESYT1) mRNA, complete cds.
AB018290 - Homo sapiens mRNA for KIAA0747 protein, partial cds.
AK025463 - Homo sapiens cDNA: FLJ21810 fis, clone HEP01030.
AL050134 - Homo sapiens mRNA; cDNA DKFZp586K011 (from clone DKFZp586K011).
AK074368 - Homo sapiens cDNA FLJ23788 fis, clone HEP21431.
AK025878 - Homo sapiens cDNA: FLJ22225 fis, clone HRC01707.
JD387624 - Sequence 368648 from Patent EP1572962.
JD420645 - Sequence 401669 from Patent EP1572962.
JD198533 - Sequence 179557 from Patent EP1572962.
JD399847 - Sequence 380871 from Patent EP1572962.
JD381094 - Sequence 362118 from Patent EP1572962.
JD477723 - Sequence 458747 from Patent EP1572962.
JD195444 - Sequence 176468 from Patent EP1572962.
JD214702 - Sequence 195726 from Patent EP1572962.
JD527638 - Sequence 508662 from Patent EP1572962.
JD241219 - Sequence 222243 from Patent EP1572962.
JD564794 - Sequence 545818 from Patent EP1572962.
JD292087 - Sequence 273111 from Patent EP1572962.
JD375519 - Sequence 356543 from Patent EP1572962.

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

Protein Q9BSJ8 (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: A0FGR7, A8K2S2, ENST00000394048.1, ENST00000394048.2, ENST00000394048.3, ENST00000394048.4, ENST00000394048.5, ENST00000394048.6, ENST00000394048.7, ENST00000394048.8, ENST00000394048.9, ESYT1 , ESYT1_HUMAN, FAM62A, KIAA0747, MBC2, NM_015292, O94848, Q6PJN4, Q9BSJ8, Q9H6J1, Q9H6W2, Q9Y416, uc318wie.1, uc318wie.2
UCSC ID: ENST00000394048.10_4
RefSeq Accession: NM_015292.3
Protein: Q9BSJ8 (aka ESYT1_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.