Human Gene TRAPPC3 (ENST00000373166.8_7) from GENCODE V47lift37
  Description: trafficking protein particle complex subunit 3, transcript variant 1 (from RefSeq NM_014408.5)
Gencode Transcript: ENST00000373166.8_7
Gencode Gene: ENSG00000054116.12_9
Transcript (Including UTRs)
   Position: hg19 chr1:36,602,173-36,615,087 Size: 12,915 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr1:36,602,804-36,614,979 Size: 12,176 Coding Exon Count: 5 

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 (chr1:36,602,173-36,615,087)mRNA (may differ from genome)Protein (180 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TPPC3_HUMAN
DESCRIPTION: RecName: Full=Trafficking protein particle complex subunit 3; AltName: Full=BET3 homolog;
FUNCTION: May play a role in vesicular transport from endoplasmic reticulum to Golgi.
SUBUNIT: Homodimer. Component of the multisubunit TRAPP (transport protein particle) complex, which includes at least TRAPPC2, TRAPPC2L, TRAPPC3, TRAPPC3L, TRAPPC4, TRAPPC5, TRAPPC8, TRAPPC9, TRAPPC10, TRAPPC11 and TRAPPC12. Heterodimer with TRAPPC6A. The heterodimer TRAPPC3-TRAPPC6A interacts with TRAPPC2L.
SUBCELLULAR LOCATION: Golgi apparatus, cis-Golgi network (By similarity). Endoplasmic reticulum (By similarity).
SIMILARITY: Belongs to the TRAPP small subunits family. BET3 subfamily.

-  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: TRAPPC3
Diseases sorted by gene-association score: tietz albinism-deafness syndrome (12), cardiac tamponade (6)

-  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: 26.03 RPKM in Adrenal Gland
Total median expression: 747.93 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 -55.70108-0.516 Picture PostScript Text
3' UTR -194.60631-0.308 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
IPR024096 - NO_sig/Golgi_transp_ligand-bd
IPR007194 - TRAPP_component
IPR016721 - TRAPP_I_complex_Bet3

Pfam Domains:
PF04051 - Transport protein particle (TRAPP) component

SCOP Domains:
111126 - Ligand-binding domain in the NO signalling and Golgi transport

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1SZ7 - X-ray 2C0J - X-ray 2CFH - X-ray MuPIT 3KXC - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O43617
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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 orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0017112 Rab guanyl-nucleotide exchange factor activity

Biological Process:
GO:0016192 vesicle-mediated transport
GO:0048193 Golgi vesicle transport
GO:0048208 COPII vesicle coating

Cellular Component:
GO:0000139 Golgi membrane
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0030008 TRAPP complex


-  Descriptions from all associated GenBank mRNAs
  AY007139 - Homo sapiens clone CDABP0066 mRNA sequence.
BC007662 - Homo sapiens trafficking protein particle complex 3, mRNA (cDNA clone MGC:2035 IMAGE:3051295), complete cds.
LF383908 - JP 2014500723-A/191411: Polycomb-Associated Non-Coding RNAs.
AJ224335 - Homo sapien mRNA for putative secretory protein, hBET3.
AK094755 - Homo sapiens cDNA FLJ37436 fis, clone BRAWH2002963, moderately similar to Homo sapiens bet3 (BET3) mRNA.
JD400248 - Sequence 381272 from Patent EP1572962.
JD265551 - Sequence 246575 from Patent EP1572962.
JD202676 - Sequence 183700 from Patent EP1572962.
JD455189 - Sequence 436213 from Patent EP1572962.
JD544589 - Sequence 525613 from Patent EP1572962.
JD561644 - Sequence 542668 from Patent EP1572962.
JD043697 - Sequence 24721 from Patent EP1572962.
JD465966 - Sequence 446990 from Patent EP1572962.
JD558519 - Sequence 539543 from Patent EP1572962.
JD304311 - Sequence 285335 from Patent EP1572962.
AF041432 - Homo sapiens bet3 (BET3) mRNA, complete cds.
JD171450 - Sequence 152474 from Patent EP1572962.
AK315610 - Homo sapiens cDNA, FLJ96691.
LF356593 - JP 2014500723-A/164096: Polycomb-Associated Non-Coding RNAs.
LF356592 - JP 2014500723-A/164095: Polycomb-Associated Non-Coding RNAs.
JD337094 - Sequence 318118 from Patent EP1572962.
LF356590 - JP 2014500723-A/164093: Polycomb-Associated Non-Coding RNAs.
JD076912 - Sequence 57936 from Patent EP1572962.
MA619485 - JP 2018138019-A/191411: Polycomb-Associated Non-Coding RNAs.
MA592170 - JP 2018138019-A/164096: Polycomb-Associated Non-Coding RNAs.
MA592169 - JP 2018138019-A/164095: Polycomb-Associated Non-Coding RNAs.
MA592167 - JP 2018138019-A/164093: Polycomb-Associated Non-Coding RNAs.

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

Protein O43617 (Reactome details) participates in the following event(s):

R-HSA-5694439 COPII coat binds TRAPPCII and RAB1:GDP
R-HSA-5694441 CSNK1D phosphorylates SEC23
R-HSA-5694418 RAB1:GTP binds USO1 and GORASP1:GOLGA2
R-HSA-5694409 Nucleotide exchange on RAB1
R-HSA-8877475 TRAPPC complexes exchange GTP for GDP on RAB1
R-HSA-204005 COPII-mediated vesicle transport
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-9007101 Rab regulation of trafficking
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A6NDN0, B2RDN2, BET3 , CDABP0066, D3DPS2, ENST00000373166.1, ENST00000373166.2, ENST00000373166.3, ENST00000373166.4, ENST00000373166.5, ENST00000373166.6, ENST00000373166.7, NM_014408, O43617, TPPC3_HUMAN, TRAPPC3 , uc318kny.1, uc318kny.2
UCSC ID: ENST00000373166.8_7
RefSeq Accession: NM_014408.5
Protein: O43617 (aka TPPC3_HUMAN or TPC3_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.