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TRAPPC3 trafficking protein particle complex subunit 3 [ Homo sapiens (human) ]

Gene ID: 27095, updated on 2-Nov-2024

Summary

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Official Symbol
TRAPPC3provided by HGNC
Official Full Name
trafficking protein particle complex subunit 3provided by HGNC
Primary source
HGNC:HGNC:19942
See related
Ensembl:ENSG00000054116 MIM:610955; AllianceGenome:HGNC:19942
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BET3
Summary
This gene encodes a component of the trafficking protein particle complex, which tethers transport vesicles to the cis-Golgi membrane. The encoded protein participates in the regulation of transport from the endoplasmic reticulum to the Golgi apparatus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
Expression
Ubiquitous expression in thyroid (RPKM 23.9), adrenal (RPKM 19.7) and 25 other tissues See more
Orthologs
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Genomic context

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See TRAPPC3 in Genome Data Viewer
Location:
1p34.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (36136572..36156053, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (35999451..36018932, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (36602173..36621654, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36553996-36554581 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36554582-36555166 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36563075-36563583 Neighboring gene ADP-ribosylserine hydrolase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 654 Neighboring gene collagen type VIII alpha 2 chain Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36579590-36580530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36580531-36581471 Neighboring gene MPRA-validated peak176 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36614757-36615417 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 655 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36625977-36626754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 746 Neighboring gene MAP7 domain containing 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:36638149-36639348 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 657 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36643121-36643768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36643769-36644414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36644415-36645060 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36653458-36654156 Neighboring gene RNA, 7SL, cytoplasmic 131, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Structure of palmitoylated BET3: insights into TRAPP complex assembly and membrane localization. Turnbull AP, et al. EMBO J, 2005 Mar 9. PMID 15692564, Free PMC Article
  2. mBet3p is required for homotypic COPII vesicle tethering in mammalian cells. Yu S, et al. J Cell Biol, 2006 Jul 31. PMID 16880271, Free PMC Article
  3. Unique self-palmitoylation activity of the transport protein particle component Bet3: a mechanism required for protein stability. Kümmel D, et al. Proc Natl Acad Sci U S A, 2006 Aug 22. PMID 16908848, Free PMC Article
  4. Entry and exit mechanisms at the cis-face of the Golgi complex. Lorente-Rodríguez A, et al. Cold Spring Harb Perspect Biol, 2011 Jul 1. PMID 21482742, Free PMC Article
  5. Structure of the Bet3-Tpc6B core of TRAPP: two Tpc6 paralogs form trimeric complexes with Bet3 and Mum2. Kümmel D, et al. J Mol Biol, 2006 Aug 4. PMID 16828797

See all (67) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TRAPPC3 expression in healthy human palatal mucosa is strongly negatively correlated with serum cotinine levels.
    Title: Whole transcriptome analysis of smoker palatal mucosa identifies multiple downregulated innate immunity genes.
  2. crystal structure
    Title: Structure of palmitoylated BET3: insights into TRAPP complex assembly and membrane localization.
  3. Bet3 functions as a cytosolic factor participating in transport from the ER to the Golgi apparatus
    Title: Mammalian Bet3 functions as a cytosolic factor participating in transport from the ER to the Golgi apparatus.
  4. mBet3p is required for the tethering and fusion of COPII vesicles to each other.
    Title: mBet3p is required for homotypic COPII vesicle tethering in mammalian cells.
  5. Bet3 has strong self-palmitoylating activity
    Title: Unique self-palmitoylation activity of the transport protein particle component Bet3: a mechanism required for protein stability.
  6. The crystal structure of human Bet3-Tpc6B heterodimer presented here represents a core sub-complex in the assembly of TRAPP.
    Title: Structure of the Bet3-Tpc6B core of TRAPP: two Tpc6 paralogs form trimeric complexes with Bet3 and Mum2.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • 1110058K12Rik

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in COPII vesicle coating NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in intra-Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in vesicle coating NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in vesicle tethering NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
  
part_of TRAPP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of TRAPP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of TRAPPII protein complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of TRAPPIII protein complex NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in cis-Golgi network membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
trafficking protein particle complex subunit 3
Names
trafficking protein particle complex 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_052857.1 RefSeqGene

    Range
    11568..24482
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001270894.2 → NP_001257823.1  trafficking protein particle complex subunit 3 isoform 2

    See identical proteins and their annotated locations for NP_001257823.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region, compared to variant 1. The encoded isoform (2) is longer than isoform 1.
    Source sequence(s)
    BC007662, CB053319, CD251784
    Consensus CDS
    CCDS72758.1
    UniProtKB/TrEMBL
    A0A087WWM0
    Related
    ENSP00000480332.1, ENST00000616395.4
    Conserved Domains (1) summary
    cd14942
    Location:15 → 177
    TRAPPC3_bet3; Bet3-TRAPPC3 subunit of the TRAPP complex

  2. NM_001270895.2 → NP_001257824.1  trafficking protein particle complex subunit 3 isoform 3

    See identical proteins and their annotated locations for NP_001257824.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an in-frame downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3 and 4 encode the same isoform (3).
    Source sequence(s)
    BC007662, BM451581, CB053319
    Consensus CDS
    CCDS59194.1
    UniProtKB/Swiss-Prot
    O43617
    Related
    ENSP00000480648.1, ENST00000617904.4
    Conserved Domains (1) summary
    cd14942
    Location:1 → 123
    TRAPPC3_bet3; Bet3-TRAPPC3 subunit of the TRAPP complex

  3. NM_001270896.2 → NP_001257825.1  trafficking protein particle complex subunit 3 isoform 3

    See identical proteins and their annotated locations for NP_001257825.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region and uses a downstream in-frame start codon compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3 and 4 encode the same isoform (3).
    Source sequence(s)
    BC007662, BG704657, BI462429, BI762992, CB053319
    Consensus CDS
    CCDS59194.1
    UniProtKB/Swiss-Prot
    O43617
    Related
    ENSP00000362256.1, ENST00000373162.5
    Conserved Domains (1) summary
    cd14942
    Location:1 → 123
    TRAPPC3_bet3; Bet3-TRAPPC3 subunit of the TRAPP complex

  4. NM_001270897.2 → NP_001257826.1  trafficking protein particle complex subunit 3 isoform 4

    See identical proteins and their annotated locations for NP_001257826.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    BC007662, BG704657, CB053319, T26006
    Consensus CDS
    CCDS72757.1
    UniProtKB/TrEMBL
    A0A087WYS5
    Related
    ENSP00000482052.1, ENST00000616074.4
    Conserved Domains (1) summary
    cd14942
    Location:15 → 103
    TRAPPC3_bet3; Bet3-TRAPPC3 subunit of the TRAPP complex

  5. NM_014408.5 → NP_055223.1  trafficking protein particle complex subunit 3 isoform 1

    See identical proteins and their annotated locations for NP_055223.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform (1).
    Source sequence(s)
    BC007662, BG704657
    Consensus CDS
    CCDS404.1
    UniProtKB/Swiss-Prot
    A6NDN0, B2RDN2, D3DPS2, O43617
    Related
    ENSP00000362261.3, ENST00000373166.8
    Conserved Domains (1) summary
    cd14942
    Location:15 → 169
    TRAPPC3_bet3; Bet3-TRAPPC3 subunit of the TRAPP complex

RNA

  1. NR_073097.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs at the 5' end and lacks two internal exons, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.
    Source sequence(s)
    BC007662, BG704657, BI462429, CB053319, HY104588

  2. NR_073098.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks three internal exons, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.
    Source sequence(s)
    AA446176, BC007662, BG704657, CB053319

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    36136572..36156053 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    35999451..36018932 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43617.1 GenPept UniProtKB/Swiss-Prot:O43617

Gene LinkOut

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