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TRAPPC2 trafficking protein particle complex 2 [ Homo sapiens (human) ]

Gene ID: 6399, updated on 6-Jan-2019

Summary

Official Symbol
TRAPPC2provided by HGNC
Official Full Name
trafficking protein particle complex 2provided by HGNC
Primary source
HGNC:HGNC:23068
See related
Ensembl:ENSG00000196459 MIM:300202
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
SEDL; SEDT; MIP2A; TRS20; ZNF547L; hYP38334; TRAPPC2P1
Summary
The protein encoded by this gene is thought to be part of a large multi-subunit complex involved in the targeting and fusion of endoplasmic reticulum-to-Golgi transport vesicles with their acceptor compartment. In addition, the encoded protein can bind c-myc promoter-binding protein 1 and block its transcriptional repression capability. Mutations in this gene are a cause of spondyloepiphyseal dysplasia tarda (SEDT). A processed pseudogene of this gene is located on chromosome 19, and other pseudogenes are found on chromosomes 8 and Y. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2010]
Expression
Ubiquitous expression in lymph node (RPKM 4.2), brain (RPKM 3.5) and 25 other tissues See more
Orthologs

Genomic context

See TRAPPC2 in Genome Data Viewer
Location:
Xp22.2
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) X NC_000023.11 (13712242..13734635, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (13730361..13752754, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985656 Neighboring gene RAB9A, member RAS oncogene family Neighboring gene OFD1, centriole and centriolar satellite protein Neighboring gene glycoprotein M6B Neighboring gene uncharacterized LOC105373138

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Spondyloepiphyseal dysplasia tarda Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2014-01-16)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2014-01-16)

ClinGen Genome Curation PagePubMed

Pathways from BioSystems

  • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
    Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
  • COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystem (from REACTOME)
    COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystemCOPII components (known as Sec13p, Sec23p, Sec24p, Sec31p, and Sar1p in yeast) traffic cargo from the endoplasmic reticulum to the ER-Golgi intermediate compartment (ERGIC). COPII-coated vesicles wer...
  • ER to Golgi Anterograde Transport, organism-specific biosystem (from REACTOME)
    ER to Golgi Anterograde Transport, organism-specific biosystemSecretory cargo destined to be secreted or to arrive at the plasma membrane (PM) leaves the ER via distinct exit sites. This cargo is destined for the Golgi apparatus for further processing.
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • RAB GEFs exchange GTP for GDP on RABs, organism-specific biosystem (from REACTOME)
    RAB GEFs exchange GTP for GDP on RABs, organism-specific biosystemHuman cells have more than 60 RAB proteins that are key regulators of intracellular membrane trafficking. These small GTPases contribute to trafficking specificity by localizing to the membranes of d...
  • Transport to the Golgi and subsequent modification, organism-specific biosystem (from REACTOME)
    Transport to the Golgi and subsequent modification, organism-specific biosystemAt least two mechanisms of transport of proteins from the ER to the Golgi have been described. One is a general flow requiring no export signals (Wieland et al, 1987; Martinez-Menarguez et al, 1999)....
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rab guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
 
ion channel binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
COPII vesicle coating TAS
Traceable Author Statement
more info
 
ER to Golgi vesicle-mediated transport NAS
Non-traceable Author Statement
more info
PubMed 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
skeletal system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
TRAPP complex IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 
endoplasmic reticulum-Golgi intermediate compartment IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
trafficking protein particle complex subunit 2
Names
sedlin

NCBI Reference Sequences (RefSeq)

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_011555.1 RefSeqGene

    Range
    4989..27382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001011658.4NP_001011658.1  trafficking protein particle complex subunit 2 isoform 1

    See identical proteins and their annotated locations for NP_001011658.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the shorter isoform (1). Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AA770629, AC003037, AK313736, DA344866
    Consensus CDS
    CCDS48082.1
    UniProtKB/Swiss-Prot
    P0DI81, P0DI82
    UniProtKB/TrEMBL
    Q6IBE5
    Related
    ENSP00000369953.1, ENST00000380579.5
    Conserved Domains (1) summary
    pfam04628
    Location:9136
    Sedlin_N; Sedlin, N-terminal conserved region
  2. NM_001128835.2NP_001122307.2  trafficking protein particle complex subunit 2 isoform 2

    See identical proteins and their annotated locations for NP_001122307.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate start codon and includes an alternate splice site in its 5' coding region, compared to variant 1. The encoded isoform (2) has a distinct and longer N-terminus, compared to isoform 1.
    Source sequence(s)
    AA770629, AC003037, DA344866, DA542477
    Consensus CDS
    CCDS48083.2
    UniProtKB/Swiss-Prot
    P0DI81
    Related
    ENSP00000392495.2, ENST00000458511.6
    Conserved Domains (1) summary
    pfam04628
    Location:43170
    Sedlin_N; Sedlin, N-terminal conserved region
  3. NM_014563.5NP_055378.1  trafficking protein particle complex subunit 2 isoform 1

    See identical proteins and their annotated locations for NP_055378.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AA770629, AC003037, BC052618, DA344866
    Consensus CDS
    CCDS48082.1
    UniProtKB/Swiss-Prot
    P0DI81, P0DI82
    UniProtKB/TrEMBL
    Q6IBE5
    Related
    ENSP00000352708.5, ENST00000359680.9
    Conserved Domains (1) summary
    pfam04628
    Location:9136
    Sedlin_N; Sedlin, N-terminal conserved region

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p12 Primary Assembly

    Range
    13712242..13734635 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545565.1XP_011543867.1  trafficking protein particle complex subunit 2 isoform X1

    See identical proteins and their annotated locations for XP_011543867.1

    UniProtKB/Swiss-Prot
    P0DI81, P0DI82
    UniProtKB/TrEMBL
    Q6IBE5
    Conserved Domains (1) summary
    pfam04628
    Location:9136
    Sedlin_N; Sedlin, N-terminal conserved region
  2. XM_011545566.2XP_011543868.1  trafficking protein particle complex subunit 2 isoform X1

    See identical proteins and their annotated locations for XP_011543868.1

    UniProtKB/Swiss-Prot
    P0DI81, P0DI82
    UniProtKB/TrEMBL
    Q6IBE5
    Conserved Domains (1) summary
    pfam04628
    Location:9136
    Sedlin_N; Sedlin, N-terminal conserved region
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