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TRAPPC4 trafficking protein particle complex 4 [ Homo sapiens (human) ]

Gene ID: 51399, updated on 8-Dec-2018

Summary

Official Symbol
TRAPPC4provided by HGNC
Official Full Name
trafficking protein particle complex 4provided by HGNC
Primary source
HGNC:HGNC:19943
See related
Ensembl:ENSG00000196655 MIM:610971
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SBDN; TRS23; PTD009; CGI-104; HSPC172; SYNBINDIN
Expression
Ubiquitous expression in testis (RPKM 25.2), adrenal (RPKM 22.1) and 25 other tissues See more
Orthologs

Genomic context

See TRAPPC4 in Genome Data Viewer
Location:
11q23.3
Exon count:
5
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (119018469..119023674)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118889241..118894384)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 84 Neighboring gene ribosomal protein L23a pseudogene 64 Neighboring gene ribosomal protein S25 Neighboring gene solute carrier family 37 member 4 Neighboring gene hypoxia up-regulated 1

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?

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.
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • 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.
  • Non-integrin membrane-ECM interactions, organism-specific biosystem (from REACTOME)
    Non-integrin membrane-ECM interactions, organism-specific biosystemSeveral non-integrin membrane proteins interact with extracellular matrix proteins. Transmembrane proteoglycans may associate with integrins and growth factor receptors to influence their function, o...
  • 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...
  • Syndecan interactions, organism-specific biosystem (from REACTOME)
    Syndecan interactions, organism-specific biosystemSyndecans are type I transmembrane proteins, with an N-terminal ectodomain that contains several consensus sequences for glycosaminoglycan (GAG) attachment and a short C-terminal cytoplasmic domain. ...
  • Syndecan-2-mediated signaling events, organism-specific biosystem (from Pathway Interaction Database)
    Syndecan-2-mediated signaling events, organism-specific biosystem
    Syndecan-2-mediated signaling events
  • 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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Rab guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
 
protein 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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendrite development ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
Component Evidence Code Pubs
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
Golgi stack ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
TRAPP complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
TRAPP complex IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
dendrite ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
synapse ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
synaptic vesicle ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 

General protein information

Preferred Names
trafficking protein particle complex subunit 4
Names
TRS23 homolog
hematopoietic stem/progenitor cell protein 172

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.

mRNA and Protein(s)

  1. NM_001318486.1NP_001305415.1  trafficking protein particle complex subunit 4 isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate coding exon compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AF105025, AP003392, BP246594, BP352757
    UniProtKB/Swiss-Prot
    Q9Y296
    Conserved Domains (1) summary
    cl21566
    Location:45103
    Sedlin_N; Sedlin, N-terminal conserved region
  2. NM_001318488.1NP_001305417.1  trafficking protein particle complex subunit 4 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AF105025, AK293977, AP003392, BP352757
    Consensus CDS
    CCDS81634.1
    UniProtKB/Swiss-Prot
    Q9Y296
    UniProtKB/TrEMBL
    B4DF86, J3KP27
    Related
    ENSP00000351896.4, ENST00000359005.8
    Conserved Domains (1) summary
    cl21566
    Location:97171
    Sedlin_N; Sedlin, N-terminal conserved region
  3. NM_001318489.1NP_001305418.1  trafficking protein particle complex subunit 4 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains two alternate neighboring splice junctions in the coding region compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AF105025, AK297422, AP003392, BP352757
    Consensus CDS
    CCDS81633.1
    UniProtKB/Swiss-Prot
    Q9Y296
    Related
    ENSP00000405033.2, ENST00000434101.6
    Conserved Domains (1) summary
    cl21566
    Location:3155
    Sedlin_N; Sedlin, N-terminal conserved region
  4. NM_001318490.1NP_001305419.1  trafficking protein particle complex subunit 4 isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate in-frame splice junction compared to variant 1. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AF105025, AP003392, BP332308, BP352757
    Consensus CDS
    CCDS81632.1
    UniProtKB/Swiss-Prot
    Q9Y296
    UniProtKB/TrEMBL
    E9PQE8
    Related
    ENSP00000436827.1, ENST00000528230.5
    Conserved Domains (1) summary
    pfam04099
    Location:3166
    Sybindin; Sybindin-like family
  5. NM_001318492.1NP_001305421.1  trafficking protein particle complex subunit 4 isoform 6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) contains an alternate splice junction compared to variant 1. The resulting isoform (6) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AF105025, AP003392, BF971819, BP352757
    UniProtKB/Swiss-Prot
    Q9Y296
    Conserved Domains (1) summary
    cl21566
    Location:11104
    Sedlin_N; Sedlin, N-terminal conserved region
  6. NM_001318494.1NP_001305423.1  trafficking protein particle complex subunit 4 isoform 7

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) lacks two consecutive coding exons compared to variant 1. The resulting isoform (7) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AF105025, AP003392, BP352757, BU624012
    Consensus CDS
    CCDS81635.1
    UniProtKB/Swiss-Prot
    Q9Y296
    UniProtKB/TrEMBL
    E9PKS9
    Related
    ENSP00000435339.1, ENST00000525303.5
    Conserved Domains (1) summary
    cl21566
    Location:3116
    Sedlin_N; Sedlin, N-terminal conserved region
  7. NM_016146.5NP_057230.1  trafficking protein particle complex subunit 4 isoform 1

    See identical proteins and their annotated locations for NP_057230.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF105025, AP003392, BP352757
    Consensus CDS
    CCDS8407.1
    UniProtKB/Swiss-Prot
    Q9Y296
    Related
    ENSP00000436005.1, ENST00000533632.5
    Conserved Domains (1) summary
    pfam04099
    Location:97209
    Sybindin; Sybindin-like family

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_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    119018469..119023674
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 PATCHES

Genomic

  1. NW_009646203.1 Reference GRCh38.p12 PATCHES

    Range
    40069..45274
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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