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

    Gene ID: 51399, updated on 10-Dec-2024

    Summary

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    Official Symbol
    TRAPPC4provided by HGNC
    Official Full Name
    trafficking protein particle complex subunit 4provided by HGNC
    Primary source
    HGNC:HGNC:19943
    See related
    Ensembl:ENSG00000196655 MIM:610971; AllianceGenome:HGNC:19943
    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; NEDESBA; SYNBINDIN
    Summary
    Involved in autophagy and endoplasmic reticulum to Golgi vesicle-mediated transport. Part of TRAPP complex. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in testis (RPKM 25.2), adrenal (RPKM 22.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TRAPPC4 in Genome Data Viewer
    Location:
    11q23.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (119018766..119024134)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (119039128..119044496)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118889476..118894844)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene centrosomal AT-AC splicing factor Neighboring gene ribosomal protein L23a pseudogene 64 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5615 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5616 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118889349-118890047 Neighboring gene ribosomal protein S25 Neighboring gene solute carrier family 37 member 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3962 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:118906707-118906861 Neighboring gene HYOU1 antisense RNA 1 Neighboring gene hypoxia up-regulated 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5617 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118927013-118927514 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118927515-118928014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5618 Neighboring gene uncharacterized LOC124902769

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Crystal structure of human synbindin reveals two conformations of longin domain. Fan S, et al. Biochem Biophys Res Commun, 2009 Jan 16. PMID 18466758
    2. The role of ERK2 in colorectal carcinogenesis is partly regulated by TRAPPC4. Weng YR, et al. Mol Carcinog, 2014 Feb. PMID 23625650
    3. Synbindin deficiency inhibits colon carcinogenesis by attenuating Wnt cascade and balancing gut microbiome. Ai L, et al. Int J Cancer, 2019 Jul 1. PMID 30561033
    4. A relatively common homozygous TRAPPC4 splicing variant is associated with an early-infantile neurodegenerative syndrome. Ghosh SG, et al. Eur J Hum Genet, 2021 Feb. PMID 32901138, Free PMC Article
    5. TRAPPC4 regulates the intracellular trafficking of PD-L1 and antitumor immunity. Ren Y, et al. Nat Commun, 2021 Sep 13. PMID 34518538, Free PMC Article

    See all (45) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A relatively common homozygous TRAPPC4 splicing variant is associated with an early-infantile neurodegenerative syndrome.
      Title: A relatively common homozygous TRAPPC4 splicing variant is associated with an early-infantile neurodegenerative syndrome.
    2. TRAPPC4 regulates the intracellular trafficking of PD-L1 and antitumor immunity.
      Title: TRAPPC4 regulates the intracellular trafficking of PD-L1 and antitumor immunity.
    3. Deficiencies in vesicular transport mediated by TRAPPC4 are associated with severe syndromic intellectual disability.
      Title: Deficiencies in vesicular transport mediated by TRAPPC4 are associated with severe syndromic intellectual disability.
    4. Findings identify a critical role of Synbindin in gut microbiome composition and Wnt signaling activation in colorectal carcinogenesis, and highlight Synbindin as an adaptor protein with multifaceted roles.
      Title: Synbindin deficiency inhibits colon carcinogenesis by attenuating Wnt cascade and balancing gut microbiome.
    5. Overexpression of TRAPPC4 increased colorectal carcinogenesis.
      Title: The role of ERK2 in colorectal carcinogenesis is partly regulated by TRAPPC4.
    6. Synbindin contributes to malignant phenotypes of GC by activating ERK on the Golgi, and synbindin is a potential biomarker and therapeutic target for GC.
      Title: Synbindin in extracellular signal-regulated protein kinase spatial regulation and gastric cancer aggressiveness.
    7. Data demonstrate that TRAPPC4 may regulate cell proliferation and apoptosis in CRC by interaction with ERK2 and phosphorylating ERK1/2 as well as modulating the subcellular location of pERK1/2 to activate the relevant signaling pathway.
      Title: TRAPPC4-ERK2 interaction activates ERK1/2, modulates its nuclear localization and regulates proliferation and apoptosis of colorectal cancer cells.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Single-cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene.
    9. The three-dimensional structure of human synbindin, which contains a longin domain and an atypical PDZ domain is presented.
      Title: Crystal structure of human synbindin reveals two conformations of longin domain.
    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

    Associated conditions

    Description Tests
    Neurodevelopmental disorder with epilepsy, spasticity, and brain atrophy
    MedGen: C5394027 OMIM: 618741 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    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 autophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in dendrite development ISS
    Inferred from Sequence or Structural Similarity
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    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 membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi stack ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    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 TRAPP complex IMP
    Inferred from Mutant Phenotype
    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 
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in presynaptic active zone IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in synaptic vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 

    General protein information

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

    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.

    mRNA and Protein(s)

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

      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
      UniProtKB/Swiss-Prot
      Q9Y296
      Conserved Domains (1) summary
      cl21566
      Location:45 → 103
      Sedlin_N; Sedlin, N-terminal conserved region

    2. NM_001318488.2 → NP_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
      Consensus CDS
      CCDS81634.1
      UniProtKB/TrEMBL
      B4DF86, J3KP27
      Related
      ENSP00000351896.4, ENST00000359005.8
      Conserved Domains (1) summary
      cl38905
      Location:4 → 167
      longin-like; Longin-like domains

    3. NM_001318489.2 → NP_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
      Consensus CDS
      CCDS81633.1
      UniProtKB/Swiss-Prot
      Q9Y296
      Related
      ENSP00000405033.2, ENST00000434101.6
      Conserved Domains (1) summary
      cd14856
      Location:4 → 151
      TRAPPC4_synbindin; Trafficking protein particle complex subunit 4

    4. NM_001318490.2 → NP_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
      Consensus CDS
      CCDS81632.1
      UniProtKB/TrEMBL
      E9PQE8
      Related
      ENSP00000436827.1, ENST00000528230.5
      Conserved Domains (1) summary
      cd14856
      Location:4 → 162
      TRAPPC4_synbindin; Trafficking protein particle complex subunit 4

    5. NM_001318492.2 → NP_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
      UniProtKB/Swiss-Prot
      Q9Y296
      Conserved Domains (1) summary
      cd14856
      Location:13 → 100
      TRAPPC4_synbindin; Trafficking protein particle complex subunit 4

    6. NM_001318494.2 → NP_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, BU624012
      Consensus CDS
      CCDS81635.1
      UniProtKB/TrEMBL
      E9PKS9
      Related
      ENSP00000435339.1, ENST00000525303.5
      Conserved Domains (1) summary
      cl38905
      Location:4 → 112
      longin-like; Longin-like domains

    7. NM_016146.6 → NP_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
      Consensus CDS
      CCDS8407.1
      UniProtKB/Swiss-Prot
      A8K3A5, B4DME1, Q9Y296
      UniProtKB/TrEMBL
      B4DF86
      Related
      ENSP00000436005.1, ENST00000533632.6
      Conserved Domains (1) summary
      cd14856
      Location:4 → 205
      TRAPPC4_synbindin; Trafficking protein particle complex subunit 4

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      119018766..119024134
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047427114.1 → XP_047283070.1  trafficking protein particle complex subunit 4 isoform X1

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_009646203.1 Reference GRCh38.p14 PATCHES

      Range
      40366..45734
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331617.1 → XP_054187592.1  trafficking protein particle complex subunit 4 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      119039128..119044496
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369106.1 → XP_054225081.1  trafficking protein particle complex subunit 4 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y296.1 GenPept UniProtKB/Swiss-Prot:Q9Y296

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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