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

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

    Summary

    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
    NEW
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    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in Golgi membrane  
    located_in Golgi stack PubMed 
    part_of TRAPP complex  
    part_of TRAPP complex PubMed 
    part_of TRAPP complex PubMed 
    part_of TRAPPII protein complex PubMed 
    part_of TRAPPIII protein complex PubMed 
    located_in cytoplasm PubMed 
    located_in cytosol  
    located_in dendrite PubMed 
    located_in endoplasmic reticulum  
    located_in postsynaptic density membrane  
    located_in presynaptic active zone  
    located_in synapse PubMed 
    located_in synaptic vesicle PubMed 

    General protein information

    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)

    NEW Try the new Transcript table

    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

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