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

    Gene ID: 6399, updated on 2-Nov-2024

    Summary

    Official Symbol
    TRAPPC2provided by HGNC
    Official Full Name
    trafficking protein particle complex subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:23068
    See related
    Ensembl:ENSG00000196459 MIM:300202; AllianceGenome:HGNC:23068
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TRAPPC2 in Genome Data Viewer
    Location:
    Xp22.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (13712245..13734620, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (13293643..13316052, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (13730364..13752739, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985656 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:13687079-13688278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20668 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:13710181-13710377 Neighboring gene RAB9A, member RAS oncogene family Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:13752241-13753440 Neighboring gene OFD1 centriole and centriolar satellite protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:13778869-13779368 Neighboring gene NANOG hESC enhancer GRCh37_chrX:13820205-13820738 Neighboring gene glycoprotein M6B Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:13845691-13846890 Neighboring gene gem nuclear organelle associated protein 8 Neighboring gene H3K27ac hESC enhancers GRCh37_chrX:14047600-14048100 and GRCh37_chrX:14048101-14048601

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Spondyloepiphyseal dysplasia tarda, X-linked not available

    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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transmembrane transporter 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 skeletal system development IMP
    Inferred from Mutant Phenotype
    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
    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 cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
     
    located_in endoplasmic reticulum-Golgi intermediate compartment IEA
    Inferred from Electronic Annotation
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in 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
    trafficking protein particle complex 2

    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.

    Genomic

    1. NG_011555.1 RefSeqGene

      Range
      5004..27379
      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
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5
      Related
      ENSP00000369953.1, ENST00000380579.6
      Conserved Domains (1) summary
      cd14825
      Location:4138
      TRAPPC2_sedlin; Trafficking protein particle complex subunit 2
    2. NM_001128835.3NP_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
      ENSP00000507474.1, ENST00000683983.1
      Conserved Domains (1) summary
      cd14825
      Location:38172
      TRAPPC2_sedlin; Trafficking protein particle complex subunit 2
    3. NM_014563.6NP_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
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5
      Related
      ENSP00000352708.5, ENST00000359680.9
      Conserved Domains (1) summary
      cd14825
      Location:4138
      TRAPPC2_sedlin; Trafficking protein particle complex subunit 2

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      13712245..13734620 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011545566.3XP_011543868.1  trafficking protein particle complex subunit 2 isoform X1

      See identical proteins and their annotated locations for XP_011543868.1

      UniProtKB/Swiss-Prot
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5
      Related
      ENSP00000392495.3, ENST00000458511.7
      Conserved Domains (1) summary
      cd14825
      Location:4138
      TRAPPC2_sedlin; Trafficking protein particle complex subunit 2
    2. XM_047442351.1XP_047298307.1  trafficking protein particle complex subunit 2 isoform X1

      UniProtKB/Swiss-Prot
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5
    3. XM_047442352.1XP_047298308.1  trafficking protein particle complex subunit 2 isoform X1

      UniProtKB/Swiss-Prot
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      13293643..13316052 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327565.1XP_054183540.1  trafficking protein particle complex subunit 2 isoform X1

      UniProtKB/Swiss-Prot
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5
    2. XM_054327564.1XP_054183539.1  trafficking protein particle complex subunit 2 isoform X1

      UniProtKB/Swiss-Prot
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5