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    TRAPPC13 trafficking protein particle complex subunit 13 [ Homo sapiens (human) ]

    Gene ID: 80006, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TRAPPC13provided by HGNC
    Official Full Name
    trafficking protein particle complex subunit 13provided by HGNC
    Primary source
    HGNC:HGNC:25828
    See related
    Ensembl:ENSG00000113597 AllianceGenome:HGNC:25828
    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
    SHLD3; C5orf44
    Summary
    Predicted to be located in cytosol. Predicted to be part of TRAPPIII protein complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in prostate (RPKM 7.6), thyroid (RPKM 6.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TRAPPC13 in Genome Data Viewer
    Location:
    5q12.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (65625027..65666233)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (66446811..66488005)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (64920854..64962060)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:64858912-64859572 Neighboring gene peptidylprolyl isomerase domain and WD repeat containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22608 Neighboring gene RNA, U6 small nuclear 540, pseudogene Neighboring gene tripartite motif containing 23 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:64934876-64935323 Neighboring gene shieldin complex subunit 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22609 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:65015266-65015462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16056 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:65018623-65019444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16058 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16057 Neighboring gene small glutamine rich tetratricopeptide repeat co-chaperone beta Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16059 Neighboring gene PRAME family member 17 pseudogene Neighboring gene neurolysin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16060 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:65220503-65221127 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:65221752-65222376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22612 Neighboring gene LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) pseudogene Neighboring gene erbb2 interacting protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. TRAPPC13 modulates autophagy and the response to Golgi stress. Ramírez-Peinado S, et al. J Cell Sci, 2017 Jul 15. PMID 28536105, Free PMC Article
    2. A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Bassik MC, et al. Cell, 2013 Feb 14. PMID 23394947, Free PMC Article
    3. Organization and assembly of the TRAPPII complex. Choi C, et al. Traffic, 2011 Jun. PMID 21453443
    4. PEA15 regulates the DNA damage-induced cell cycle checkpoint and oncogene-directed transformation. Nagarajan A, et al. Mol Cell Biol, 2014 Jun. PMID 24710276, Free PMC Article
    5. TRAPP Complexes in Secretion and Autophagy. Kim JJ, et al. Front Cell Dev Biol, 2016. PMID 27066478, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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

    Clone Names

    • FLJ13611, FLJ26957, MGC48585

    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 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
    part_of TRAPPII protein complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of TRAPPIII protein complex 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
    		  

    General protein information

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    Preferred Names
    trafficking protein particle complex subunit 13
    Names
    REV7-interacting novel NHEJ regulator 1
    Trs65-related
    UPF0533 protein C5orf44
    trafficking protein particle complex 13

    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_001093755.2 → NP_001087224.1  trafficking protein particle complex subunit 13 isoform 1

      See identical proteins and their annotated locations for NP_001087224.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC008560, AK023673, AL713699, BC012006, BM664695, DB145758, N67829
      Consensus CDS
      CCDS47221.1
      UniProtKB/TrEMBL
      B7ZLB5
      Related
      ENSP00000409231.2, ENST00000438419.6
      Conserved Domains (1) summary
      pfam06159
      Location:65 → 298
      DUF974; Protein of unknown function (DUF974)

    2. NM_001093756.2 → NP_001087225.1  trafficking protein particle complex subunit 13 isoform 3

      See identical proteins and their annotated locations for NP_001087225.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 3).
      Source sequence(s)
      AC008560, AK023673, AL713699, BC117128, BM664695, DB145758, N67829
      Consensus CDS
      CCDS47223.1
      UniProtKB/TrEMBL
      B7ZLB7
      Related
      ENSP00000231526.4, ENST00000231526.8
      Conserved Domains (1) summary
      pfam06159
      Location:65 → 292
      DUF974; Protein of unknown function (DUF974)

    3. NM_001243737.2 → NP_001230666.1  trafficking protein particle complex subunit 13 isoform 4

      See identical proteins and their annotated locations for NP_001230666.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks an exon and uses an alternate splice site in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AC008560, BC142994, DB145758
      Consensus CDS
      CCDS58950.1
      UniProtKB/TrEMBL
      B7ZLB5
      Related
      ENSP00000423405.1, ENST00000505553.5
      Conserved Domains (1) summary
      pfam06159
      Location:65 → 292
      DUF974; Protein of unknown function (DUF974)

    4. NM_001365342.1 → NP_001352271.1  trafficking protein particle complex subunit 13 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC008560, DA236226
      Conserved Domains (1) summary
      pfam06159
      Location:1 → 135
      DUF974; Protein of unknown function (DUF974)

    5. NM_001365343.1 → NP_001352272.1  trafficking protein particle complex subunit 13 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC008560, DA236226
      Conserved Domains (1) summary
      pfam06159
      Location:1 → 135
      DUF974; Protein of unknown function (DUF974)

    6. NM_024941.4 → NP_079217.2  trafficking protein particle complex subunit 13 isoform 2

      See identical proteins and their annotated locations for NP_079217.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 2).
      Source sequence(s)
      AC008560, AK023673, AL713699, BC117128, BM664695, DB145758, N67829
      Consensus CDS
      CCDS47222.1
      UniProtKB/Swiss-Prot
      A5PLN9, Q17RZ9, Q49A23, Q4JHG0, Q6MZG4, Q8TCM2, Q9H8I3
      UniProtKB/TrEMBL
      B7ZLB7
      Related
      ENSP00000382367.3, ENST00000399438.8
      Conserved Domains (1) summary
      pfam06159
      Location:65 → 298
      DUF974; Protein of unknown function (DUF974)

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      65625027..65666233
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      66446811..66488005
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_003545.1: Suppressed sequence

      Description
      NR_003545.1: This RefSeq was removed because it is now thought that this transcript represents a coding variant on another locus, SHLD3.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A5PLN9.2 GenPept UniProtKB/Swiss-Prot:A5PLN9

    Gene LinkOut

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

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