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    TRAPPC12 trafficking protein particle complex subunit 12 [ Homo sapiens (human) ]

    Gene ID: 51112, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TRAPPC12provided by HGNC
    Official Full Name
    trafficking protein particle complex subunit 12provided by HGNC
    Primary source
    HGNC:HGNC:24284
    See related
    Ensembl:ENSG00000171853 MIM:614139; AllianceGenome:HGNC:24284
    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
    PEBAS; TTC15; CGI-87; TTC-15
    Summary
    Involved in several processes, including endoplasmic reticulum to Golgi vesicle-mediated transport; positive regulation of protein localization to kinetochore; and regulation of kinetochore assembly. Located in several cellular components, including endoplasmic reticulum-Golgi intermediate compartment; kinetochore; and perinuclear region of cytoplasm. Part of TRAPP complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 6.2), brain (RPKM 2.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TRAPPC12 in Genome Data Viewer
    Location:
    2p25.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (3379694..3479565)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (3401815..3501615)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (3383465..3483336)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15222 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3172751-3173696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3182069-3182826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3183585-3184342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3184343-3185098 Neighboring gene Sharpr-MPRA regulatory region 8446 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:3202367-3202905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3204190-3204746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15224 Neighboring gene EARP complex and GARP complex interacting protein 1 Neighboring gene MPRA-validated peak3584 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:3237853-3239052 Neighboring gene Sharpr-MPRA regulatory region 3808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15226 Neighboring gene VISTA enhancer hs1385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3284251-3284751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3289510-3290088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3290089-3290666 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3310431-3310601 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3323251-3323862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3326607-3327134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3327135-3327662 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3358809-3358982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15229 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15227 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3381914-3382430 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3382431-3382947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11109 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3402817-3403742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3403743-3404668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3404669-3405592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3416341-3416841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3415840-3416340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3434408-3434908 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3437307-3437557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3463593-3464106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3464459-3465326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3475415-3475916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3475917-3476416 Neighboring gene TRAPPC12 antisense RNA 1 Neighboring gene uncharacterized LOC112268321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11111 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3522968-3523489 Neighboring gene acireductone dioxygenase 1

    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. Mutations in TRAPPC12 Manifest in Progressive Childhood Encephalopathy and Golgi Dysfunction. Milev MP, et al. Am J Hum Genet, 2017 Aug 3. PMID 28777934, Free PMC Article
    2. Mammalian TRAPPIII Complex positively modulates the recruitment of Sec13/31 onto COPII vesicles. Zhao S, et al. Sci Rep, 2017 Feb 27. PMID 28240221, Free PMC Article
    3. TRAMM/TrappC12 plays a role in chromosome congression, kinetochore stability, and CENP-E recruitment. Milev MP, et al. J Cell Biol, 2015 Apr 27. PMID 25918224, Free PMC Article
    4. TRAPP Complexes in Secretion and Autophagy. Kim JJ, et al. Front Cell Dev Biol, 2016. PMID 27066478, Free PMC Article
    5. C4orf41 and TTC-15 are mammalian TRAPP components with a role at an early stage in ER-to-Golgi trafficking. Scrivens PJ, et al. Mol Biol Cell, 2011 Jun 15. PMID 21525244, Free PMC Article

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TRAPPC12, but not TRAPPC8, bound to Sec13/Sec31A tetramer but each Sec protein alone could not interact with TRAPPC12.
      Title: Mammalian TRAPPIII Complex positively modulates the recruitment of Sec13/31 onto COPII vesicles.
    2. The authors report that variants in TRAPPC12 result in progressive childhood encephalopathy. Fibroblasts derived from three affected individuals showed a fragmented Golgi that could be rescued by expression of wild-type TRAPPC12.
      Title: Mutations in TRAPPC12 Manifest in Progressive Childhood Encephalopathy and Golgi Dysfunction.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
    MedGen: C5567229 OMIM: 617669 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of trafficking protein particle complex 12 (TRAPPC12) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ36862, FLJ44560

    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 Golgi organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 metaphase chromosome alignment IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of protein localization to kinetochore IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of kinetochore assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vesicle tethering NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    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 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
    		  
    colocalizes_with endoplasmic reticulum-Golgi intermediate compartment IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in kinetochore IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    colocalizes_with perinuclear region of cytoplasm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    trafficking protein particle complex subunit 12
    Names
    TPR repeat protein 15
    tetratricopeptide repeat domain 15
    tetratricopeptide repeat protein 15
    trafficking of membranes and mitosis
    trafficking protein particle complex 12

    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_001321102.2 → NP_001308031.1  trafficking protein particle complex subunit 12

      Status: VALIDATED

      Source sequence(s)
      AC114810, AK098327
      Consensus CDS
      CCDS1652.1
      UniProtKB/Swiss-Prot
      B3KV01, D6W4Y2, Q8WVT3, Q8WVW1, Q9Y395
      UniProtKB/TrEMBL
      Q8N9N0
      Related
      ENSP00000371544.2, ENST00000382110.6
      Conserved Domains (4) summary
      sd00006
      Location:546 → 573
      TPR; TPR repeat [structural motif]
      pfam11035
      Location:61 → 134
      SnAPC_2_like; Small nuclear RNA activating complex subunit 2, SNAP190 Myb
      pfam13414
      Location:622 → 685
      TPR_11; TPR repeat
      pfam13424
      Location:581 → 652
      TPR_12; Tetratricopeptide repeat

    2. NM_016030.6 → NP_057114.5  trafficking protein particle complex subunit 12

      See identical proteins and their annotated locations for NP_057114.5

      Status: VALIDATED

      Source sequence(s)
      AF151845, BC014164, BC017475, DA031172
      Consensus CDS
      CCDS1652.1
      UniProtKB/Swiss-Prot
      B3KV01, D6W4Y2, Q8WVT3, Q8WVW1, Q9Y395
      UniProtKB/TrEMBL
      Q8N9N0
      Related
      ENSP00000324318.5, ENST00000324266.10
      Conserved Domains (4) summary
      sd00006
      Location:546 → 573
      TPR; TPR repeat [structural motif]
      pfam11035
      Location:61 → 134
      SnAPC_2_like; Small nuclear RNA activating complex subunit 2, SNAP190 Myb
      pfam13414
      Location:622 → 685
      TPR_11; TPR repeat
      pfam13424
      Location:581 → 652
      TPR_12; Tetratricopeptide repeat

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      3379694..3479565
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011510350.3 → XP_011508652.1  trafficking protein particle complex subunit 12 isoform X1

      UniProtKB/TrEMBL
      Q8N9N0
      Conserved Domains (4) summary
      sd00006
      Location:508 → 535
      TPR; TPR repeat [structural motif]
      pfam11035
      Location:61 → 134
      SnAPC_2_like; Small nuclear RNA activating complex subunit 2, SNAP190 Myb
      pfam13414
      Location:584 → 647
      TPR_11; TPR repeat
      pfam13424
      Location:543 → 614
      TPR_12; Tetratricopeptide repeat

    2. XM_047444637.1 → XP_047300593.1  trafficking protein particle complex subunit 12 isoform X1

    3. XM_011510352.3 → XP_011508654.1  trafficking protein particle complex subunit 12 isoform X2

      Conserved Domains (1) summary
      pfam11035
      Location:61 → 134
      SnAPC_2_like; Small nuclear RNA activating complex subunit 2, SNAP190 Myb

    4. XM_047444639.1 → XP_047300595.1  trafficking protein particle complex subunit 12 isoform X3

    5. XM_047444638.1 → XP_047300594.1  trafficking protein particle complex subunit 12 isoform X2

    6. XM_011510353.3 → XP_011508655.1  trafficking protein particle complex subunit 12 isoform X4

      Conserved Domains (1) summary
      pfam11035
      Location:61 → 134
      SnAPC_2_like; Small nuclear RNA activating complex subunit 2, SNAP190 Myb

    7. XM_011510354.3 → XP_011508656.1  trafficking protein particle complex subunit 12 isoform X5

      Conserved Domains (1) summary
      pfam11035
      Location:61 → 134
      SnAPC_2_like; Small nuclear RNA activating complex subunit 2, SNAP190 Myb

    8. XM_011510355.3 → XP_011508657.1  trafficking protein particle complex subunit 12 isoform X6

      UniProtKB/TrEMBL
      Q53QD4
      Conserved Domains (4) summary
      TIGR02795
      Location:234 → 293
      tol_pal_ybgF; tol-pal system protein YbgF
      sd00006
      Location:231 → 258
      TPR; TPR repeat [structural motif]
      pfam13414
      Location:307 → 370
      TPR_11; TPR repeat
      pfam13424
      Location:266 → 337
      TPR_12; Tetratricopeptide repeat

    9. XM_011510356.2 → XP_011508658.1  trafficking protein particle complex subunit 12 isoform X7

      See identical proteins and their annotated locations for XP_011508658.1

      UniProtKB/TrEMBL
      A0A0J9YXQ9, Q53QD4
      Conserved Domains (3) summary
      sd00006
      Location:190 → 217
      TPR; TPR repeat [structural motif]
      cl26002
      Location:199 → 379
      TPR_11; TPR repeat
      cl26250
      Location:193 → 252
      TPR_6; Tetratricopeptide repeat

    RNA

    1. XR_426956.4 RNA Sequence

    2. XR_007076381.1 RNA Sequence

    3. XR_001738761.2 RNA Sequence

    4. XR_007076382.1 RNA Sequence

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187522.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      9876..89035
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      3401815..3501615
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054342395.1 → XP_054198370.1  trafficking protein particle complex subunit 12 isoform X1

    2. XM_054342396.1 → XP_054198371.1  trafficking protein particle complex subunit 12 isoform X1

    3. XM_054342397.1 → XP_054198372.1  trafficking protein particle complex subunit 12 isoform X2

    4. XM_054342399.1 → XP_054198374.1  trafficking protein particle complex subunit 12 isoform X3

    5. XM_054342398.1 → XP_054198373.1  trafficking protein particle complex subunit 12 isoform X2

    6. XM_054342400.1 → XP_054198375.1  trafficking protein particle complex subunit 12 isoform X4

    7. XM_054342401.1 → XP_054198376.1  trafficking protein particle complex subunit 12 isoform X5

    8. XM_054342403.1 → XP_054198378.1  trafficking protein particle complex subunit 12 isoform X7

      UniProtKB/TrEMBL
      A0A0J9YXQ9

    9. XM_054342402.1 → XP_054198377.1  trafficking protein particle complex subunit 12 isoform X6

    RNA

    1. XR_008486387.1 RNA Sequence

    2. XR_008486386.1 RNA Sequence

    3. XR_008486385.1 RNA Sequence

    4. XR_008486388.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WVT3.3 GenPept UniProtKB/Swiss-Prot:Q8WVT3

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