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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TRAPPC6B Gene

protein-coding   GIFtS: 50
GCID: GC14M039617

trafficking protein particle complex 6B

 Explore 1 disease affiliated with
TRAPPC6B via our new
 Human Malady Compendium 
Biological research products
for TRAPPC6B
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Trafficking Protein Particle Complex 6B1 2
TPC62
Trafficking Protein Particle Complex Subunit 6B2

External Ids:    HGNC: 230661   Entrez Gene: 1225532   Ensembl: ENSG000001824007   OMIM: 6103975   UniProtKB: Q86SZ23   

Export aliases for TRAPPC6B gene to outside databases

Previous GC identifers: GC14M037607 GC14M038686 GC14M019731


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for TRAPPC6B:
TRAPPC6B is a component of TRAPP complexes, which are tethering complexes involved in vesicle transport (Kummel et al.,
2005 (PubMed 16025134)).(supplied by OMIM, Mar 2008)

UniProtKB/Swiss-Prot: TPC6B_HUMAN, Q86SZ2
Function: May play a role in vesicular transport from endoplasmic reticulum to Golgi (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000014.8  NC_018925.1  NT_026437.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the TRAPPC6B gene promoter:
         POU2F2 (Oct-2.1)   Oct-B1   oct-B3   oct-B2   POU2F2   POU2F2C   POU2F1   POU2F1a   POU2F2B   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTRAPPC6B promoter sequence
   Search SABiosciences Chromatin IP Primers for TRAPPC6B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TRAPPC6B


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 14q21.1   Ensembl cytogenetic band:  14q21.1   HGNC cytogenetic band: 14q13.3

TRAPPC6B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TRAPPC6B gene location

GeneLoc information about chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14M039617:  view genomic region     (about GC identifiers)

Start:
39,617,015 bp from pter      End:
39,639,736 bp from pter
Size:
22,722 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: TPC6B_HUMAN, Q86SZ2 (See protein sequence)
Recommended Name: Trafficking protein particle complex subunit 6B  
Size: 158 amino acids; 17983 Da
Subunit: Part of the multisubunit TRAPP (transport protein particle) complex. Homodimer. Heterodimer with TRAPPC3
Subcellular location: Golgi apparatus, cis-Golgi network (By similarity). Endoplasmic reticulum (By similarity)
Sequence caution: Sequence=CAD62341.1; Type=Erroneous initiation;
3 PDB 3D structures from and Proteopedia for TRAPPC6B:
2BJN (3D)        2CFH (3D)        3KXC (3D)    
Secondary accessions: B3KPS2 Q5JPD6 Q86U35 Q86X35
Alternative splicing: 2 isoforms:  Q86SZ2-1   Q86SZ2-2   

Explore the universe of human proteins at neXtProt for TRAPPC6B: NX_Q86SZ2

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q86SZ2

  • TRAPPC6B Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001073005.1  NP_803235.1  

    ENSEMBL proteins: 
     ENSP00000330289   ENSP00000335171   ENSP00000452236   ENSP00000450670   ENSP00000451711  

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    Uscn Proteins for TRAPPC6B

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005783endoplasmic reticulum IEA--
    GO:0005794Golgi apparatus IEA--


    TRAPPC6B for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    TRAPPC6B for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR007194 TRAPP_component
     IPR024096 NO_sig/Golgi_transp_ligand-bd

    Graphical View of Domain Structure for InterPro Entry Q86SZ2

    ProtoNet protein and cluster: Q86SZ2

    1 Blocks protein family: IPB007194 Transport protein particle (TRAPP) component

    UniProtKB/Swiss-Prot: TPC6B_HUMAN, Q86SZ2
    Similarity: Belongs to the TRAPP small subunits family. BET3 subfamily


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: TPC6B_HUMAN, Q86SZ2
    Function: May play a role in vesicular transport from endoplasmic reticulum to Golgi (By similarity)

    miRNA
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    hsa-miR-579 hsa-miR-34b* hsa-miR-328 hsa-miR-125a-5p hsa-miR-136 hsa-miR-3942-5p hsa-miR-500a hsa-miR-486-5p
    SwitchGear 3'UTR luciferase reporter plasmidTRAPPC6B 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRAPPC6B

    1 GenomeRNAi human phenotype for TRAPPC6B:
     Decreased viability with pacli 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TRAPPC6B

    STRING Interaction Network Preview (showing 5 interactants - click image to see 12)

    5/23 Interacting proteins for TRAPPC6B (Q86SZ22, 3 ENSP000003302894) via UniProtKB, MINT, STRING, and/or I2D (see all 23)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TRAPPC3O436172, 3, ENSP000003622614MINT-6785068 MINT-6785053 MINT-6784845 I2D: score=3 STRING: ENSP00000362261
    COPS5Q929053, ENSP000003505124I2D: score=5 STRING: ENSP00000350512
    TRAPPC4Q9Y2963, ENSP000003518964I2D: score=1 STRING: ENSP00000351896
    TRAPPC2P0DI813, ENSP000003527084I2D: score=1 STRING: ENSP00000352708
    ACO2Q997983I2D: score=5 
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016192vesicle-mediated transport IEA--


    TRAPPC6B for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for TRAPPC6B

    1 DrugBank Compound for TRAPPC6B    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    S-PALMITOYL-L-CYSTEINE-- --target--10592235

    Search CenterWatch for drugs/clinical trials and news about TRAPPC6B / TPC6B 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for TRAPPC6B gene (2 alternative transcripts): 
    NM_001079537.1  NM_177452.3  

    Unigene Cluster for TRAPPC6B:

    Trafficking protein particle complex 6B
    Hs.13303  [show with all ESTs]
    Unigene Representative Sequence: NM_001079537
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000469361(uc001wut.1 uc001wuu.1 uc001wuv.1 uc010tqd.1)
    ENST00000330149 ENST00000347691 ENST00000557764 ENST00000555269 ENST00000554018
    ENST00000556765

    miRNA
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    8/32 QIAGEN miScript miRNA Assays for microRNAs that regulate TRAPPC6B (see all 32):
    hsa-miR-579 hsa-miR-34b* hsa-miR-328 hsa-miR-125a-5p hsa-miR-136 hsa-miR-3942-5p hsa-miR-500a hsa-miR-486-5p
    SwitchGear 3'UTR luciferase reporter plasmidTRAPPC6B 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AK025437.1 AK056690.1 AK294339.1 AK310730.1 AK315900.1 AL833179.1 BC047328.1 BX161510.1 
    BX248013.1 

    8 DOTS entries:

    DT.451669  DT.100790168  DT.92425367  DT.75171886  DT.100773795  DT.120757479  DT.120757494  DT.40122444 

    24/150 AceView cDNA sequences (see all 150):

    AA625846 AI567135 AI521496 BM468117 BU626821 T32517 BU735689 AW118812 
    CD676093 AI129609 AI216550 AA911836 AA782655 AA927711 W49617 BF434452 
    NM_177452 AA504210 AK025437 CA422147 AI378461 AI378472 AL833179 CR614282 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for TRAPPC6B    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7a · 7b
    SP1:                    -     -                                                         
    SP2:                    -     -           -                 -     -                     
    SP3:                    -     -           -                                             
    SP4:                    -                 -                                             
    SP5:                                                                                    


    ECgene alternative splicing isoforms for TRAPPC6B

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    TRAPPC6B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AAAGGACAAG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See TRAPPC6B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TRAPPC6B

    SOURCE GeneReport for Unigene cluster: Hs.13303
        SABiosciences Custom PCR Arrays for TRAPPC6B
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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for TRAPPC6B gene from 8/32 species (see all 32)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves TRAPPC6B1 trafficking protein particle complex 6B 83.97(n)
    94.3(a)
      423337  NM_001252160.1  NP_001239089.1 
    lizard
    (Anolis carolinensis)
    Reptilia TRAPPC6B6
    --
    94(a)
    1 ↔ 1
    1(23963820-23974561)
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC526682 hypothetical protein MGC52668 78.85(n)    BC044077.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc663042 hypothetical protein MGC66304 75.02(n)   393634  BC057509.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG61961 CG6196 55.19(n)
    55.63(a)
      41866  NM_142193.3  NP_650450.1 
    worm
    (Caenorhabditis elegans)
    Secernentea CELE_K08H10.91 Protein K08H10.9 52.66(n)
    48.55(a)
      179394  NM_073170.4  NP_505571.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT3G050001 Transport protein particle (TRAPP) component 58.2(n)
    53.28(a)
      819661  NM_111372.3  NP_187151.1 
    rice
    (Oryza sativa)
    Liliopsida Os09g02449001 hypothetical protein 56.61(n)
    55.17(a)
      4346489  NM_001069192.2  NP_001062657.2 


    ENSEMBL Gene Tree for TRAPPC6B (if available)
    TreeFam Gene Tree for TRAPPC6B (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for TRAPPC6B gene
    TRAPPC6A2  
    1 SIMAP similar gene for TRAPPC6B using alignment to 5 protein entries:     TPC6B_HUMAN (see all proteins):
    TRAPPC6A

    TRAPPC6B for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/522 NCBI SNPs in TRAPPC6B are shown (see all 522    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 14 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs603420721,2
    --39616610(+) ACCTCC/TGACTC 2 -- int10--------
    rs1406951201,2
    --39616618(+) CTCCCA/GGGTTC 2 -- int10--------
    rs786832191,2
    F,--39616845(+) ATGTAT/CGGCAT 2 -- int11Minor allele frequency- C:0.14WA 118
    rs80112441,2
    C,F,A,H,--39616856(+) TAAGGC/TAACAA 2 -- int110Minor allele frequency- T:0.26NS EA NA WA 752
    rs1446563691,2
    --39617030(+) TTCTTC/TAGTAC 2 -- ut310--------
    rs28691,2
    C,F,O,A,H,--39617103(+) TTCAAT/CTGTCC 2 -- ut3127Minor allele frequency- C:0.20MN NS EA NA WA 2896
    rs171088521,2
    C,F,--39617116(+) TACTAA/TTTTTT 2 -- ut314Minor allele frequency- T:0.09NA WA 252
    rs732915411,2
    C,F,--39617195(+) TATACC/ACAAAG 2 -- ut313Minor allele frequency- A:0.20WA CSA 122
    rs745567591,2
    C,F,--39617268(+) GATTGG/ATTAAT 2 -- ut311Minor allele frequency- A:0.14WA 118
    rs1146806511,2
    F,--39617436(+) TGCTGG/CCAAAT 2 -- ut311Minor allele frequency- C:0.03WA 118

    HapMap Linkage Disequilibrium report for TRAPPC6B (39617015 - 39639736 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for TRAPPC6B
         2 CNVs: 5740 66627

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    TRAPPC6B for disorders           About GeneDecksing

    OMIM gene information: 610397    OMIM disorders: --

    1 disease for TRAPPC6B:    About MalaCards
    malaria


    Export disorders for TRAPPC6B gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for TRAPPC6B gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with TRAPPC6B)
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    1. The structure of the TRAPP subunit TPC6 suggests a model for a TRAPP subcomplex. (PubMed id 16025134)1, 2 Kuemmel D....Heinemann U. (2005)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    5. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    6. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    7. C4orf41 and TTC-15 are mammalian TRAPP components wit h a role at an early stage in ER-to-Golgi trafficking. (PubMed id 21525244)1 Scrivens P.J....Sacher M. (2011)
    8. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)
    9. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    10. A mouse TRAPP-related protein is involved in pigmentation. (PubMed id 16697553)1 Gwynn B....Peters L.L. (2006)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 122553 HGNC: 23066 AceView: TRAPPC6B Ensembl:ENSG00000182400 euGenes: HUgn122553
    ECgene: TRAPPC6B H-InvDB: TRAPPC6B

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for TRAPPC6B Pharmacogenomics, SNPs, Pathways

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