TRAPPC6A Gene
protein-coding GIFtS: 50
GCID: GC19M045666
|
|
trafficking protein particle complex 6A
| |
Aliases for TRAPPC6A gene
(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 6A1 2 | | TRS331 2 | | TRAPP Complex Subunit 6A2 3 | | HSPC2891 | | MGC26501 | | Trafficking Protein Particle Complex Subunit 6A2 |
Export aliases for TRAPPC6A gene to outside databasesPrevious GC identifers: GC00U913616 GC19M050360 GC19M042096 |
Summaries for TRAPPC6A gene(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 TRAPPC6A: This gene encodes a component of the trafficking protein particle complex, which tethers transport vesicles to thecis-Golgi membrane. Loss of expression of the related gene in mouse affects coat and eye pigmentation, suggesting thatthe encoded protein may be involved in melanosome biogenesis. Alternatively spliced transcript variants encodingmultiple isoforms have been observed for this gene. (provided by RefSeq, Aug 2012) UniProtKB/Swiss-Prot: TPC6A_HUMAN, O75865Function: May play a role in vesicular transport during the biogenesis of melanosomes (By similarity)
|
Genomic Views for TRAPPC6A gene
(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_000019.9 NC_018930.1 NT_011109.16
Regulatory elements: SABiosciences Regulatory transcription factor binding sites in the TRAPPC6A gene promoter: AREB6 AP-2rep ER-alpha NF-1 NF-1/L Olf-1 Other transcription factors
Search SABiosciences Chromatin IP Primers for TRAPPC6A
Epigenetics:
|  | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TRAPPC6A |
Genomic Location: Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 19q13.32 Ensembl cytogenetic band: 19q13.32 HGNC cytogenetic band: 19q13.32TRAPPC6A Gene in genomic location: bands according to Ensembl, locations according to
(and/or Entrez Gene and/or Ensembl if different)

GeneLoc information about chromosome 19 GeneLoc Exon Structure GeneLoc location for GC19M045666: view genomic region
(about GC identifiers)
Start:
|
45,666,186 bp from pter |
End:
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45,681,495 bp from pter |
Size:
|
15,310 bases |
Orientation:
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minus strand |
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Proteins for TRAPPC6A gene
(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: TPC6A_HUMAN, O75865 (See
protein sequence)Recommended Name: Trafficking protein particle complex subunit 6A Size: 159 amino acids; 17605 Da
Subunit: Part of the multisubunit TRAPP (transport protein particle) complex. Heterodimer with TRAPPC3. The heterodimerTRAPPC3-TRAPPC6A interacts with TRAPPC2L. Interacts with TRAPPC2L
Subcellular location: Golgi apparatus, cis-Golgi network (By similarity). Endoplasmic reticulum (By similarity)
Sequence caution: Sequence=AAC62259.1; Type=Erroneous initiation; Sequence=AAF28967.1; Type=Erroneous initiation;
2 PDB 3D structures from and Proteopedia for TRAPPC6A:2C0J (3D)
  2J3T (3D)
 
Secondary accessions: Q9BQ45 Q9P092Alternative splicing: 2 isoforms: O75865-1 O75865-2 Explore the universe of human proteins at neXtProt for TRAPPC6A: NX_O75865
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_O75865 TRAPPC6A Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (4 alternative transcripts):
NP_001257820.1 NP_001257821.1 NP_001257822.1 NP_077013.1 ENSEMBL proteins: ENSP00000006275 ENSP00000468363 ENSP00000468612 ENSP00000468182 Human Recombinant Protein Products:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005783 | endoplasmic reticulum |
IEA | -- | | GO:0005794 | Golgi apparatus |
IEA | -- |
TRAPPC6A for ontologies About GeneDecksing
TRAPPC6A Antibody Products: Assay Products for TRAPPC6A: |
Protein
Domains / Families for TRAPPC6A gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
TRAPPC6A for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry O75865ProtoNet protein and cluster: O75865 1 Blocks protein family: IPB007194 Transport protein particle (TRAPP) component
UniProtKB/Swiss-Prot: TPC6A_HUMAN, O75865Similarity: Belongs to the TRAPP small subunits family. BET3 subfamily |
Function for TRAPPC6A gene
(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: TPC6A_HUMAN, O75865Function: May play a role in vesicular transport during the biogenesis of melanosomes (By similarity)
Clone Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for TRAPPC6A (see all 3) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for TRAPPC6A OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
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Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005515 | protein binding |
IPI | -- |
TRAPPC6A for ontologies About GeneDecksing
1 GenomeRNAi human phenotype for TRAPPC6A: Animal Models: 3 MGI mutant phenotypes (inferred from 1 allele ) (MGI details for Trappc6a):
TRAPPC6A for phenotypes About GeneDecksing
|
Pathways & Interactions for TRAPPC6A gene
(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 TRAPPC6A
STRING Interaction
Network Preview (showing 5 interactants - click image to see 12)
 5/16 Interacting proteins for TRAPPC6A (O758651, 2, 3 ENSP000000062754) via UniProtKB, MINT, STRING, and/or I2D (see all 16)| Interactant | Interaction Details |
|---|
| GeneCard | External ID(s) |
|---|
| HOXA1 | P496392, 3, ENSP000003432464 | MINT-67909 I2D:
score=5 STRING: ENSP00000343246 | | TRAPPC3 | O436172, 3, ENSP000003622614 | MINT-6785415 MINT-6785068 MINT-6784856 MINT-66356 MINT-6785038 I2D:
score=5 STRING: ENSP00000362261 | | EFS | O432812, 3, ENSP000002167334 | MINT-67460 I2D:
score=5 STRING: ENSP00000216733 | | SSSCA1 | O602322, 3, ENSP000003123184 | MINT-67028 I2D:
score=5 STRING: ENSP00000312318 | | RAD54B | Q9Y6202, 3, ENSP000003366064 | MINT-67956 I2D:
score=5 STRING: ENSP00000336606 | About this table
Gene Ontology (GO): 1 biological process term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0016192 | vesicle-mediated transport |
IEA | -- |
TRAPPC6A for ontologies About GeneDecksing
|
Drugs & Compounds for TRAPPC6A gene(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 Tocris compounds for TRAPPC6A
1 DrugBank Compound for TRAPPC6A About this table
Search CenterWatch for drugs/clinical trials and news about TRAPPC6A / TPC6A 
|
Transcripts for TRAPPC6A gene(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 TRAPPC6A gene (4 alternative transcripts): NM_001270891.1 NM_001270892.1 NM_001270893.1 NM_024108.2 Unigene Cluster for TRAPPC6A: Trafficking protein particle complex 6A Hs.466929 [show with all ESTs]Unigene Representative Sequence: BM4240285 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000006275(uc002pav.3 uc002paw.3) ENST00000588062 ENST00000585934 ENST00000592647 ENST00000587818
Clone Products: |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for TRAPPC6A (see all 3) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for TRAPPC6A OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector: TRAPPC6A (NM_024108) | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for TRAPPC6A | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TRAPPC6A  |
Additional cDNA sequence: AF161407.1 BC001907.1 BC004450.1 FJ418644.1 7 DOTS entries: DT.121485076 DT.100771267 DT.413120 DT.95161826 DT.75185340 DT.75180803 DT.97861865 24/109 AceView cDNA sequences (see all 109): BM453945 BQ576105 BM781446 BF435031 BU734927 BQ691918 BM701569 BC004450 BM781486 BC001907 CA424931 CD671132 AI492665 BQ028679 BG575310 BM841123 BM558363 NM_024108 AI168147 CA418444 AA614444 BQ636932 AI291016 BG748962 GeneLoc Exon Structure
3 Alternative Splicing Database (ASD) splice patterns (SP) for TRAPPC6A About this scheme
| ExUns: | 1a | · | 1b | · | 1c | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5 | ^ | 6a | · | 6b | · | 6c | |
| SP1: | |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | |
| SP2: | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |
| SP3: | |   | |   | - |   | - |   | |   | |   | |   | |   | |   | |   |
ECgene alternative splicing isoforms for TRAPPC6A
|
Expression for TRAPPC6A gene
(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
| TRAPPC6A expression in normal human tissues (normalized intensities) See probesets specificity/sensitivity at GeneAnnot About this imageBioGPS CGAP TAG: GCGGATACTG
About this image See TRAPPC6A Protein Expression from SPIRE MOPED and PaxDB Genevestigator expression for TRAPPC6A
SOURCE GeneReport for Unigene cluster: Hs.466929 SABiosciences Custom PCR Arrays for TRAPPC6A
Primer Products: |  | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for TRAPPC6A Browse OriGene validated miRNA SYBR primer pairs
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Orthologs for TRAPPC6A gene
(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 TRAPPC6A gene from 6/22 species (see all 22) About this table
| Organism |
Taxonomic classification |
Gene |
Description |
Human Similarity |
Orthology Type |
Details |
mouse (Mus musculus) |
Mammalia |
Trappc6a1 , 5 |
trafficking protein particle complex 6A1, 5 |
85.12(n)1 83.02(a)1 |
  |
7 (9.92 cM)5 670911 NM_025960.31 NP_080236.21 195086705 |
zebrafish (Danio rerio) |
Actinopterygii |
trappc6bl6 |
trafficking protein particle complex 6b-like |
57(a) |
1 ↔ 1 |
15(14108999-14116135) |
fruit fly (Drosophila melanogaster) |
Insecta |
CG61966 |
-- |
46(a) |
1 → many |
3R(11176067-11176741) |
worm (Caenorhabditis elegans) |
Secernentea |
K08H10.96 |
Protein K08H10.9 |
36(a) |
1 → many |
V(9991828-9992768) |
thale cress (Arabidopsis thaliana) |
eudicotyledons |
AT3G050006 |
Transport protein particle (TRAPP) component |
31(a) |
1 → many |
3(1387175-1388756) |
rice (Oryza sativa) |
Liliopsida |
---- |
transport protein particle component, Bet3, domain...transport protein particle component, Bet3, domain... |
34(a)33(a) |
many ↔ manymany ↔ many |
9(3368499-3375004) 7(11279309-11284331) |
ENSEMBL Gene Tree for TRAPPC6A (if available) TreeFam Gene Tree for TRAPPC6A (if available)  |
Paralogs for TRAPPC6A gene(Paralogs according to
1HomoloGene, 2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68) About This Section
| Paralogs for TRAPPC6A gene
- TRAPPC6B2
1 SIMAP similar gene for TRAPPC6A using alignment to 4 protein entries: TPC6A_HUMAN (see all proteins):TRAPPC6B
TRAPPC6A for paralogs About GeneDecksing
|
Genomic Variants for TRAPPC6A gene(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
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical significance | Chr 19 pos | Sequence | # | AA Chg | Type | More | # | Allele freq | Pop | Total sample | More |
|---|
HapMap Linkage Disequilibrium report for TRAPPC6A (45666186 - 45681495 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions) Database of Genomic Variants (DGV): 2 variations for TRAPPC6A 2 CNVs: 5103 5343  | SABiosciences Cancer Mutation PCR Assays |
|  | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing TRAPPC6A |
|
Disorders
/ Diseases for TRAPPC6A gene
(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
|
TRAPPC6A for disorders About GeneDecksing
OMIM gene information: 610396
OMIM disorders: --
1 disease for TRAPPC6A: About MalaCardsmalaria Export disorders for TRAPPC6A gene to outside databases
|
Publications for TRAPPC6A gene (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 TRAPPC6A gene, integrated from 9 sources (see all 15): (articles sorted by number of sources associating them with TRAPPC6A) | |  | Utopia: connect your pdf to the dynamic world of online information |
- Biochemical and crystallographic studies reveal a specific interaction between TRAPP subunits Trs33p and Bet3p. (PubMed id 16262728)1, 2 Kim M.-S.... Sacher M. (2005)
- 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)
- The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)1, 2 Grimwood J.... Lucas S.M. (2004)
- Entry and exit mechanisms at the cis-face of the Golgi complex. (PubMed id 21482742)1 Lorente-Rodriguez A. and Barlowe C. (2011)
- Alzheimer's disease genes are associated with measures of cognitive ageing in the lothian birth cohorts of 1921 and 1936. (PubMed id 21766012)1 Hamilton G....Deary I.J. (2011)
- 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)
- Genome-wide association studies in an isolated founde r population from the Pacific Island of Kosrae. (PubMed id 19197348)1 Lowe J.K....Friedman J.M. (2009)
- TRAPPC2L is a novel, highly conserved TRAPP-interacting protein. (PubMed id 19416478)2 Scrivens P.J.... Sacher M. (2009)
- Distinct isocomplexes of the TRAPP trafficking factor coexist inside human cells. (PubMed id 18930054)1 Kummel D....Heinemann U. (2008)
- A mouse TRAPP-related protein is involved in pigmentation. (PubMed id 16697553)1 Gwynn B....Peters L.L. (2006)
|
External Searches for TRAPPC6A gene
(in PubMed,
OMIM, and NCBI Bookshelf) About This Section
|
|
Genome Databases showing TRAPPC6A gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing TRAPPC6A gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing TRAPPC6A gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL, Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot) About This Section
|
| Name | Description |
| PharmGKB entry for TRAPPC6A | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for TRAPPC6A gene: Search GeneIP for patents involving TRAPPC6A
GeneCards and IP: Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products for TRAPPC6A gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences), In Situ Hybridization Assays from Advanced Cell Diagnostics About This Section
|
 | |
 | |
 |
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