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TRAPPC6A trafficking protein particle complex subunit 6A [ Homo sapiens (human) ]

Gene ID: 79090, updated on 2-Nov-2024

Summary

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Official Symbol
TRAPPC6Aprovided by HGNC
Official Full Name
trafficking protein particle complex subunit 6Aprovided by HGNC
Primary source
HGNC:HGNC:23069
See related
Ensembl:ENSG00000007255 MIM:610396; AllianceGenome:HGNC:23069
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
TRS33
Summary
This gene encodes a component of the trafficking protein particle complex, which tethers transport vesicles to the cis-Golgi membrane. Loss of expression of the related gene in mouse affects coat and eye pigmentation, suggesting that the encoded protein may be involved in melanosome biogenesis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2012]
Expression
Ubiquitous expression in kidney (RPKM 18.2), spleen (RPKM 12.2) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See TRAPPC6A in Genome Data Viewer
Location:
19q13.32
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (45162933..45178237, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (47988066..48003370, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (45666191..45681495, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene protein phosphatase 1 regulatory subunit 37 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45632987-45633488 Neighboring gene Sharpr-MPRA regulatory region 10789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45638457-45639261 Neighboring gene MPRA-validated peak3514 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14786 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45641146-45641718 Neighboring gene eukaryotic translation initiation factor 5A pseudogene 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45656063-45656688 Neighboring gene uncharacterized LOC105372420 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:45657908-45658134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45658871-45659588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45663890-45664522 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14787 Neighboring gene NTPase KAP family P-loop domain containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45680873-45681816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14788 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14789 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:45682829-45683329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45683755-45684256 Neighboring gene Sharpr-MPRA regulatory region 2997 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14790 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10758 Neighboring gene biogenesis of lysosomal organelles complex 1 subunit 3 Neighboring gene Sharpr-MPRA regulatory region 12921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45719170-45719704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45720327-45721022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45721023-45721716 Neighboring gene exocyst complex component 3 like 2 Neighboring gene exocyst complex component 3 like 4 pseudogene

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Missense mutation in TRAPPC6A identified in patients with a neurodevelopmental syndrome, affects stability of the TRAPP complex.
    Title: A missense mutation in TRAPPC6A leads to build-up of the protein, in patients with a neurodevelopmental syndrome and dysmorphic features.
  2. Host cellular protein TRAPPC6ADelta interacts with influenza A virus M2 protein and regulates viral propagation by modulating M2 trafficking.
    Title: Host Cellular Protein TRAPPC6AΔ Interacts with Influenza A Virus M2 Protein and Regulates Viral Propagation by Modulating M2 Trafficking.
  3. Mapping and characterization of mouse Trappc6a, along with a description of the human homolog.
    Title: A mouse TRAPP-related protein is involved in pigmentation.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae.
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)

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

  • MGC2650

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 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 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 TRAPPIII protein complex NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in cis-Golgi network 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 IEA
Inferred from Electronic Annotation
more info
  
is_active_in trans-Golgi network IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
trafficking protein particle complex subunit 6A
Names
TRAPP complex subunit 6A
trafficking protein particle complex 6A

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.

Genomic

  1. NG_033044.1 RefSeqGene

    Range
    5007..20311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001270891.2 → NP_001257820.1  trafficking protein particle complex subunit 6A isoform 2

    See identical proteins and their annotated locations for NP_001257820.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as TRAPPC6Adelta29-42) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AF161407, BC001907, CN256687
    Consensus CDS
    CCDS59397.1
    UniProtKB/Swiss-Prot
    K7ERB1, K7ERQ4, O75865, Q9BQ45, Q9P092
    UniProtKB/TrEMBL
    B7TZ90
    Related
    ENSP00000468612.1, ENST00000585934.1
    Conserved Domains (1) summary
    cd14944
    Location:3 → 157
    TRAPPC6A_Trs33; Trs33 subunit of the TRAPP complex

  2. NM_001270892.2 → NP_001257821.1  trafficking protein particle complex subunit 6A isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the coding region, which results in a frameshift, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC001907, CN256686, CN256687
    Consensus CDS
    CCDS59395.1
    UniProtKB/Swiss-Prot
    O75865
    Related
    ENSP00000468182.1, ENST00000592647.1

  3. NM_001270893.2 → NP_001257822.1  trafficking protein particle complex subunit 6A isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has multiple differences in the coding region, one of which results in a frameshift, compared to variant 1. The encoded isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC001907, BI462720
    Consensus CDS
    CCDS59396.1
    UniProtKB/Swiss-Prot
    O75865
    Related
    ENSP00000468363.1, ENST00000588062.5

  4. NM_024108.3 → NP_077013.1  trafficking protein particle complex subunit 6A isoform 1

    See identical proteins and their annotated locations for NP_077013.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    BC001907, CN256687
    Consensus CDS
    CCDS12655.1
    UniProtKB/Swiss-Prot
    O75865
    Related
    ENSP00000006275.3, ENST00000006275.8
    Conserved Domains (1) summary
    cd14944
    Location:3 → 171
    TRAPPC6A_Trs33; Trs33 subunit of the TRAPP complex

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    45162933..45178237 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439420.1 → XP_047295376.1  trafficking protein particle complex subunit 6A isoform X2

  2. XM_047439419.1 → XP_047295375.1  trafficking protein particle complex subunit 6A isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    47988066..48003370 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322116.1 → XP_054178091.1  trafficking protein particle complex subunit 6A isoform X2

  2. XM_054322115.1 → XP_054178090.1  trafficking protein particle complex subunit 6A isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75865.2 GenPept UniProtKB/Swiss-Prot:O75865

Gene LinkOut

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