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TRAPPC4 Gene(Protein Coding)

Trafficking Protein Particle Complex 4

GCID:
GC11P119018
GIFtS:
54
Genes Participants
UDN Logo

Aliases for TRAPPC4 Gene

Aliases for TRAPPC4 Gene

  • Trafficking Protein Particle Complex 4 2 3 5
  • Hematopoietic Stem/Progenitor Cell Protein 172 3 4
  • TRS23 Homolog 3 4
  • Synbindin 3 4
  • SBDN 3 4
  • Trafficking Protein Particle Complex Subunit 4 3
  • CGI-104 3
  • HSPC172 3
  • PTD009 3
  • TRS23 3

External Ids for TRAPPC4 Gene

Previous GeneCards Identifiers for TRAPPC4 Gene

  • GC11P118923
  • GC11P118426
  • GC11P118394
  • GC11P114828
  • GC11P118889

Summaries for TRAPPC4 Gene

GeneCards Summary for TRAPPC4 Gene

TRAPPC4 (Trafficking Protein Particle Complex 4) is a Protein Coding gene. Among its related pathways are Transport to the Golgi and subsequent modification and Syndecan-2-mediated signaling events. GO annotations related to this gene include Rab guanyl-nucleotide exchange factor activity.

UniProtKB/Swiss-Prot for TRAPPC4 Gene

  • May play a role in vesicular transport from endoplasmic reticulum to Golgi.

Gene Wiki entry for TRAPPC4 Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRAPPC4 Gene

Genomics for TRAPPC4 Gene

Products:

  1. Regulatory Element

Regulatory Elements for TRAPPC4 Gene

Enhancers for TRAPPC4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11F119024 1.4 Ensembl ENCODE 97.8 +9.5 9501 7.3 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 KLF13 TRAPPC4 VPS11 SLC37A4 PIR60932
GH11F119015 1.1 ENCODE 72.8 -0.4 -372 4.6 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 YY1 TRAPPC4 BCL9L ARCN1 ENSG00000254909 UBE4A RPS25 RPL23AP64 ENSG00000254428 ENSG00000222529 FOXR1
GH11F119020 0.8 ENCODE 98.1 +3.2 3236 1.9 ELF3 PKNOX1 RARA YY1 GATA4 CREM HMG20B CEBPB TBX21 NR2F2 TRAPPC4 RPS25 PIR60932 SLC37A4
GH11F118996 1.1 ENCODE 63.5 -20.4 -20375 3.2 PKNOX1 CREB3L1 MLX ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF143 FOS TRAPPC4 ENSG00000255121 GC11P119002
GH11F119016 0.7 ENCODE 73.4 -3.0 -2967 0.2 CTCF RAD21 ZBTB40 TEAD3 YY1 ZNF121 POLR2H POLR2A THRAP3 KDM1A TRAPPC4 LOC101929133 BCL9L UBE4A ENSG00000254909 RPL23AP64 ENSG00000254428 DDX6 MIR3656
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TRAPPC4 on UCSC Golden Path with GeneCards custom track

Promoters for TRAPPC4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000112326 68 3001 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 YY1

Transcription factor binding sites by QIAGEN in the TRAPPC4 gene promoter:

Genomic Location for TRAPPC4 Gene

Chromosome:
11
Start:
119,018,432 bp from pter
End:
119,025,454 bp from pter
Size:
7,023 bases
Orientation:
Plus strand

Genomic View for TRAPPC4 Gene

Genes around TRAPPC4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRAPPC4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRAPPC4 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TRAPPC4 Gene

Proteins for TRAPPC4 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for TRAPPC4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y296-TPPC4_HUMAN
    Recommended name:
    Trafficking protein particle complex subunit 4
    Protein Accession:
    Q9Y296
    Secondary Accessions:
    • A8K3A5
    • B4DME1

    Protein attributes for TRAPPC4 Gene

    Size:
    219 amino acids
    Molecular mass:
    24340 Da
    Quaternary structure:
    • Component of the multisubunit TRAPP (transport protein particle) complex, which includes at least TRAPPC2, TRAPPC2L, TRAPPC3, TRAPPC3L, TRAPPC4, TRAPPC5, TRAPPC8, TRAPPC9, TRAPPC10, TRAPPC11 and TRAPPC12. Interacts with SDC2 (By similarity).
    • Component of the multisubunit TRAPP (transport protein particle) complex, which includes at least TRAPPC2, TRAPPC2L, TRAPPC3, TRAPPC3L, TRAPPC4, TRAPPC5, TRAPPC8, TRAPPC9, TRAPPC10, TRAPPC11 and TRAPPC12. Interacts with SDC2 (By similarity).

    Three dimensional structures from OCA and Proteopedia for TRAPPC4 Gene

    Alternative splice isoforms for TRAPPC4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRAPPC4 Gene

Protein Expression for TRAPPC4 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TRAPPC4 Gene

  • Ubiquitination at Lys 41
  • Modification sites at PhosphoSitePlus

Other Protein References for TRAPPC4 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for TRAPPC4

No data available for DME Specific Peptides for TRAPPC4 Gene

Domains & Families for TRAPPC4 Gene

Gene Families for TRAPPC4 Gene

HGNC:

Protein Domains for TRAPPC4 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TRAPPC4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y296

UniProtKB/Swiss-Prot:

TPPC4_HUMAN :
  • Belongs to the TRAPP small subunits family. TRAPPC4 subfamily.
Family:
  • Belongs to the TRAPP small subunits family. TRAPPC4 subfamily.
genes like me logo Genes that share domains with TRAPPC4: view

Function for TRAPPC4 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for TRAPPC4 Gene

UniProtKB/Swiss-Prot Function:
May play a role in vesicular transport from endoplasmic reticulum to Golgi.

Gene Ontology (GO) - Molecular Function for TRAPPC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17110339
GO:0017112 Rab guanyl-nucleotide exchange factor activity IBA --
genes like me logo Genes that share ontologies with TRAPPC4: view
genes like me logo Genes that share phenotypes with TRAPPC4: view

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TRAPPC4 Gene

Localization for TRAPPC4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRAPPC4 Gene

Golgi apparatus, cis-Golgi network. Endoplasmic reticulum.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TRAPPC4 gene
Compartment Confidence
cytosol 5
golgi apparatus 5
endoplasmic reticulum 4
mitochondrion 2
cytoskeleton 1
nucleus 1

Gene Ontology (GO) - Cellular Components for TRAPPC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005795 Golgi stack ISS 11018053
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with TRAPPC4: view

Pathways & Interactions for TRAPPC4 Gene

genes like me logo Genes that share pathways with TRAPPC4: view

Gene Ontology (GO) - Biological Process for TRAPPC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006888 ER to Golgi vesicle-mediated transport IBA --
GO:0016192 vesicle-mediated transport IEA --
GO:0016358 dendrite development ISS 11018053
GO:0043547 positive regulation of GTPase activity IEA --
genes like me logo Genes that share ontologies with TRAPPC4: view

No data available for SIGNOR curated interactions for TRAPPC4 Gene

Drugs & Compounds for TRAPPC4 Gene

Products:

  1. Drug

(1) Drugs for TRAPPC4 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
S-PALMITOYL-L-CYSTEINE Experimental Pharma Target 0
genes like me logo Genes that share compounds with TRAPPC4: view

Transcripts for TRAPPC4 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for TRAPPC4 Gene

(7) REFSEQ mRNAs :
(10) Additional mRNA sequences :
(354) Selected AceView cDNA sequences:
(15) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TRAPPC4 Gene

Trafficking protein particle complex 4:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for TRAPPC4 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b · 3c · 3d ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b · 7c
SP1: - - -
SP2: - - - -
SP3: - - - - -
SP4: - - - -
SP5: -
SP6:
SP7:

Relevant External Links for TRAPPC4 Gene

GeneLoc Exon Structure for
TRAPPC4
ECgene alternative splicing isoforms for
TRAPPC4

Expression for TRAPPC4 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRAPPC4 Gene

mRNA expression in normal human tissues for TRAPPC4 Gene
mRNA expression by BioGPS for TRAPPC4 GenemRNA expression by GTEx for TRAPPC4 Gene

Protein differential expression in normal tissues from HIPED for TRAPPC4 Gene

This gene is overexpressed in Bone (14.8) and Serum (10.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TRAPPC4 Gene



Protein tissue co-expression partners for TRAPPC4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TRAPPC4 Gene:

TRAPPC4

SOURCE GeneReport for Unigene cluster for TRAPPC4 Gene:

Hs.132760
genes like me logo Genes that share expression patterns with TRAPPC4: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for TRAPPC4 Gene

Orthologs for TRAPPC4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TRAPPC4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia TRAPPC4 34 35
  • 100 (n)
oppossum
(Monodelphis domestica)
 Mammalia TRAPPC4 35
  • 96 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia TRAPPC4 35
  • 92 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Trappc4 34 16 35
  • 91.17 (n)
rat
(Rattus norvegicus)
 Mammalia Trappc4 34
  • 90.72 (n)
dog
(Canis familiaris)
 Mammalia TRAPPC4 34 35
  • 90.56 (n)
cow
(Bos Taurus)
 Mammalia TRAPPC4 34 35
  • 90.41 (n)
chicken
(Gallus gallus)
 Aves TRAPPC4 34 35
  • 78.54 (n)
lizard
(Anolis carolinensis)
 Reptilia TRAPPC4 35
  • 88 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia trappc4 34
  • 76.56 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.11434 34
zebrafish
(Danio rerio)
 Actinopterygii trappc4 34 35
  • 75.95 (n)
zgc73260 34
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP008106 34
  • 61.37 (n)
fruit fly
(Drosophila melanogaster)
 Insecta Trs23 34 35
  • 61.03 (n)
worm
(Caenorhabditis elegans)
 Secernentea F36D4.2 34
  • 53.24 (n)
trpp-4 35
  • 47 (a)
 OneToOne
K. lactis yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0D12144g 34
  • 50.15 (n)
A. gosspyii yeast
(Ashbya gossypii)
 Saccharomycetes AGOS_AFR459W 34
  • 45.57 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes TRS23 34 35 37
  • 43.55 (n)
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT5G02280 34
  • 58.81 (n)
rice
(Oryza sativa)
 Liliopsida Os07g0454700 34
  • 56.92 (n)
bread mold
(Neurospora crassa)
 Ascomycetes NCU11085 34
  • 57.2 (n)
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes trs23 34
  • 56.77 (n)
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.7090 34
Species where no ortholog for TRAPPC4 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TRAPPC4 Gene

ENSEMBL:
Gene Tree for TRAPPC4 (if available)
TreeFam:
Gene Tree for TRAPPC4 (if available)

Paralogs for TRAPPC4 Gene

No data available for Paralogs for TRAPPC4 Gene

Variants for TRAPPC4 Gene

Sequence variations from dbSNP and Humsavar for TRAPPC4 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs10696222 -- 119,019,832(+) TTAAA(-/AAT)CTTTT intron-variant, upstream-variant-2KB
rs10892321 -- 119,018,404(+) GGCAA(A/G)AGGCG upstream-variant-2KB
rs111230411 -- 119,022,424(+) CTTTA(C/G)AAAAA intron-variant
rs111322300 -- 119,023,168(+) CCATA(C/T)TGGCC intron-variant
rs111345266 -- 119,023,057(+) CCTTC(C/T)GGGTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TRAPPC4 Gene

Variant ID Type Subtype PubMed ID
nsv983067 CNV duplication 23825009
nsv826101 CNV gain 20364138

Variation tolerance for TRAPPC4 Gene

Residual Variation Intolerance Score: 25.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.37; 85.44% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TRAPPC4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRAPPC4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRAPPC4 Gene

Disorders for TRAPPC4 Gene

Relevant External Links for TRAPPC4

Genetic Association Database (GAD)
TRAPPC4
Human Genome Epidemiology (HuGE) Navigator
TRAPPC4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TRAPPC4

No disorders were found for TRAPPC4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TRAPPC4 Gene

Publications for TRAPPC4 Gene

  1. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai C.-H. … Lin W.-C. (Genome Res. 2000) 2 3 4 64
  2. C4orf41 and TTC-15 are mammalian TRAPP components with a role at an early stage in ER-to-Golgi trafficking. (PMID: 21525244) Scrivens P.J. … Sacher M. (Mol. Biol. Cell 2011) 3 4 64
  3. Crystal structure of human synbindin reveals two conformations of longin domain. (PMID: 18466758) Fan S. … Gong W. (Biochem. Biophys. Res. Commun. 2009) 3 22 64
  4. Single-cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene. (PMID: 20035503) Elstner M. … Turnbull D.M. (Ann. Neurol. 2009) 3 46 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for TRAPPC4 Gene

Sources for TRAPPC4 Gene

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