Aliases for TRAPPC4 Gene

Aliases for TRAPPC4 Gene

  • Trafficking Protein Particle Complex 4 2 3 5
  • Hematopoietic Stem/Progenitor Cell Protein 172 3 4
  • Trafficking Protein Particle Complex Subunit 4 3 4
  • TRS23 Homolog 3 4
  • SBDN 3 4
  • SYNBINDIN 3
  • Synbindin 4
  • 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 Vesicle-mediated transport and Transport to the Golgi and subsequent modification. Gene Ontology (GO) annotations related to this gene include Rab guanyl-nucleotide exchange factor activity. An important paralog of this gene is TRAPPC1.

UniProtKB/Swiss-Prot Summary for TRAPPC4 Gene

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

Gene Wiki entry for TRAPPC4 Gene

Additional gene information for TRAPPC4 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRAPPC4 Gene

Genomics for TRAPPC4 Gene

GeneHancer (GH) Regulatory Elements for TRAPPC4 Gene

Promoters and enhancers for TRAPPC4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J119015 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 822.7 -0.3 -258 4.9 SIN3A SP1 ZBTB40 SIX5 FOXA1 ZBTB6 RBPJ POLR2A NR2F6 ATF1 TRAPPC4 ENSG00000283704 RPS25 piR-31150 lnc-RPS25-2 BCL9L ENSG00000254909 RPL23AP64 UBE4A ENSG00000245869
GH11J119024 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas 97.8 +9.7 9710 7.7 SP1 CTCF SREBF1 FOXA1 MLX RBPJ SMARCE1 POLR2A USF2 NR2F1 SLC37A4 TRAPPC4 VPS11 RPL5P30 IFT46 ENSG00000255121 MPZL2 CD3G CD3D CD3E
GH11J118996 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 63.5 -20.4 -20374 3.2 ZBTB40 MLX RBPJ SMARCE1 POLR2A NR2F1 NR2F6 CREB1 HCFC1 MIXL1 CCDC84 ENSG00000255121 TRAPPC4 RPL23AP64 lnc-RPS25-3
GH11J119020 Enhancer 0.8 ENCODE 98 +3.2 3236 1.9 FOXA1 NR2F6 CREB1 MIXL1 HLF ELF3 SP1 CEBPG CEBPA RXRA piR-37181 TRAPPC4 RPS25 ENSG00000283704
GH11J119025 Enhancer 0.7 Ensembl ENCODE 100.7 +5.4 5369 0.8 GATAD2B OSR2 HIC1 ZNF513 FEZF1 GLIS1 DMAP1 piR-37181 TRAPPC4 RPS25 SLC37A4 lnc-SLC37A4-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TRAPPC4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TRAPPC4 gene promoter:
  • AML1a
  • Gfi-1
  • HNF-4alpha1
  • Ik-2
  • ITF-2
  • NF-1
  • NF-1/L
  • Nkx6-1
  • Tal-1beta

Genomic Locations for TRAPPC4 Gene

Genomic Locations for TRAPPC4 Gene
chr11:119,018,432-119,025,454
(GRCh38/hg38)
Size:
7,023 bases
Orientation:
Plus strand
chr11:118,889,142-118,896,164
(GRCh37/hg19)
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 StructureGene Density

RefSeq DNA sequence for TRAPPC4 Gene

Proteins for TRAPPC4 Gene

  • 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).

    Three dimensional structures from OCA and Proteopedia for TRAPPC4 Gene

    Alternative splice isoforms for TRAPPC4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRAPPC4 Gene

Post-translational modifications for TRAPPC4 Gene

  • Ubiquitination at Lys41
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TRAPPC4 Gene

Domains & Families for TRAPPC4 Gene

Gene Families for TRAPPC4 Gene

Protein Domains for TRAPPC4 Gene

Suggested Antigen Peptide Sequences for TRAPPC4 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55104, moderately similar to Trafficking protein particle complex subunit4 (B4DME1_HUMAN)
  • TRS23 homolog (TPPC4_HUMAN)

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

Molecular function for TRAPPC4 Gene

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

Phenotypes From GWAS Catalog for TRAPPC4 Gene

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 21873635
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

CRISPR Products

Clone 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 4
golgi apparatus 4
endoplasmic reticulum 3
mitochondrion 1
nucleus 1
cytoskeleton 0

Subcellular locations from the

Human Protein Atlas (HPA)

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:0006888 ER to Golgi vesicle-mediated transport IBA 21873635
GO:0016192 vesicle-mediated transport IEA --
GO:0016358 dendrite development ISS 11018053
GO:0048208 COPII vesicle coating TAS --
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

(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

CRISPR Products

Clone 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

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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

Evidence on tissue expression from TISSUES for TRAPPC4 Gene

  • Nervous system(4.8)
  • Lung(4.4)
  • Blood(4.2)
genes like me logo Genes that share expression patterns with TRAPPC4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 32
  • 100 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TRAPPC4 33
  • 96 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TRAPPC4 33
  • 92 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Trappc4 17 33 32
  • 91.17 (n)
rat
(Rattus norvegicus)
Mammalia Trappc4 32
  • 90.72 (n)
dog
(Canis familiaris)
Mammalia TRAPPC4 33 32
  • 90.56 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TRAPPC4 33 32
  • 90.41 (n)
OneToOne
chicken
(Gallus gallus)
Aves TRAPPC4 33 32
  • 78.54 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TRAPPC4 33
  • 88 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia trappc4 32
  • 76.56 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.11434 32
zebrafish
(Danio rerio)
Actinopterygii trappc4 33 32
  • 75.95 (n)
OneToOne
zgc73260 32
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008106 32
  • 61.37 (n)
fruit fly
(Drosophila melanogaster)
Insecta Trs23 33 32
  • 61.03 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea F36D4.2 32
  • 53.24 (n)
trpp-4 33
  • 47 (a)
OneToOne
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D12144g 32
  • 50.15 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR459W 32
  • 45.57 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRS23 35 33 32
  • 43.55 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G02280 32
  • 58.81 (n)
rice
(Oryza sativa)
Liliopsida Os07g0454700 32
  • 56.92 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU11085 32
  • 57.2 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes trs23 32
  • 56.77 (n)
sea squirt
(Ciona savignyi)
Ascidiacea Cin.7090 32
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7090 32
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)
Aminode:
Evolutionary constrained regions (ECRs) for TRAPPC4: view image

Paralogs for TRAPPC4 Gene

Paralogs for TRAPPC4 Gene

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

Variants for TRAPPC4 Gene

Sequence variations from dbSNP and Humsavar for TRAPPC4 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs11006 benign, Glycogen storage disease, type I 119,024,492(+) A/G downstream_transcript_variant
rs886047744 uncertain-significance, Glycogen storage disease, type I 119,024,550(+) G/A/C downstream_transcript_variant
rs886047745 uncertain-significance, Glycogen storage disease, type I 119,024,612(+) G/A downstream_transcript_variant
rs886047746 uncertain-significance, Glycogen storage disease, type I 119,024,627(+) A/G downstream_transcript_variant
rs1000178354 -- 119,021,545(+) C/T intron_variant

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

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

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)

Additional Variant Information 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

Additional Disease Information for TRAPPC4

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

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 CH … Lin W (Genome research 2000) 2 3 4 56
  2. C4orf41 and TTC-15 are mammalian TRAPP components with a role at an early stage in ER-to-Golgi trafficking. (PMID: 21525244) Scrivens PJ … Sacher M (Molecular biology of the cell 2011) 3 4 56
  3. Single-cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene. (PMID: 20035503) Elstner M … Turnbull DM (Annals of neurology 2009) 3 43 56
  4. Crystal structure of human synbindin reveals two conformations of longin domain. (PMID: 18466758) Fan S … Gong W (Biochemical and biophysical research communications 2009) 3 23 56
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 56

Products for TRAPPC4 Gene

Sources for TRAPPC4 Gene