Free for academic non-profit institutions. Other users need a Commercial license

Aliases for TRAPPC2 Gene

Aliases for TRAPPC2 Gene

  • Trafficking Protein Particle Complex 2 2 3 5
  • Sedlin 3 4
  • SEDL 3 4
  • Trafficking Protein Particle Complex Subunit 2 3
  • Spondyloepiphyseal Dysplasia, Late 2
  • TRAPPC2P1 3
  • HYP38334 3
  • ZNF547L 3
  • MIP2A 3
  • TRS20 3
  • SEDT 3

External Ids for TRAPPC2 Gene

Previous HGNC Symbols for TRAPPC2 Gene

  • SEDL

Previous GeneCards Identifiers for TRAPPC2 Gene

  • GC00U913615
  • GC0XM013492

Summaries for TRAPPC2 Gene

Entrez Gene Summary for TRAPPC2 Gene

  • The protein encoded by this gene is thought to be part of a large multi-subunit complex involved in the targeting and fusion of endoplasmic reticulum-to-Golgi transport vesicles with their acceptor compartment. In addition, the encoded protein can bind c-myc promoter-binding protein 1 and block its transcriptional repression capability. Mutations in this gene are a cause of spondyloepiphyseal dysplasia tarda (SEDT). A processed pseudogene of this gene is located on chromosome 19, and other pseudogenes are found on chromosomes 8 and Y. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2010]

GeneCards Summary for TRAPPC2 Gene

TRAPPC2 (Trafficking Protein Particle Complex 2) is a Protein Coding gene. Diseases associated with TRAPPC2 include Spondyloepiphyseal Dysplasia Tarda, X-Linked and Spondyloepiphyseal Dysplasia With Congenital Joint Dislocations. Among its related pathways are Metabolism of proteins and Transport to the Golgi and subsequent modification. Gene Ontology (GO) annotations related to this gene include transcription factor binding and ion channel binding. An important paralog of this gene is TRAPPC2B.

UniProtKB/Swiss-Prot for TRAPPC2 Gene

  • Prevents transcriptional repression and induction of cell death by ENO1 (By similarity). May play a role in vesicular transport from endoplasmic reticulum to Golgi.

Gene Wiki entry for TRAPPC2 Gene

Additional gene information for TRAPPC2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRAPPC2 Gene

Genomics for TRAPPC2 Gene

GeneHancer (GH) Regulatory Elements for TRAPPC2 Gene

Promoters and enhancers for TRAPPC2 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
GH0XI013732 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 +0.0 11 5.2 HDGF PKNOX1 CLOCK SMAD1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 OFD1 TRAPPC2
GH0XI013687 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE 9.6 +43.0 43038 7.2 PKNOX1 ARNT SIN3A DMAP1 ZNF2 YY1 POLR2B SP3 SMARCB1 KAT8 RAB9A OFD1 TCEANC TRAPPC2 ATXN3L
GH0XI013696 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 9.1 +36.3 36259 3.9 HDGF ATF1 PKNOX1 SMAD1 INSM2 KLF17 ZNF366 ATF7 IKZF2 CREM RAB9A OFD1 TRAPPC2
GH0XI013720 Enhancer 0.9 Ensembl ENCODE 14.8 +12.8 12837 3.2 INSM2 ZNF664 ZNF366 ZNF639 SCRT1 SMARCE1 ZNF362 ZNF189 CBFA2T3 ZEB2 TRAPPC2 RAB9A OFD1
GH0XI013715 Enhancer 0.6 Ensembl ENCODE 15 +16.9 16876 4.3 ZFP69B ZNF362 ZNF692 TRAPPC2 OFD1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TRAPPC2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TRAPPC2 gene promoter:

Genomic Locations for TRAPPC2 Gene

Genomic Locations for TRAPPC2 Gene
chrX:13,712,242-13,734,635
(GRCh38/hg38)
Size:
22,394 bases
Orientation:
Minus strand
chrX:13,730,361-13,752,754
(GRCh37/hg19)

Genomic View for TRAPPC2 Gene

Genes around TRAPPC2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRAPPC2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRAPPC2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRAPPC2 Gene

Proteins for TRAPPC2 Gene

  • Protein details for TRAPPC2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P0DI81-TPC2A_HUMAN
    Recommended name:
    Trafficking protein particle complex subunit 2
    Protein Accession:
    P0DI81
    Secondary Accessions:
    • A6NEG0
    • O14582
    • Q9HD16

    Protein attributes for TRAPPC2 Gene

    Size:
    140 amino acids
    Molecular mass:
    16445 Da
    Quaternary structure:
    • Can homodimerize. Component of the multisubunit TRAPP (transport protein particle) complex, which includes TRAPPC2, TRAPPC2L, TRAPPC3, TRAPPC3L, TRAPPC4, TRAPPC5, TRAPPC8, TRAPPC9, TRAPPC10, TRAPPC11 and TRAPPC12. Interacts with ENO1, PITX1 and SF1.
    Miscellaneous:
    • A paralogous gene encoding an identical protein appears to have arisen by retrotransposition of a cDNA from this locus and to have acquired a promoter and non-coding 5 UTR from the ZNF547 gene.

    Alternative splice isoforms for TRAPPC2 Gene

neXtProt entry for TRAPPC2 Gene

Post-translational modifications for TRAPPC2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for TRAPPC2 Gene

Domains & Families for TRAPPC2 Gene

Gene Families for TRAPPC2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for TRAPPC2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for TRAPPC2 Gene

Graphical View of Domain Structure for InterPro Entry

P0DI81

UniProtKB/Swiss-Prot:

TPC2A_HUMAN :
  • Belongs to the TRAPP small subunits family. Sedlin subfamily.
Family:
  • Belongs to the TRAPP small subunits family. Sedlin subfamily.
genes like me logo Genes that share domains with TRAPPC2: view

Function for TRAPPC2 Gene

Molecular function for TRAPPC2 Gene

UniProtKB/Swiss-Prot Function:
Prevents transcriptional repression and induction of cell death by ENO1 (By similarity). May play a role in vesicular transport from endoplasmic reticulum to Golgi.

Gene Ontology (GO) - Molecular Function for TRAPPC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11134351
GO:0008134 transcription factor binding IPI 11134351
GO:0017112 Rab guanyl-nucleotide exchange factor activity TAS --
GO:0044325 ion channel binding IPI 12681486
genes like me logo Genes that share ontologies with TRAPPC2: view
genes like me logo Genes that share phenotypes with TRAPPC2: view

Human Phenotype Ontology for TRAPPC2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TRAPPC2 Gene

MGI Knock Outs for TRAPPC2:

Animal Model Products

miRNA for TRAPPC2 Gene

miRTarBase miRNAs that target TRAPPC2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for TRAPPC2 Gene

Localization for TRAPPC2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRAPPC2 Gene

Cytoplasm, perinuclear region. Endoplasmic reticulum-Golgi intermediate compartment. Nucleus. Cytoplasm. Note=Localized in perinuclear granular structures. {ECO:0000269 PubMed:11031107}.

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 TRAPPC2 gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 5
cytosol 5
golgi apparatus 2
cytoskeleton 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (3)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRAPPC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005622 intracellular IEA --
GO:0005634 nucleus IDA,ISS 25918224
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with TRAPPC2: view

Pathways & Interactions for TRAPPC2 Gene

genes like me logo Genes that share pathways with TRAPPC2: view

Gene Ontology (GO) - Biological Process for TRAPPC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IMP 10431248
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IDA 11134351
GO:0006810 transport IEA --
GO:0006888 ER to Golgi vesicle-mediated transport NAS 10431248
genes like me logo Genes that share ontologies with TRAPPC2: view

No data available for SIGNOR curated interactions for TRAPPC2 Gene

Drugs & Compounds for TRAPPC2 Gene

No Compound Related Data Available

Transcripts for TRAPPC2 Gene

Unigene Clusters for TRAPPC2 Gene

Trafficking protein particle complex 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TRAPPC2 Gene

No ASD Table

Relevant External Links for TRAPPC2 Gene

GeneLoc Exon Structure for
TRAPPC2
ECgene alternative splicing isoforms for
TRAPPC2

Expression for TRAPPC2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TRAPPC2 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for TRAPPC2 Gene



NURSA nuclear receptor signaling pathways regulating expression of TRAPPC2 Gene:

TRAPPC2

SOURCE GeneReport for Unigene cluster for TRAPPC2 Gene:

Hs.592238

mRNA Expression by UniProt/SwissProt for TRAPPC2 Gene:

P0DI81-TPC2A_HUMAN
Tissue specificity: Expressed in brain, heart, kidney, liver, lung, pancreas, placenta, skeletal muscle, fetal cartilage, fibroblasts, placenta and lymphocytes.

Evidence on tissue expression from TISSUES for TRAPPC2 Gene

  • Nervous system(3.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TRAPPC2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • immune
  • nervous
  • respiratory
  • skeleton
Regions:
Head and neck:
  • eye
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
Thorax:
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with TRAPPC2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues and Protein tissue co-expression partners for TRAPPC2 Gene

Orthologs for TRAPPC2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TRAPPC2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TRAPPC2 33 34
  • 100 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 97 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 97 (a)
ManyToMany
-- 34
  • 90 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia 0610009B22Rik 34
  • 95 (a)
ManyToMany
Trappc2 33 16 34
  • 90.71 (n)
dog
(Canis familiaris)
Mammalia TRAPPC2 33 34
  • 93.65 (n)
rat
(Rattus norvegicus)
Mammalia Trappc2 33
  • 93.1 (n)
cow
(Bos Taurus)
Mammalia TRAPPC2 33 34
  • 91.9 (n)
chicken
(Gallus gallus)
Aves TRAPPC2 33 34
  • 83.33 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 96 (a)
ManyToMany
-- 34
  • 90 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia trappc2 33
  • 79.76 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.18543 33
zebrafish
(Danio rerio)
Actinopterygii egfl6 34
  • 92 (a)
ManyToMany
trappc2 33 34
  • 78.57 (n)
Dr.16486 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002528 33
  • 65.7 (n)
fruit fly
(Drosophila melanogaster)
Insecta l(3)72Dh 33 34
  • 62.08 (n)
worm
(Caenorhabditis elegans)
Secernentea sedl-1 33 34
  • 56.13 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR246W 33
  • 54.23 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D15763g 33
  • 52.93 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRS20 33 34 36
  • 50.13 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G80500 33
  • 59.26 (n)
rice
(Oryza sativa)
Liliopsida Os02g0613600 33
  • 59.01 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 69 (a)
OneToMany
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes trs20 33
  • 53.88 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU11174 33
  • 50.25 (n)
Species where no ortholog for TRAPPC2 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 TRAPPC2 Gene

ENSEMBL:
Gene Tree for TRAPPC2 (if available)
TreeFam:
Gene Tree for TRAPPC2 (if available)

Paralogs for TRAPPC2 Gene

Paralogs for TRAPPC2 Gene

(1) SIMAP similar genes for TRAPPC2 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with TRAPPC2: view

Variants for TRAPPC2 Gene

Sequence variations from dbSNP and Humsavar for TRAPPC2 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs104894948 pathogenic, Spondyloepiphyseal dysplasia tarda, Spondyloepiphyseal dysplasia tarda (SEDT) [MIM:313400] 13,716,080(-) A/G coding_sequence_variant, missense_variant
rs104894949 pathogenic, Spondyloepiphyseal dysplasia tarda 13,714,501(-) G/T coding_sequence_variant, stop_gained
rs1057515788 uncertain-significance, Spondyloepiphyseal dysplasia 13,712,347(-) C/T 3_prime_UTR_variant
rs1057515789 uncertain-significance, Spondyloepiphyseal dysplasia 13,713,216(-) G/A 3_prime_UTR_variant
rs1057515790 uncertain-significance, Spondyloepiphyseal dysplasia 13,713,450(-) /AAAAAAA 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for TRAPPC2 Gene

Variant ID Type Subtype PubMed ID
nsv528634 CNV gain 19592680

Variation tolerance for TRAPPC2 Gene

Gene Damage Index Score: 0.07; 1.53% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRAPPC2 Gene

Human Gene Mutation Database (HGMD)
TRAPPC2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRAPPC2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRAPPC2 Gene

Disorders for TRAPPC2 Gene

MalaCards: The human disease database

(5) MalaCards diseases for TRAPPC2 Gene - From: HGMD, OMIM, ClinVar, GTR, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TPC2A_HUMAN
  • Spondyloepiphyseal dysplasia tarda (SEDT) [MIM:313400]: X-linked recessive disorder of endochondral bone formation. {ECO:0000269 PubMed:10431248, ECO:0000269 PubMed:11349230, ECO:0000269 PubMed:11424925}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TRAPPC2

genes like me logo Genes that share disorders with TRAPPC2: view

No data available for Genatlas for TRAPPC2 Gene

Publications for TRAPPC2 Gene

  1. Human wild-type SEDL protein functionally complements yeast Trs20p but some naturally occurring SEDL mutants do not. (PMID: 14597397) Gécz J … de Barros Lopes M (Gene 2003) 2 3 4 58
  2. A missense mutation in the SEDL gene results in delayed onset of X linked spondyloepiphyseal dysplasia in a large pedigree. (PMID: 11424925) Grunebaum E … Roifman CM (Journal of medical genetics 2001) 3 4 22 58
  3. Identification of the gene (SEDL) causing X-linked spondyloepiphyseal dysplasia tarda. (PMID: 10431248) Gedeon AK … Gécz J (Nature genetics 1999) 3 4 22 58
  4. TRAMM/TrappC12 plays a role in chromosome congression, kinetochore stability, and CENP-E recruitment. (PMID: 25918224) Milev MP … Sacher M (The Journal of cell biology 2015) 3 4 58
  5. 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 58

Products for TRAPPC2 Gene

Sources for TRAPPC2 Gene

Content
Loading form....