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

TMED3 Gene(Protein Coding)

Transmembrane P24 Trafficking Protein 3

GCID:
GC15P079311
GIFtS:
43
Genes Participants
UDN Logo

Aliases for TMED3 Gene

Aliases for TMED3 Gene

  • Transmembrane P24 Trafficking Protein 3 2 3 5
  • Transmembrane Emp24 Protein Transport Domain Containing 3 2 3
  • P24 Family Protein Gamma-4 3 4
  • Membrane Protein P24B 3 4
  • P24gamma4 3 4
  • C15orf22 3 4
  • P26 3 4
  • Transmembrane Emp24 Domain-Containing Protein 3 3
  • Testis Tissue Sperm-Binding Protein Li 48e 3
  • Transmembrane Emp24 Domain Containing 3 2
  • Chromosome 15 Open Reading Frame 22 2
  • Integral Type I Protein 3
  • P24g4 3
  • P24B 3

External Ids for TMED3 Gene

Previous HGNC Symbols for TMED3 Gene

  • C15orf22

Previous GeneCards Identifiers for TMED3 Gene

  • GC15P077391
  • GC15P079603
  • GC15P056361

Summaries for TMED3 Gene

GeneCards Summary for TMED3 Gene

TMED3 (Transmembrane P24 Trafficking Protein 3) is a Protein Coding gene. Diseases associated with TMED3 include Keratoconus. Among its related pathways are Transport to the Golgi and subsequent modification and Metabolism of proteins. An important paralog of this gene is TMED7.

UniProtKB/Swiss-Prot for TMED3 Gene

  • Potential role in vesicular protein trafficking, mainly in the early secretory pathway. Contributes to the coupled localization of TMED2 and TMED10 in the cis-Golgi network.

Additional gene information for TMED3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TMED3 Gene

Genomics for TMED3 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for TMED3 Gene

Promoters and enhancers for TMED3 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
GH15I079310 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 +0.5 500 2 PKNOX1 ATF1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B ZNF48 POLR2B ELK1 TMED3 KIAA1024 GC15P079414
GH15I079987 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 4.5 +677.9 677948 4 CTCF MEIS2 PKNOX1 MAX EBF1 RAD21 RELA GATA3 SCRT2 HNF4G ENSG00000279719 BCL2A1 RNU6-667P ST20 TMED3 ZFAND6 LOC100420205
GH15I078969 Enhancer 1 Ensembl ENCODE 5.5 -340.7 -340665 1.7 CEBPG ZNF644 THRB RAD21 RARA YY1 TEAD3 POLR2A HNF4G MIXL1 RASGRF1 TMED3 GC15M078960 LOC100129540
GH15I079370 Enhancer 0.5 ENCODE 5.1 +59.9 59872 0.2 MEIS2 TEAD4 TAL1 CEBPB HMBOX1 CBFA2T3 CEBPG KIAA1024 RNU6-667P TMED3 GC15P079414
GH15I079364 Enhancer 0.4 ENCODE 5.2 +54.6 54554 2.3 MAFG NFE2 KIAA1024 RNU6-667P TMED3 GC15P079414
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TMED3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TMED3 gene promoter:

Genomic Locations for TMED3 Gene

Genomic Locations for TMED3 Gene
chr15:79,311,062-79,427,432
(GRCh38/hg38)
Size:
116,371 bases
Orientation:
Plus strand
chr15:79,603,404-79,704,334
(GRCh37/hg19)

Genomic View for TMED3 Gene

Genes around TMED3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TMED3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TMED3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TMED3 Gene

Proteins for TMED3 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for TMED3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y3Q3-TMED3_HUMAN
    Recommended name:
    Transmembrane emp24 domain-containing protein 3
    Protein Accession:
    Q9Y3Q3
    Secondary Accessions:
    • A8K069
    • B4DN05
    • Q2T9F8

    Protein attributes for TMED3 Gene

    Size:
    217 amino acids
    Molecular mass:
    24777 Da
    Quaternary structure:
    • Monomer in endoplasmic reticulum, endoplasmic reticulum-Golgi intermediate compartment and cis-Golgi network. Interacts (via C-terminus) with COPG1; the interaction involves dimeric TMED3; however, there are conflicting reports on the interaction. Interacts with GORASP1 and GORASP2 (By similarity).

    Alternative splice isoforms for TMED3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TMED3 Gene

Protein Expression for TMED3 Gene

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

Post-translational modifications for TMED3 Gene

No Post-translational modifications

Other Protein References for TMED3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TMED3 Gene

Domains & Families for TMED3 Gene

Gene Families for TMED3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Predicted secreted proteins
  • Transporters

Protein Domains for TMED3 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TMED3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y3Q3

UniProtKB/Swiss-Prot:

TMED3_HUMAN :
  • Belongs to the EMP24/GP25L family.
Family:
  • Belongs to the EMP24/GP25L family.
genes like me logo Genes that share domains with TMED3: view

Function for TMED3 Gene

Products:

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

Molecular function for TMED3 Gene

UniProtKB/Swiss-Prot Function:
Potential role in vesicular protein trafficking, mainly in the early secretory pathway. Contributes to the coupled localization of TMED2 and TMED10 in the cis-Golgi network.

Phenotypes From GWAS Catalog for TMED3 Gene

genes like me logo Genes that share phenotypes with TMED3: view

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TMED3 Gene

Localization for TMED3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TMED3 Gene

Endoplasmic reticulum-Golgi intermediate compartment membrane; Single-pass type I membrane protein. Golgi apparatus, cis-Golgi network membrane; Single-pass type I membrane protein. Golgi apparatus, Golgi stack membrane; Single-pass type I membrane protein. Endoplasmic reticulum membrane; Single-pass type I membrane protein. Cytoplasmic vesicle, COPI-coated vesicle membrane; Single-pass type I membrane protein. Note=Probably cycles between compartments of the early secretatory pathway. {ECO:0000269 PubMed:10852829}.

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 TMED3 gene
Compartment Confidence
endoplasmic reticulum 5
golgi apparatus 5
mitochondrion 2
plasma membrane 1
extracellular 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TMED3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005783 endoplasmic reticulum IDA,IEA 12237308
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005793 endoplasmic reticulum-Golgi intermediate compartment IDA 12237308
GO:0005794 Golgi apparatus IDA 12237308
genes like me logo Genes that share ontologies with TMED3: view

Pathways & Interactions for TMED3 Gene

genes like me logo Genes that share pathways with TMED3: view

Gene Ontology (GO) - Biological Process for TMED3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006888 ER to Golgi vesicle-mediated transport TAS --
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER TAS --
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with TMED3: view

No data available for SIGNOR curated interactions for TMED3 Gene

Drugs & Compounds for TMED3 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for TMED3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for TMED3 Gene

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

Unigene Clusters for TMED3 Gene

Transmembrane emp24 protein transport domain containing 3:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for TMED3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d
SP1: - - -
SP2: -
SP3: - -
SP4:

Relevant External Links for TMED3 Gene

GeneLoc Exon Structure for
TMED3
ECgene alternative splicing isoforms for
TMED3

Expression for TMED3 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TMED3 Gene

mRNA expression in normal human tissues for TMED3 Gene
mRNA expression by BioGPS for TMED3 GenemRNA expression by GTEx for TMED3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TMED3 Gene

This gene is overexpressed in Skin (15.8), Hair follicle (15.1), and Breast (8.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TMED3 Gene



NURSA nuclear receptor signaling pathways regulating expression of TMED3 Gene:

TMED3

SOURCE GeneReport for Unigene cluster for TMED3 Gene:

Hs.513058

Evidence on tissue expression from TISSUES for TMED3 Gene

  • Lung(4.6)
  • Skin(4.6)
  • Kidney(4.2)
  • Nervous system(3.8)
  • Pancreas(2.8)
  • Intestine(2.2)
genes like me logo Genes that share expression patterns with TMED3: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TMED3 Gene

Orthologs for TMED3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for TMED3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia TMED3 33 34
  • 99.39 (n)
cow
(Bos Taurus)
 Mammalia TMED3 34
  • 91 (a)
 OneToOne
LOC539132 33
  • 89.4 (n)
dog
(Canis familiaris)
 Mammalia TMED3 33 34
  • 88.05 (n)
mouse
(Mus musculus)
 Mammalia Tmed3 33 16 34
  • 87.54 (n)
rat
(Rattus norvegicus)
 Mammalia Tmed3 33
  • 87.1 (n)
oppossum
(Monodelphis domestica)
 Mammalia TMED3 34
  • 75 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia TICAM2 34
  • 5 (a)
 ManyToMany
chicken
(Gallus gallus)
 Aves TMED3 33 34
  • 78.35 (n)
zebrafish
(Danio rerio)
 Actinopterygii tmed3 33 34
  • 66.3 (n)
wufb09b11 33
fruit fly
(Drosophila melanogaster)
 Insecta p24-1 34
  • 44 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea F57B10.5 34
  • 50 (a)
 OneToMany
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes EMP24 34
  • 22 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.9127 34
  • 49 (a)
 OneToMany
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.11649 33
Species where no ortholog for TMED3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • 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 (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for TMED3 Gene

ENSEMBL:
Gene Tree for TMED3 (if available)
TreeFam:
Gene Tree for TMED3 (if available)

Paralogs for TMED3 Gene

Paralogs for TMED3 Gene

(4) SIMAP similar genes for TMED3 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with TMED3: view

Variants for TMED3 Gene

Sequence variations from dbSNP and Humsavar for TMED3 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1000018760 -- 79,396,404(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000027629 -- 79,420,160(+) AAAAA/AAAAAA downstream_transcript_variant
rs1000027917 -- 79,354,747(+) G/T genic_downstream_transcript_variant, intron_variant
rs1000039156 -- 79,354,904(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000077196 -- 79,383,553(+) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TMED3 Gene

Variant ID Type Subtype PubMed ID
nsv474241 CNV novel sequence insertion 20440878
nsv524829 CNV loss 19592680

Variation tolerance for TMED3 Gene

Residual Variation Intolerance Score: 72.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.16; 51.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TMED3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TMED3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TMED3 Gene

Disorders for TMED3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TMED3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
keratoconus
  • conical cornea
- elite association - COSMIC cancer census association via MalaCards
Search TMED3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for TMED3

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TMED3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TMED3 Gene

Publications for TMED3 Gene

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4 58
  2. 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 58
  3. Oligomeric state and stoichiometry of p24 proteins in the early secretory pathway. (PMID: 12237308) Jenne N … Wieland FT (The Journal of biological chemistry 2002) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58

Products for TMED3 Gene

Sources for TMED3 Gene

Content
Loading form....