This gene is a member of a family of genes encoding transport proteins located in the endoplasmic reticulum and the Golgi. A similar gene in mouse is the target of microRNA miR-296, which is part of an imprinted cluster. [provided by RefSeq, Jul 2016] See more...

Aliases for TMED9 Gene

Aliases for TMED9 Gene

  • Transmembrane P24 Trafficking Protein 9 2 3 5
  • P24alpha2 2 3 4
  • Transmembrane Emp24 Protein Transport Domain Containing 9 2 3
  • Transmembrane Emp24 Domain-Containing Protein 9 3 4
  • P24 Family Protein Alpha-2 3 4
  • Glycoprotein 25L2 3 4
  • HSGP25L2G 2 3
  • GMP25 3 4
  • P24a2 2 3
  • P25 3 4
  • GP25L2 4
  • TMED9 5

External Ids for TMED9 Gene

Previous GeneCards Identifiers for TMED9 Gene

  • GC05P176952
  • GC05P171938
  • GC05P177019

Summaries for TMED9 Gene

Entrez Gene Summary for TMED9 Gene

  • This gene is a member of a family of genes encoding transport proteins located in the endoplasmic reticulum and the Golgi. A similar gene in mouse is the target of microRNA miR-296, which is part of an imprinted cluster. [provided by RefSeq, Jul 2016]

GeneCards Summary for TMED9 Gene

TMED9 (Transmembrane P24 Trafficking Protein 9) is a Protein Coding gene. Diseases associated with TMED9 include Hereditary Spastic Paraplegia. Among its related pathways are Transport to the Golgi and subsequent modification and Metabolism of proteins. Gene Ontology (GO) annotations related to this gene include syntaxin binding. An important paralog of this gene is TMED4.

UniProtKB/Swiss-Prot Summary for TMED9 Gene

  • Appears to be involved in vesicular protein trafficking, mainly in the early secretory pathway. In COPI vesicle-mediated retrograde transport involved in the coatomer recruitment to membranes of the early secretory pathway. Increases coatomer-dependent activity of ARFGAP2. Thought to play a crucial role in the specific retention of p24 complexes in cis-Golgi membranes; specifically contributes to the coupled localization of TMED2 and TMED10 in the cis-Golgi network. May be involved in organization of intracellular membranes, such as of the ER-Golgi intermediate compartment and the Golgi apparatus. Involved in ER localization of PTPN2 isoform PTPB.

Additional gene information for TMED9 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TMED9 Gene

Genomics for TMED9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TMED9 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
GH05J177591 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 606.4 +0.4 368 2.1 PRDM10 TFE3 SIX5 IKZF1 KDM1A ZNF692 POLR2A TARDBP JUND LARP7 TMED9 FAM153CP lnc-FAM193B-2 B4GALT7
GH05J177552 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 11.9 -38.0 -38019 3.2 HNRNPL CREB1 GATAD2A CTCF PRDM10 TFE3 SIX5 IKZF1 KDM1A ZNF692 ENSG00000272459 FAM193B LOC105377750 lnc-DDX41-4 DOK3 DDX41 TMED9 B4GALT7 FAM153A lnc-DDX41-3
GH05J177542 Enhancer 1.4 FANTOM5 ENCODE dbSUPER 11.8 -46.2 -46200 6.3 CEBPG GATAD2A PRDM10 ZNF629 TFE3 ZNF692 RCOR2 JUND PRDM1 PHF21A DOK3 ENSG00000272459 DDX41 TMED9 PDLIM7 MXD3 DBN1 RAB24 GRK6 NSD1
GH05J177599 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 5.4 +7.5 7498 3.8 SP1 PRDM10 ZNF629 TFE3 SIX5 NFKBIZ POLR2A ZNF692 BACH1 LARP7 B4GALT7 HSALNG0046955 PDLIM7 ZNF346 DDX41 ZNF346-IT1 FAM153A TMED9 lnc-FAM193B-2
GH05J177586 Enhancer 0.3 Ensembl 23.1 -5.4 -5402 1.2 SPI1 TMED9 FAM153CP FAM193B DDX41 ENSG00000247679 RMND5B B4GALT7 piR-60946
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TMED9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TMED9

Top Transcription factor binding sites by QIAGEN in the TMED9 gene promoter:
  • AML1a
  • AP-1
  • c-Fos
  • c-Jun
  • c-Myc
  • E47
  • ER-alpha
  • FosB
  • Fra-1
  • Max1

Genomic Locations for TMED9 Gene

Genomic Locations for TMED9 Gene
chr5:177,592,203-177,597,242
(GRCh38/hg38)
Size:
5,040 bases
Orientation:
Plus strand
chr5:177,019,159-177,023,125
(GRCh37/hg19)
Size:
3,967 bases
Orientation:
Plus strand

Genomic View for TMED9 Gene

Genes around TMED9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TMED9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TMED9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TMED9 Gene

Proteins for TMED9 Gene

  • Protein details for TMED9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BVK6-TMED9_HUMAN
    Recommended name:
    Transmembrane emp24 domain-containing protein 9
    Protein Accession:
    Q9BVK6
    Secondary Accessions:
    • Q14437
    • Q8WZ61

    Protein attributes for TMED9 Gene

    Size:
    235 amino acids
    Molecular mass:
    27277 Da
    Quaternary structure:
    • Monomer and homodimer in endoplasmic reticulum. Predominantly monomeric and to lesser extent homodimeric in endoplasmic reticulum-Golgi intermediate compartment and cis-Golgi network. Probably oligomerizes with other members of the EMP24/GP25L family such as TMED2, TMED7 and TMED10. Interacts with TMED5. Interacts (via C-terminus) with COPG1; the interaction involves dimeric TMED9. Interacts with PTPN2 and SPAST. Interacts with STX17; the interaction is direct.
    SequenceCaution:
    • Sequence=AAL35268.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=CAA62380.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

neXtProt entry for TMED9 Gene

Post-translational modifications for TMED9 Gene

  • N-linked glycosylated containing high mannose.
  • Glycosylation at Asn125
  • Ubiquitination at Lys160 and Lys180
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • TMED9_HUMAN (1846)

Other Protein References for TMED9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TMED9 Gene

Domains & Families for TMED9 Gene

Gene Families for TMED9 Gene

Protein Domains for TMED9 Gene

InterPro:
Blocks:
  • emp24/gp25L/p24 family
ProtoNet:

Suggested Antigen Peptide Sequences for TMED9 Gene

GenScript: Design optimal peptide antigens:
  • Glycoprotein 25L2 (TMED9_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BVK6

UniProtKB/Swiss-Prot:

TMED9_HUMAN :
  • Belongs to the EMP24/GP25L family.
Family:
  • Belongs to the EMP24/GP25L family.
genes like me logo Genes that share domains with TMED9: view

Function for TMED9 Gene

Molecular function for TMED9 Gene

UniProtKB/Swiss-Prot Function:
Appears to be involved in vesicular protein trafficking, mainly in the early secretory pathway. In COPI vesicle-mediated retrograde transport involved in the coatomer recruitment to membranes of the early secretory pathway. Increases coatomer-dependent activity of ARFGAP2. Thought to play a crucial role in the specific retention of p24 complexes in cis-Golgi membranes; specifically contributes to the coupled localization of TMED2 and TMED10 in the cis-Golgi network. May be involved in organization of intracellular membranes, such as of the ER-Golgi intermediate compartment and the Golgi apparatus. Involved in ER localization of PTPN2 isoform PTPB.

Phenotypes From GWAS Catalog for TMED9 Gene

Gene Ontology (GO) - Molecular Function for TMED9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16595549
GO:0019905 syntaxin binding IPI 21545355
genes like me logo Genes that share ontologies with TMED9: view
genes like me logo Genes that share phenotypes with TMED9: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TMED9

Clone Products

  • Addgene plasmids for TMED9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TMED9 Gene

Localization for TMED9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TMED9 Gene

Endoplasmic reticulum membrane. Single-pass type I membrane protein. Golgi apparatus, cis-Golgi network membrane. Single-pass type I membrane protein. Endoplasmic reticulum-Golgi intermediate compartment membrane. Single-pass type I membrane protein. Golgi apparatus, trans-Golgi network membrane. Single-pass type I membrane protein. Note=Cycles between compartments of the early secretatory pathway.

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 TMED9 gene
Compartment Confidence
endoplasmic reticulum 5
golgi apparatus 5
extracellular 4
cytosol 3
peroxisome 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
nucleus 1
endosome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for TMED9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005783 endoplasmic reticulum IBA,IDA 12237308
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005793 endoplasmic reticulum-Golgi intermediate compartment IDA 12237308
GO:0005794 Golgi apparatus IBA,IDA 12237308
genes like me logo Genes that share ontologies with TMED9: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TMED9 Gene

Pathways & Interactions for TMED9 Gene

genes like me logo Genes that share pathways with TMED9: view

Gene Ontology (GO) - Biological Process for TMED9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IBA 21873635
GO:0006888 ER to Golgi vesicle-mediated transport TAS --
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER TAS --
GO:0007030 Golgi organization IMP 18287528
GO:0010638 positive regulation of organelle organization IMP 18287528
genes like me logo Genes that share ontologies with TMED9: view

No data available for SIGNOR curated interactions for TMED9 Gene

Drugs & Compounds for TMED9 Gene

No Compound Related Data Available

Transcripts for TMED9 Gene

mRNA/cDNA for TMED9 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TMED9

Clone Products

  • Addgene plasmids for TMED9

Alternative Splicing Database (ASD) splice patterns (SP) for TMED9 Gene

No ASD Table

Relevant External Links for TMED9 Gene

GeneLoc Exon Structure for
TMED9

Expression for TMED9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TMED9 Gene

Protein differential expression in normal tissues from HIPED for TMED9 Gene

This gene is overexpressed in Nasal epithelium (32.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TMED9 Gene



Protein tissue co-expression partners for TMED9 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TMED9

SOURCE GeneReport for Unigene cluster for TMED9 Gene:

Hs.279929

Evidence on tissue expression from TISSUES for TMED9 Gene

  • Skin(4.7)
  • Liver(4.7)
  • Nervous system(4.2)
  • Lung(3.8)
  • Pancreas(3.7)
  • Kidney(3.3)
  • Intestine(2.5)
  • Blood(2.3)
  • Eye(2.3)
  • Spleen(2.1)
  • Heart(2)
genes like me logo Genes that share expression patterns with TMED9: 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 TMED9 Gene

Orthologs for TMED9 Gene

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

Orthologs for TMED9 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TMED9 30 31
  • 99.29 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TMED9 31
  • 92 (a)
OneToOne
LOC481444 30
  • 91.35 (n)
Cow
(Bos Taurus)
Mammalia TMED9 30 31
  • 89.79 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Tmed9 30 17 31
  • 87.52 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Tmed9 30
  • 87.09 (n)
Oppossum
(Monodelphis domestica)
Mammalia TMED9 31
  • 87 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TMED9 31
  • 54 (a)
OneToOne
Chicken
(Gallus gallus)
Aves -- 31
  • 51 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia TMED9 31
  • 85 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia tmed9 30
  • 75.4 (n)
Zebrafish
(Danio rerio)
Actinopterygii tmed9 30 31
  • 78.99 (n)
OneToOne
sbcb294 30
Fruit Fly
(Drosophila melanogaster)
Insecta eca 31
  • 64 (a)
ManyToMany
p24-2 31
  • 51 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea Y60A3A.9 31
  • 67 (a)
ManyToMany
T08D2.1 31
  • 55 (a)
ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ERP5 31
  • 29 (a)
ManyToMany
ERP6 31
  • 29 (a)
ManyToMany
ERP1 31 33
  • 26 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 66 (a)
OneToMany
Species where no ortholog for TMED9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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 Vase (Ciona intestinalis)
  • 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)
  • Wheat (Triticum aestivum)

Evolution for TMED9 Gene

ENSEMBL:
Gene Tree for TMED9 (if available)
TreeFam:
Gene Tree for TMED9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TMED9: view image

Paralogs for TMED9 Gene

(5) SIMAP similar genes for TMED9 Gene using alignment to 1 proteins:

  • TMED9_HUMAN
genes like me logo Genes that share paralogs with TMED9: view

Variants for TMED9 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TMED9 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
rs869025249 Uncertain Significance: Monoclonal B-Cell Lymphocytosis 177,592,291(+) T/A MISSENSE_VARIANT
rs57960711 - p.Thr16Ser

Additional dbSNP identifiers (rs#s) for TMED9 Gene

Structural Variations from Database of Genomic Variants (DGV) for TMED9 Gene

Variant ID Type Subtype PubMed ID
nsv5149 CNV insertion 18451855

Variation tolerance for TMED9 Gene

Residual Variation Intolerance Score: 38.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.15; 39.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TMED9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TMED9

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TMED9 Gene

Disorders for TMED9 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TMED9 Gene - From: GeneCards

Disorder Aliases PubMed IDs
hereditary spastic paraplegia
  • spastic paraplegia 3, autosomal dominant
- elite association - COSMIC cancer census association via MalaCards
Search TMED9 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with TMED9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TMED9 Gene

Publications for TMED9 Gene

  1. Syntaxin 17 cycles between the ER and ERGIC and is required to maintain the architecture of ERGIC and Golgi. (PMID: 21545355) Muppirala M … Swarup G (Biology of the cell 2011) 3 4
  2. The cargo receptors Surf4, endoplasmic reticulum-Golgi intermediate compartment (ERGIC)-53, and p25 are required to maintain the architecture of ERGIC and Golgi. (PMID: 18287528) Mitrovic S … Hauri HP (Molecular biology of the cell 2008) 3 4
  3. Evidence for a role of transmembrane protein p25 in localization of protein tyrosine phosphatase TC48 to the ER. (PMID: 16595549) Gupta V … Swarup G (Journal of cell science 2006) 3 4
  4. 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
  5. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. (PMID: 12754519) Zhang H … Aebersold R (Nature biotechnology 2003) 3 4

Products for TMED9 Gene

  • Signalway ELISA kits for TMED9
  • Signalway Proteins for TMED9

Sources for TMED9 Gene