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THBD Gene(Protein Coding)

Thrombomodulin

GCID:
GC20M023026
GIFtS:
54
Genes Participants
UDN Logo

Aliases for THBD Gene

Aliases for THBD Gene

  • Thrombomodulin 2 3 3 5
  • CD141 Antigen 3 4
  • Fetomodulin 3 4
  • THRM 3 4
  • TM 3 4
  • THPH12 3
  • AHUS6 3
  • BDCA3 3
  • CD141 3

External Ids for THBD Gene

Previous GeneCards Identifiers for THBD Gene

  • GC20M023014
  • GC20M023021
  • GC20M022974

Summaries for THBD Gene

Entrez Gene Summary for THBD Gene

  • The protein encoded by this intronless gene is an endothelial-specific type I membrane receptor that binds thrombin. This binding results in the activation of protein C, which degrades clotting factors Va and VIIIa and reduces the amount of thrombin generated. Mutations in this gene are a cause of thromboembolic disease, also known as inherited thrombophilia. [provided by RefSeq, Jul 2008]

GeneCards Summary for THBD Gene

THBD (Thrombomodulin) is a Protein Coding gene. Diseases associated with THBD include Thrombophilia Due To Thrombomodulin Defect and Hemolytic Uremic Syndrome, Atypical 6. Among its related pathways are Complement and coagulation cascades and Response to elevated platelet cytosolic Ca2+. Gene Ontology (GO) annotations related to this gene include calcium ion binding and transmembrane signaling receptor activity. An important paralog of this gene is CD93.

UniProtKB/Swiss-Prot for THBD Gene

  • Thrombomodulin is a specific endothelial cell receptor that forms a 1:1 stoichiometric complex with thrombin. This complex is responsible for the conversion of protein C to the activated protein C (protein Ca). Once evolved, protein Ca scissions the activated cofactors of the coagulation mechanism, factor Va and factor VIIIa, and thereby reduces the amount of thrombin generated.

Gene Wiki entry for THBD Gene

Additional gene information for THBD Gene

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

Genomics for THBD Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for THBD Gene

Promoters and enhancers for THBD 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
GH20I023047 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 553.7 -0.2 -191 5 CLOCK ATF1 SIN3A GLIS2 ARID2 ZNF143 ATF7 ZNF263 SP3 NCOA1 THBD GC20P023049 CD93 GZF1 GC20P023047 GC20P023071
GH20I023141 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 17.7 -102.3 -102268 22 PKNOX1 SMAD1 FOXA2 MLX ARID4B YBX1 DMAP1 IRF4 SLC30A9 POLR2B CD93 NXT1 THBD ENSG00000230387 GZF1 CST3 ENSG00000279164 RNA5SP478 LOC100505664
GH20I023245 Enhancer 1.3 FANTOM5 Ensembl ENCODE 13.1 -196.2 -196159 0.6 HDGF ARNT NEUROD1 YBX1 ZNF2 ZBTB7B IRF4 TCF12 ZNF280A ARID2 NXT1 THBD CD93 NAPB ENSG00000230387 ENSG00000277901
GH20I023080 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 6.5 -34.8 -34756 8 CTCF PKNOX1 TAF1 JUN ETV1 TAL1 MAX EBF1 ZIC2 RAD21 CD93 THBD GZF1 ENSG00000279447
GH20I023059 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 8.1 -11.7 -11657 3.4 MEIS2 CTCF PKNOX1 JUN TEAD4 TAL1 MAX EBF1 FEZF1 RAD21 CD93 ENSG00000234646 LOC101929707 THBD GC20P023071 GC20P023049
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around THBD on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for THBD Gene

Genomic Locations for THBD Gene
chr20:23,045,633-23,049,741
(GRCh38/hg38)
Size:
4,109 bases
Orientation:
Minus strand
chr20:23,026,270-23,030,378
(GRCh37/hg19)

Genomic View for THBD Gene

Genes around THBD on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for THBD Gene

Proteins for THBD Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    P07204-TRBM_HUMAN
    Recommended name:
    Thrombomodulin
    Protein Accession:
    P07204
    Secondary Accessions:
    • Q8IV29
    • Q9UC32

    Protein attributes for THBD Gene

    Size:
    575 amino acids
    Molecular mass:
    60329 Da
    Quaternary structure:
    • Interacts with ITGAL, ITGAM and ITGB2.

    Three dimensional structures from OCA and Proteopedia for THBD Gene

neXtProt entry for THBD Gene

Protein Expression for THBD Gene

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

Post-translational modifications for THBD Gene

  • N-glycosylated.
  • The iron and 2-oxoglutarate dependent 3-hydroxylation of aspartate and asparagine is (R) stereospecific within EGF domains.
  • Glycosylation at posLast=4747, isoforms=115, posLast=116116, isoforms=382, isoforms=409, posLast=490490, and isoforms=492

Other Protein References for THBD Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for THBD Gene

Domains & Families for THBD Gene

Gene Families for THBD Gene

HGNC:
Human Protein Atlas (HPA):
  • Candidate cardiovascular disease genes
  • CD markers
  • Disease related genes
  • Predicted membrane proteins

Protein Domains for THBD Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for THBD Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P07204

UniProtKB/Swiss-Prot:

TRBM_HUMAN :
  • Extracellular region (481-515) contains a binding side for alpha-L/beta-2 and alpha-M/beta-2 integrin.
Domain:
  • Extracellular region (481-515) contains a binding side for alpha-L/beta-2 and alpha-M/beta-2 integrin.
genes like me logo Genes that share domains with THBD: view

Function for THBD Gene

Products:

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

Molecular function for THBD Gene

GENATLAS Biochemistry:
thrombomodulin coagulation factor complexing with thrombin,the complex activating PROC,with mutations in the promoter region putatively associated with a risk for arterial thrombosis and myocardial infarction
UniProtKB/Swiss-Prot Function:
Thrombomodulin is a specific endothelial cell receptor that forms a 1:1 stoichiometric complex with thrombin. This complex is responsible for the conversion of protein C to the activated protein C (protein Ca). Once evolved, protein Ca scissions the activated cofactors of the coagulation mechanism, factor Va and factor VIIIa, and thereby reduces the amount of thrombin generated.

Phenotypes From GWAS Catalog for THBD Gene

Gene Ontology (GO) - Molecular Function for THBD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity TAS 2822087
GO:0004888 transmembrane signaling receptor activity IEA --
GO:0005509 calcium ion binding IEA,TAS --
GO:0005515 protein binding IPI 14691232
genes like me logo Genes that share ontologies with THBD: view
genes like me logo Genes that share phenotypes with THBD: view

Human Phenotype Ontology for THBD Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for THBD Gene

MGI Knock Outs for THBD:

Animal Model Products

Clone Products

  • R&D Systems cDNA Clones for THBD (Thrombomodulin/BDCA-3)

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for THBD Gene

Localization for THBD Gene

Subcellular locations from UniProtKB/Swiss-Prot for THBD Gene

Membrane; Single-pass type I membrane protein.

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 THBD gene
Compartment Confidence
plasma membrane 5
extracellular 4
cytoskeleton 2
nucleus 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for THBD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IEA --
GO:0005774 vacuolar membrane IEA --
GO:0005886 plasma membrane IEA,TAS --
GO:0005887 integral component of plasma membrane TAS,IEA --
GO:0009986 cell surface IDA 17379830
genes like me logo Genes that share ontologies with THBD: view

Pathways & Interactions for THBD Gene

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

Gene Ontology (GO) - Biological Process for THBD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
GO:0007565 female pregnancy IEA --
GO:0007596 blood coagulation TAS --
GO:0007599 hemostasis IEA --
GO:0010165 response to X-ray IEA --
genes like me logo Genes that share ontologies with THBD: view

No data available for SIGNOR curated interactions for THBD Gene

Drugs & Compounds for THBD Gene

Products:

  1. Drug

(77) Drugs for THBD Gene - From: DrugBank, PharmGKB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Warfarin Approved Pharma 505
Dexibuprofen Approved, Investigational Pharma Target, modulator 0
Drotrecogin alfa Approved, Investigational, Withdrawn Pharma Target 0
Ibuprofen Approved Pharma Channel blocker, Target, modulator 547

(61) Additional Compounds for THBD Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with THBD: view

Transcripts for THBD Gene

Products:

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

mRNA/cDNA for THBD Gene

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

Unigene Clusters for THBD Gene

Thrombomodulin:
Representative Sequences:

Clone Products

  • R&D Systems cDNA Clones for THBD (Thrombomodulin/BDCA-3)

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

No ASD Table

Relevant External Links for THBD Gene

GeneLoc Exon Structure for
THBD
ECgene alternative splicing isoforms for
THBD

Expression for THBD Gene

Products:

  1. Primer

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

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for THBD Gene

This gene is overexpressed in Pancreas (55.9).

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



NURSA nuclear receptor signaling pathways regulating expression of THBD Gene:

THBD

SOURCE GeneReport for Unigene cluster for THBD Gene:

Hs.2030

mRNA Expression by UniProt/SwissProt for THBD Gene:

P07204-TRBM_HUMAN
Tissue specificity: Endothelial cells are unique in synthesizing thrombomodulin.

Evidence on tissue expression from TISSUES for THBD Gene

  • Lung(4.7)
  • Nervous system(4.5)
  • Heart(3.5)
  • Blood(3.2)
  • Spleen(3.2)
  • Lymph node(2.6)
  • Muscle(2.5)
  • Skin(2.5)
  • Kidney(2.2)
  • Liver(2.1)
  • Pancreas(2.1)
  • Bone marrow(2)
  • Intestine(2)

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • urinary
Organs:
Head and neck:
  • brain
  • ear
  • head
Thorax:
  • heart
  • lung
Abdomen:
  • kidney
  • liver
  • pancreas
General:
  • blood
  • blood vessel
  • coagulation system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with THBD: view

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for THBD Gene

Orthologs for THBD Gene

This gene was present in the common ancestor of chordates.

Orthologs for THBD Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia THBD 33 34
  • 99.25 (n)
dog
(Canis familiaris)
 Mammalia THBD 33 34
  • 80.45 (n)
cow
(Bos Taurus)
 Mammalia THBD 33 34
  • 77.93 (n)
mouse
(Mus musculus)
 Mammalia Thbd 33 16 34
  • 73.53 (n)
rat
(Rattus norvegicus)
 Mammalia Thbd 33
  • 71.95 (n)
oppossum
(Monodelphis domestica)
 Mammalia THBD 34
  • 46 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia THBD 34
  • 40 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves THBD 33 34
  • 58.88 (n)
tropical clawed frog
(Silurana tropicalis)
 Amphibia thbd 33
  • 49.37 (n)
zebrafish
(Danio rerio)
 Actinopterygii THBD 34
  • 27 (a)
 OneToOne
Species where no ortholog for THBD 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for THBD Gene

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

Paralogs for THBD Gene

Paralogs for THBD Gene

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

Variants for THBD Gene

Sequence variations from dbSNP and Humsavar for THBD Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1039499682 uncertain-significance, Atypical hemolytic uremic syndrome 23,045,908(-) C/T 3_prime_UTR_variant
rs1042579 benign, Atypical hemolytic uremic syndrome 23,048,087(-) G/A/T coding_sequence_variant, missense_variant
rs1042580 benign, Atypical hemolytic uremic syndrome 23,046,984(-) T/C 3_prime_UTR_variant
rs113252822 likely-benign, Atypical hemolytic uremic syndrome 23,046,007(-) A/G 3_prime_UTR_variant
rs11696919 likely-benign, Atypical hemolytic uremic syndrome 23,047,426(-) T/C 3_prime_UTR_variant

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

Variant ID Type Subtype PubMed ID
esv2758789 CNV loss 17122850
nsv482065 CNV gain 20164927

Variation tolerance for THBD Gene

Residual Variation Intolerance Score: 78.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.10; 69.11% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for THBD Gene

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

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

Disorders for THBD Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
thrombophilia due to thrombomodulin defect
  • thph12
hemolytic uremic syndrome, atypical 6
  • hemolytic uremic syndrome, atypical, susceptibility to, 6
thrombosis
  • thrombosis of blood vessel
dengue shock syndrome
  • dss
sarcomatoid mesothelioma
  • malignant fibrous mesothelioma
- elite association - COSMIC cancer census association via MalaCards
Search THBD in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TRBM_HUMAN
  • Hemolytic uremic syndrome atypical 6 (AHUS6) [MIM:612926]: An atypical form of hemolytic uremic syndrome. It is a complex genetic disease characterized by microangiopathic hemolytic anemia, thrombocytopenia, renal failure and absence of episodes of enterocolitis and diarrhea. In contrast to typical hemolytic uremic syndrome, atypical forms have a poorer prognosis, with higher death rates and frequent progression to end-stage renal disease. {ECO:0000269 PubMed:19625716, ECO:0000269 PubMed:20513133}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. Other genes may play a role in modifying the phenotype.
  • Thrombophilia due to thrombomodulin defect (THPH12) [MIM:614486]: A hemostatic disorder characterized by a tendency to thrombosis. {ECO:0000269 PubMed:12139752, ECO:0000269 PubMed:7811989, ECO:0000269 PubMed:9198186}. Note=The disease may be caused by mutations affecting the gene represented in this entry. The role of thrombomodulin in thrombosis is controversial. It is likely that genetic or environmental risk factors in addition to THBD variation are involved in the pathogenesis of venous thrombosis.

Genatlas disease for THBD Gene

thrombosis,recurrent

Additional Disease Information for THBD

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with THBD: view

Publications for THBD Gene

  1. Thrombomodulin mutations in atypical hemolytic-uremic syndrome. (PMID: 19625716) Delvaeye M … Conway EM (The New England journal of medicine 2009) 3 4 22 44 58
  2. Thrombomodulin Ala455Val polymorphism and risk of coronary heart disease. (PMID: 11245641) Wu KK … Atherosclerosis Risk in Communities Study (ARIC) Investigators (Circulation 2001) 3 4 22 44 58
  3. Mutations in alternative pathway complement proteins in American patients with atypical hemolytic uremic syndrome. (PMID: 20513133) Maga TK … Smith RJ (Human mutation 2010) 3 4 44 58
  4. Thrombomodulin gene polymorphisms or haplotypes as potential risk factors for venous thromboembolism: a population-based case-control study. (PMID: 15842356) Heit JA … Melton LJ (Journal of thrombosis and haemostasis : JTH 2005) 3 22 44 58
  5. Genetic risk for restenosis after coronary balloon angioplasty. (PMID: 15135268) Horibe H … Yokota M (Atherosclerosis 2004) 3 22 44 58

Products for THBD Gene

Sources for THBD Gene

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