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RNA category is based on mRNA expression levels in the analyzed samples (RNA assay description). The categories include: tissue/cell line enriched, group enriched, tissue/cell line enhanced, expressed in all, mixed and not detected. RNA category is calculated separately for The Cancer Genome Atlas (TCGA) data from cancer tissues and internally generated Human Protein Atlas (HPA) data from normal tissues and cell lines.
TCGA (cancer tissue):
Expressed in all
HPA (cell line):
Cell line enhanced (BJ, BJ hTERT+, RT4)
HPA (normal tissue):
Tissue enhanced (adrenal gland)
Protein evidencei
Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence, or iv) not available.
Evidence at protein level
IMMUNOHISTOCHEMISTRY DATA RELIABILITY
Reliability score - normal tissuesi
Reliability score (score description), divided into Enhanced, Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between antibody staining pattern, available RNA-Seq and gene/protein characterization data, as well as similarity between independent antibodies targeting the same protein.
Kaplan-Meier plots for all cancers where high expression of this gene has significant (p<0.001) association with patient survival are shown in this summary. Whether the prognosis is favourable or unfavourable is indicated in brackets. Each Kaplan-Meier plot is clickable and redirects to a detailed page that includes individual expression and survival data for patients with the selected cancer.
RNA expression overview shows RNA-seq data from The Cancer Genome Atlas (TCGA).
TCGA dataseti
RNA-seq data in 17 cancer types are reported as median FPKM (number Fragments Per Kilobase of exon per Million reads), generated by the The Cancer Genome Atlas (TCGA). RNA cancer tissue category is calculated based on mRNA expression levels across all 17 cancer tissues and include: cancer tissue enriched, cancer group enriched, cancer tissue enhanced, expressed in all, mixed and not detected. To access cancer specific RNA and prognostic data, click on the cancer name. The cancer types are color-coded according to which type of normal organ the cancer originates from.
Antibody staining in 20 different cancers is summarized by a selection of four standard cancer tissue samples representative of the overall staining pattern. From left: colorectal cancer, breast cancer, prostate cancer and lung cancer. An additional fifth image can be added as a complement. The assay and annotation is described here. Note that samples used for immunohistochemistry by the Human Protein Atlas do not correspond to samples in the TCGA dataset.
Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.
Gene name
TBX3 (HGNC Symbol)
Synonyms
TBX3-ISO, UMS, XHL
Description
T-box 3 (HGNC Symbol)
Entrez gene summary
This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. This protein is a transcriptional repressor and is thought to play a role in the anterior/posterior axis of the tetrapod forelimb. Mutations in this gene cause ulnar-mammary syndrome, affecting limb, apocrine gland, tooth, hair, and genital development. Alternative splicing of this gene results in three transcript variants encoding different isoforms; however, the full length nature of one variant has not been determined. [provided by RefSeq, Jul 2008]
The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.
At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.
Under the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50). The region with the lowest possible identity is always selected for antigen design, with a maximum identity of 60% allowed for designing a single-target antigen (read more).
The curve in blue displays the predicted antigenicity i.e. the tendency for different regions of the protein to generate an immune response, with peak regions being predicted to be more antigenic.The curve shows average values based on a sliding window approach using an in-house propensity scale. (read more).
If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.
Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.
TBX3-001
TBX3-002
PROTEIN INFORMATIONi
The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.
The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.
The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.
The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
Predicted intracellular proteins Plasma proteins Transcription factors Immunoglobulin fold Cancer-related genes Mutated cancer genes Mutational cancer driver genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Other Mutations COSMIC Nonsense Mutations COSMIC Missense Mutations COSMIC Frameshift Mutations Disease related genes Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000978 [RNA polymerase II core promoter proximal region sequence-specific DNA binding] GO:0001078 [transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding] GO:0001085 [RNA polymerase II transcription factor binding] GO:0001102 [RNA polymerase II activating transcription factor binding] GO:0001501 [skeletal system development] GO:0003677 [DNA binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006357 [regulation of transcription from RNA polymerase II promoter] GO:0007275 [multicellular organism development] GO:0007569 [cell aging] GO:0008284 [positive regulation of cell proliferation] GO:0008595 [anterior/posterior axis specification, embryo] GO:0009887 [animal organ morphogenesis] GO:0030539 [male genitalia development] GO:0030540 [female genitalia development] GO:0030879 [mammary gland development] GO:0032275 [luteinizing hormone secretion] GO:0035115 [embryonic forelimb morphogenesis] GO:0035136 [forelimb morphogenesis] GO:0042733 [embryonic digit morphogenesis] GO:0043066 [negative regulation of apoptotic process] GO:0043565 [sequence-specific DNA binding] GO:0045662 [negative regulation of myoblast differentiation] GO:0045787 [positive regulation of cell cycle] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0046884 [follicle-stimulating hormone secretion] GO:0048332 [mesoderm morphogenesis] GO:0090398 [cellular senescence]
SCAMPI predicted membrane proteins Predicted intracellular proteins Plasma proteins Transcription factors Immunoglobulin fold Cancer-related genes Mutated cancer genes Mutational cancer driver genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Other Mutations COSMIC Nonsense Mutations COSMIC Missense Mutations COSMIC Frameshift Mutations Disease related genes Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000978 [RNA polymerase II core promoter proximal region sequence-specific DNA binding] GO:0001078 [transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding] GO:0001085 [RNA polymerase II transcription factor binding] GO:0001102 [RNA polymerase II activating transcription factor binding] GO:0001501 [skeletal system development] GO:0001568 [blood vessel development] GO:0001701 [in utero embryonic development] GO:0001947 [heart looping] GO:0003007 [heart morphogenesis] GO:0003151 [outflow tract morphogenesis] GO:0003167 [atrioventricular bundle cell differentiation] GO:0003677 [DNA binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006357 [regulation of transcription from RNA polymerase II promoter] GO:0007275 [multicellular organism development] GO:0007569 [cell aging] GO:0008284 [positive regulation of cell proliferation] GO:0008595 [anterior/posterior axis specification, embryo] GO:0009887 [animal organ morphogenesis] GO:0010159 [specification of animal organ position] GO:0019827 [stem cell population maintenance] GO:0021761 [limbic system development] GO:0030539 [male genitalia development] GO:0030540 [female genitalia development] GO:0030857 [negative regulation of epithelial cell differentiation] GO:0030879 [mammary gland development] GO:0032275 [luteinizing hormone secretion] GO:0035050 [embryonic heart tube development] GO:0035108 [limb morphogenesis] GO:0035115 [embryonic forelimb morphogenesis] GO:0035116 [embryonic hindlimb morphogenesis] GO:0035136 [forelimb morphogenesis] GO:0042127 [regulation of cell proliferation] GO:0042733 [embryonic digit morphogenesis] GO:0043066 [negative regulation of apoptotic process] GO:0043565 [sequence-specific DNA binding] GO:0045662 [negative regulation of myoblast differentiation] GO:0045787 [positive regulation of cell cycle] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0046884 [follicle-stimulating hormone secretion] GO:0048332 [mesoderm morphogenesis] GO:0055007 [cardiac muscle cell differentiation] GO:0060021 [palate development] GO:0060412 [ventricular septum morphogenesis] GO:0060444 [branching involved in mammary gland duct morphogenesis] GO:0060596 [mammary placode formation] GO:0060923 [cardiac muscle cell fate commitment] GO:0060931 [sinoatrial node cell development] GO:0090398 [cellular senescence] GO:2000648 [positive regulation of stem cell proliferation]
The Human Protein Atlas project is funded
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