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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):
Expressed in all
HPA (normal tissue):
Expressed in all
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
PDCD6 (HGNC Symbol)
Synonyms
ALG-2, PEF1B
Description
Programmed cell death 6 (HGNC Symbol)
Entrez gene summary
This gene encodes a calcium-binding protein belonging to the penta-EF-hand protein family. Calcium binding is important for homodimerization and for conformational changes required for binding to other protein partners. This gene product participates in T cell receptor-, Fas-, and glucocorticoid-induced programmed cell death. In mice deficient for this gene product, however, apoptosis was not blocked suggesting this gene product is functionally redundant. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is also located on the short arm of chromosome 5. [provided by RefSeq, May 2012]
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.
PDCD6-001
PDCD6-006
PDCD6-008
PDCD6-011
PDCD6-012
PDCD6-201
PDCD6-202
PDCD6-203
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.
O75340 [Direct mapping] Programmed cell death protein 6
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Transporters Primary Active Transporters Predicted intracellular proteins Plasma proteins Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
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GO:0001525 [angiogenesis] GO:0001938 [positive regulation of endothelial cell proliferation] GO:0004198 [calcium-dependent cysteine-type endopeptidase activity] GO:0005509 [calcium ion binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005737 [cytoplasm] GO:0005768 [endosome] GO:0005783 [endoplasmic reticulum] GO:0005789 [endoplasmic reticulum membrane] GO:0006508 [proteolysis] GO:0006886 [intracellular protein transport] GO:0006915 [apoptotic process] GO:0006919 [activation of cysteine-type endopeptidase activity involved in apoptotic process] GO:0010595 [positive regulation of endothelial cell migration] GO:0016020 [membrane] GO:0030948 [negative regulation of vascular endothelial growth factor receptor signaling pathway] GO:0031410 [cytoplasmic vesicle] GO:0031965 [nuclear membrane] GO:0032007 [negative regulation of TOR signaling] GO:0034605 [cellular response to heat] GO:0036324 [vascular endothelial growth factor receptor-2 signaling pathway] GO:0042802 [identical protein binding] GO:0042803 [protein homodimerization activity] GO:0043280 [positive regulation of cysteine-type endopeptidase activity involved in apoptotic process] GO:0043495 [protein anchor] GO:0045766 [positive regulation of angiogenesis] GO:0046872 [metal ion binding] GO:0046983 [protein dimerization activity] GO:0048306 [calcium-dependent protein binding] GO:0051592 [response to calcium ion] GO:0051898 [negative regulation of protein kinase B signaling] GO:0060090 [binding, bridging] GO:0070062 [extracellular exosome] GO:0070971 [endoplasmic reticulum exit site] GO:0097190 [apoptotic signaling pathway]
The Human Protein Atlas project is funded
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