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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):
Mixed
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
Protein expression normal tissuei
A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation.
"Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile.
Cytoplasmic expression at variable levels in selected tissues, most abundant in heart muscle.
IMMUNOHISTOCHEMISTRY DATA RELIABILITY
Data reliability descriptioni
Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.
Antibody staining mainly consistent with RNA expression data. Caution, targets protein from more than one gene.
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.
Gene product is not prognostic.
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RNA EXPRESSION OVERVIEWi
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.
For each cancer, color-coded bars indicate the percentage of patients (maximum 12 patients) with high and medium protein expression level. The cancer types are color-coded according to which type of normal organ the cancer originates from. Low or not detected protein expression results in a white bar. Mouse-over function shows details about expression level and normal tissue of origin. The images and annotations can be accessed by clicking on the cancer name or protein expression bar. If more than one antibody is analyzed, the tabs at the top of the staining summary section can be used to toggle between the different antibodies.
Most malignant cells were negative. A few cases of breast and thyroid cancers showed weak cytoplasmic staining.
Cancer tissues displayed weak to moderate cytoplasmic positivity. Several cases of melanomas, skin, renal and liver cancers were negative.
Several cases of liver and endometrial cancers showed moderate to strong cytoplasmic staining while lung cancers displayed moderate positivity. Several renal and pancreatic cancers exhibited weak to moderate cytoplasmic and membranous staining. Remaining cancer tissues were weakly stained or negative.
Moderate to strong cytoplasmic positivity was observed in a few gliomas. A few cases of thyroid, urothelial, testicular, colorectal, prostate and endometrial cancers showed weak to moderate cytoplasmic immunoreactivity. Remaining cancer tissues were generally negative.
GENE INFORMATIONi
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
CAMK2D (HGNC Symbol)
Synonyms
CAMKD
Description
Calcium/calmodulin dependent protein kinase II delta (HGNC Symbol)
Entrez gene summary
The product of this gene belongs to the serine/threonine protein kinase family and to the Ca(2+)/calmodulin-dependent protein kinase subfamily. Calcium signaling is crucial for several aspects of plasticity at glutamatergic synapses. In mammalian cells, the enzyme is composed of four different chains: alpha, beta, gamma, and delta. The product of this gene is a delta chain. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Distinct isoforms of this chain have different expression patterns.[provided by RefSeq, Nov 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.
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.
Q13557 [Direct mapping] Calcium/calmodulin-dependent protein kinase type II subunit delta A0A024RDK3 [Target identity:100%; Query identity:100%] Calcium/calmodulin-dependent protein kinase (CaM kinase) II delta, isoform CRA_a
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Enzymes ENZYME proteins Transferases Kinases CAMK Ser/Thr protein kinases Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Plasma proteins Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
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GO:0000165 [MAPK cascade] GO:0000166 [nucleotide binding] GO:0001558 [regulation of cell growth] GO:0002026 [regulation of the force of heart contraction] GO:0003254 [regulation of membrane depolarization] GO:0004672 [protein kinase activity] GO:0004674 [protein serine/threonine kinase activity] GO:0004683 [calmodulin-dependent protein kinase activity] GO:0005088 [Ras guanyl-nucleotide exchange factor activity] GO:0005515 [protein binding] GO:0005516 [calmodulin binding] GO:0005524 [ATP binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005737 [cytoplasm] GO:0005829 [cytosol] GO:0005886 [plasma membrane] GO:0006357 [regulation of transcription from RNA polymerase II promoter] GO:0006468 [protein phosphorylation] GO:0007399 [nervous system development] GO:0008016 [regulation of heart contraction] GO:0010613 [positive regulation of cardiac muscle hypertrophy] GO:0010649 [regulation of cell communication by electrical coupling] GO:0010666 [positive regulation of cardiac muscle cell apoptotic process] GO:0010880 [regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum] GO:0010881 [regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion] GO:0016020 [membrane] GO:0016301 [kinase activity] GO:0016310 [phosphorylation] GO:0016529 [sarcoplasmic reticulum] GO:0016740 [transferase activity] GO:0018105 [peptidyl-serine phosphorylation] GO:0018107 [peptidyl-threonine phosphorylation] GO:0019871 [sodium channel inhibitor activity] GO:0030154 [cell differentiation] GO:0030666 [endocytic vesicle membrane] GO:0031432 [titin binding] GO:0032469 [endoplasmic reticulum calcium ion homeostasis] GO:0033017 [sarcoplasmic reticulum membrane] GO:0034704 [calcium channel complex] GO:0042383 [sarcolemma] GO:0042803 [protein homodimerization activity] GO:0043005 [neuron projection] GO:0043547 [positive regulation of GTPase activity] GO:0044325 [ion channel binding] GO:0046777 [protein autophosphorylation] GO:0051259 [protein oligomerization] GO:0055119 [relaxation of cardiac muscle] GO:0060314 [regulation of ryanodine-sensitive calcium-release channel activity] GO:0060333 [interferon-gamma-mediated signaling pathway] GO:0060341 [regulation of cellular localization] GO:0071277 [cellular response to calcium ion] GO:0086003 [cardiac muscle cell contraction] GO:0086091 [regulation of heart rate by cardiac conduction] GO:0098901 [regulation of cardiac muscle cell action potential] GO:0098909 [regulation of cardiac muscle cell action potential involved in regulation of contraction] GO:1900034 [regulation of cellular response to heat] GO:1901725 [regulation of histone deacetylase activity] GO:1901844 [regulation of cell communication by electrical coupling involved in cardiac conduction] GO:1901897 [regulation of relaxation of cardiac muscle] GO:1902306 [negative regulation of sodium ion transmembrane transport] GO:1902514 [regulation of calcium ion transmembrane transport via high voltage-gated calcium channel] GO:2000650 [negative regulation of sodium ion transmembrane transporter activity]
D6R938 [Direct mapping] Calcium/calmodulin-dependent protein kinase (CaM kinase) II delta, isoform CRA_e; Calcium/calmodulin-dependent protein kinase type II subunit delta
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Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Protein evidence (Ezkurdia et al 2014)
The Human Protein Atlas project is funded
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