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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.
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 expressioni
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.
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 scorei
Reliability score (score description), divided into Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between the staining pattern of one antibody or several antibodies with RNA-seq data and available gene/protein characterization data.
Below is an overview of RNA and protein expression data generated in the Human Protein Atlas project. Analyzed tissues are divided into color-coded groups according to which functional features they have in common. For each group, a list of included tissues is accessed by clicking on group name, group symbol, RNA bar, or protein bar. Subsequent selection of a particular tissue in this list links to the image data page. Images of selected tissues give a visual summary of the protein expression profile furthest to the right. The gray human body provides links to a histology dictionary when clicking on any part of the figure.
RNA expression (TPM)i
RNA-seq results generated in HPA are reported as number of transcripts per million (TPM). Each bar represents the highest expression score found in a particular group of tissues. The assay is described more in detail in Assays & Annotation.
Protein expression (score)i
Each bar represents the highest expression score found in a particular group of tissues. Protein expression scores are based on a best estimate of the "true" protein expression from a knowledge-based annotation, described more in detail under Assays & annotation. For genes where more than one antibody has been used, a collective score is set displaying the estimated true protein expression.
Protein expression data is shown for each of the 44 tissues. The color-coding is based on tissues with functional features in common. Mouse-over function shows protein score for analyzed cell types found in a selected tissue. To access image data click on tissue name or bar. Annotation of protein expression is described in detail in Assays & annotation.
For genes with available protein data for which a knowledge-based annotation gave inconclusive results, no protein expression data is displayed in the protein expression data overview, however, all immunohistochemical images are still available and the annotation data can be found under Primary data.
Organ
Expression
Alphabetical
RNA EXPRESSION OVERVIEWi
RNA expression overview shows RNA-data from three different sources: Internally generated Human Protein Atlas (HPA) RNA-seq data, RNA-seq data from the Genotype-Tissue Expression (GTEx) project and CAGE data from FANTOM5 project. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
HPA dataseti
HPA dataset RNA-seq tissue data is reported as mean TPM (transcripts per million), corresponding to mean values of the different individual samples from each tissue. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar. The RNA-seq assay is described in detail in Assays & Annotation.
RNA tissue category HPA HPA RNA tissue category (category description) is calculated based on mRNA expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all
GTEx dataseti
GTEx dataset RNA-seq data are reported as median RPKM (reads per kilobase per million mapped reads), generated by the Genotype-Tissue Expression (GTEx) project. More information can be found in Assays & Annotation.
RNA tissue category GTEx GTEx RNA tissue category (category description) is calculated based on mRNA expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all
FANTOM5 dataseti
FANTOM5 dataset Tissue data obtained through Cap Analysis of Gene Expression (CAGE) are reported as Tags Per Million, generated by the FANTOM5 project. More information can be found in Assays & Annotation.
RNA tissue category FANTOM5 FANTOM5 RNA tissue category (category description) is calculated based on gene expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all
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) (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:0000082 [G1/S transition of mitotic cell cycle] GO:0000165 [MAPK cascade] GO:0000186 [activation of MAPKK activity] GO:0001558 [regulation of cell growth] GO:0001666 [response to hypoxia] GO:0002026 [regulation of the force of heart contraction] GO:0002028 [regulation of sodium ion transport] 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: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:0006816 [calcium ion transport] GO:0007173 [epidermal growth factor receptor signaling pathway] GO:0007264 [small GTPase mediated signal transduction] GO:0007265 [Ras protein signal transduction] GO:0007268 [synaptic transmission] GO:0007411 [axon guidance] GO:0008016 [regulation of heart contraction] GO:0008286 [insulin receptor signaling pathway] GO:0008543 [fibroblast growth factor receptor signaling pathway] GO:0010389 [regulation of G2/M transition of mitotic cell cycle] 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:0014704 [intercalated disc] GO:0014911 [positive regulation of smooth muscle cell migration] GO:0016020 [membrane] GO:0016529 [sarcoplasmic reticulum] GO:0018105 [peptidyl-serine phosphorylation] GO:0018107 [peptidyl-threonine phosphorylation] GO:0019221 [cytokine-mediated signaling pathway] GO:0019871 [sodium channel inhibitor activity] GO:0030007 [cellular potassium ion homeostasis] GO:0030315 [T-tubule] GO:0030666 [endocytic vesicle membrane] GO:0031432 [titin binding] GO:0031594 [neuromuscular junction] GO:0032469 [endoplasmic reticulum calcium ion homeostasis] GO:0033017 [sarcoplasmic reticulum membrane] GO:0034605 [cellular response to heat] GO:0034704 [calcium channel complex] GO:0035022 [positive regulation of Rac protein signal transduction] GO:0038095 [Fc-epsilon receptor signaling pathway] GO:0042383 [sarcolemma] GO:0042803 [protein homodimerization activity] GO:0043025 [neuronal cell body] GO:0043194 [axon initial segment] GO:0043234 [protein complex] GO:0044325 [ion channel binding] GO:0045087 [innate immune response] GO:0046777 [protein autophosphorylation] GO:0048010 [vascular endothelial growth factor receptor signaling pathway] GO:0048011 [neurotrophin TRK receptor signaling pathway] GO:0048471 [perinuclear region of cytoplasm] GO:0048661 [positive regulation of smooth muscle cell proliferation] GO:0050998 [nitric-oxide synthase binding] GO:0051259 [protein oligomerization] GO:0055119 [relaxation of cardiac muscle] GO:0060048 [cardiac muscle contraction] GO:0060314 [regulation of ryanodine-sensitive calcium-release channel activity] GO:0060333 [interferon-gamma-mediated signaling pathway] GO:0060341 [regulation of cellular localization] GO:0061049 [cell growth involved in cardiac muscle cell development] GO:0070374 [positive regulation of ERK1 and ERK2 cascade] 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 generation of L-type calcium current] 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)
