CLIP3 protein expression summary - The Human Protein Atlas

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CLIP3

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HUMAN PROTEIN ATLAS SUMMARYⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Proteinⁱ Full gene name according to HGNC.	CAP-Gly domain containing linker protein 3
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	CLIP3 (CLIPR-59, RSNL1)
Tissue specificityⁱ ??The RNA specificity category is based on mRNA expression levels in the consensus dataset which is calculated from the RNA expression levels in samples from HPA and GTEX. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. Read more	Tissue enhanced (brain)
Tissue expression clusterⁱ The RNA data was used to cluster genes according to their expression across tissues. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Non-specific - Angiogenesis (mainly)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Cell type enhanced (Horizontal cells, Bipolar cells, Inhibitory neurons, Muller glia cells, Granulosa cells, Excitatory neurons, Peritubular cells)
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Granulosa cells - Unknown function (mainly)
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed blood cell samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Not detected in immune cells
Brain specificityⁱ The regional specificity category is based on mRNA expression levels in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. All brain expression profiles are based on data from HPA. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category Read more	Low human brain regional specificity
Cancer prognostic summary	Prognostic marker in renal cancer (unfavorable) and pancreatic cancer (favorable)
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location. Read more	Intracellular
Protein function (UniProt)ⁱ Useful information about the protein provided by UniProt.	Functions as a cytoplasmic linker protein. Involved in TGN-endosome dynamics. May modulate the cellular compartmentalization of AKT kinase family and promote its cell membrane localization, thereby playing a role in glucose transport in adipocytes.... show less
Gene summary (Entrez)ⁱ Useful information about the gene from Entrez	This gene encodes a member of the cytoplasmic linker protein 170 family. Members of this protein family contain a cytoskeleton-associated protein glycine-rich domain and mediate the interaction of microtubules with cellular organelles. The encoded protein plays a role in T cell apoptosis by facilitating the association of tubulin and the lipid raft ganglioside GD3. The encoded protein also functions as a scaffold protein mediating membrane localization of phosphorylated protein kinase B. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2010]... show less

TISSUEⁱ Summary of data presented in the Tissue section, with a representative image of protein expression (left) and an interactive chart showing the tissue-specific mRNA expression (right). The image and the chart are clickable and will redirect to more Tissue data. This section contains information regarding the expression profiles of protein-coding genes in normal human tissue, both on the mRNA and protein level. The protein expression data is derived from antibody-based protein profiling using immunohistochemistry. Read more

Tissue expression clusterⁱ The RNA data was used to cluster genes according to their expression across tissues. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Non-specific - Angiogenesis (mainly)
Tissue specificityⁱ The RNA specificity category is based on mRNA expression levels in the consensus dataset which is calculated from the RNA expression levels in samples from HPA and GTEX. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. Read more	Tissue enhanced (brain)
Tissue distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA and GTEX. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in many
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. Read more	Estimation of protein expression could not be performed. View primary data.

BRAINⁱ Summary of data presented in the Brain Atlas and a representative image of mRNA expression in the human brain. The image is clickable and will redirect to more Brain Atlas data. The Brain Atlas explores the protein expression in the mammalian brain by visualization and integration of data from three mammalian species (human, pig and mouse). Transcriptomics data combined with affinity-based protein in situ localization down to single cell level is available in a brain-centric sub atlas of the Human Protein Atlas. Read more

Human regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. All brain expression profiles are based on data from HPA. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Low region specificity
Pig regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. All brain expression profiles are based on data from HPA. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Low region specificity
Mouse regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. All brain expression profiles are based on data from HPA. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Low region specificity

SINGLE CELL TYPEⁱ Summary of data presented in the Single cell Type section, with an interactive chart showing the cell type-specific mRNA expression. The chart is clickable and will redirect to more Cell Type data. This section contains information about single cell type RNA expression based on scRNAseq of human tissues. The data also covers transcriptomics analysis of human blood and cultured cell lines. Read more

Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Granulosa cells - Unknown function (mainly)
Cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Cell type enhanced (Horizontal cells, Bipolar cells, Inhibitory neurons, Muller glia cells, Granulosa cells, Excitatory neurons, Peritubular cells)

TISSUE CELL TYPEⁱ

Fibroblasts

Classificationⁱ

Core cell type enriched

PATHOLOGYⁱ Summary of data presented in the Pathology section, with representative images of protein expression in cancer (left) and correlation between mRNA expression and patient survival (right). Images are clickable and redirect to pages with more Pathology data. This section contains mRNA and protein expression data from 17 different forms of human cancer, as well as correlation analysis of mRNA expression and patient survival. The protein expression data is derived from antibody-based protein profiling using immunohistochemistry. Read more
	Renal cancer p<0.001
Prognostic summary	Prognostic marker in renal cancer (unfavorable) and pancreatic cancer (favorable)
Cancer specificityⁱ Specificity of RNA expression in 17 cancer types is categorized as either cancer enriched, group enriched, cancer enhanced, low cancer specificity and not detected. Read more	Cancer enhanced (glioma)
Cancer distributionⁱ Distribution of RNA expression in 17 cancer types is categorized as either detected in single, detected in some, detected in many, detected in all, or not detected. Read more	Detected in all

IMMUNE CELLⁱ Summary of data presented in the Immune Cell section and a representative image of mRNA expression in immune cells in the blood. The image is clickable and will redirect to more immune cell related data. The Immune Cell section contains information regarding single cell type mRNA expression profiles of protein-coding genes in various immune cells in the blood, e.g. B-cells and granulocytes. Read more

Immune cell expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	NK-cells - Transcription (mainly)
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Not detected in immune cells

BLOOD PROTEINⁱ Summary of data presented in the Blood proteins section and a representative image of the concentration in plasma and related function for the protein in plasma. The image is clickable and will redirect to more data. The Blood proteins section contains plasma levels of proteins detected in human blood and an analysis of the human secretome (including annotation of the genes predicted to be actively secreted to human blood) is also presented. Read more
Detected in blood by immunoassayⁱ The blood-based immunoassay category applies to actively secreted proteins and is based on plasma or serum protein concentrations established with enzyme-linked immunosorbent assays, compiled from a literature search. The categories include: detected and not detected, where detection refers to a concentration found in the literature search. Read more	No (not applicable)
Detected in blood by mass spectrometryⁱ Detection or not of the gene in blood, based on spectral count estimations from a publicly available mass spectrometry-based plasma proteomics data set obtained from the PeptideAtlas.	No
Detected in blood by proximity extension assayⁱ Detection or not of the gene in blood, based on proximity extension assays (Olink) for a longitudinal wellness study covering 76 individuals with three visits during two years. Read more	No

SUBCELLULARⁱ Summary of data presented in the Cell Atlas and a representative image of subcellular localization. The Cell Atlas provides RNA expression data derived from RNA sequencing of a large panel of cell lines and protein localization data derived from antibody-based profiling by immunofluorescence confocal microscopy, using a subset of cell lines selected based on RNA expression. Read more

Main locationⁱ Main subcellular location(s) and reliability score(s) for the encoded protein(s) in human cells. The main location(s) may be characterized by presence in all tested cell lines and/or ihigher staining intensity compared to the potential additional location(s). If available, links to overrepresentation analyses in Reactome, a free, open-source, curated and peer reviewed biological pathway database, are provided. An analysis is done for the corresponding gene set of the proteome localizing to the main and additional locations of the protein on this page, respectively. Read more	Not available

CELL LINEⁱ Summary of data presented in the Cell Line section and a representative image of mRNA expression across different human cell lines. The image is clickable and will redirect to more cell line data. This section contains information regarding mRNA expression profiles of human protein-coding genes for a large variety of cell lines. Read more

Cell line expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Mesenchymal cell lines - ECM organization (mainly)
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Cell line enhanced (ASC TERT1, fHDF/TERT166, HSkMC, hTERT-RPE1)
Cell type distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in many

METABOLIC

Metabolic info	Not available

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	CLIP3 (HGNC Symbol)
Synonyms	CLIPR-59, RSNL1
Description	CAP-Gly domain containing linker protein 3 (HGNC Symbol)
Chromosome	19
Cytoband	q13.12
Chromosome location (bp)	36014660 - 36033343
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	4
Protein evidence	Evidence at protein level (all genes)
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more
Ensembl	ENSG00000105270 (version 103.38)
Entrez gene	25999
UniProt	Q96DZ5 (UniProt - Evidence at protein level)
neXtProt	NX_Q96DZ5
Antibodypedia	CLIP3 antibodies

PROTEIN BROWSERⁱ

CLIP3-201

CLIP3-204

CLIP3-205

CLIP3-206

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.
Splice variant	UniProt	Protein class	Gene ontology	Length & mass	Signal peptide (predicted)	Transmembrane regions (predicted)
CLIP3-201 ENSP00000353732 ENST00000360535	Q96DZ5 [Direct mapping] CAP-Gly domain-containing linker protein 3 Show all	SPOCTOPUS predicted membrane proteins Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014) Show all	GO:0001934 [positive regulation of protein phosphorylation] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005737 [cytoplasm] GO:0005794 [Golgi apparatus] GO:0005795 [Golgi stack] GO:0005802 [trans-Golgi network] GO:0005829 [cytosol] GO:0005886 [plasma membrane] GO:0008017 [microtubule binding] GO:0010803 [regulation of tumor necrosis factor-mediated signaling pathway] GO:0010828 [positive regulation of glucose transmembrane transport] GO:0016020 [membrane] GO:0018230 [peptidyl-L-cysteine S-palmitoylation] GO:0031115 [negative regulation of microtubule polymerization] GO:0031122 [cytoplasmic microtubule organization] GO:0031901 [early endosome membrane] GO:0032588 [trans-Golgi network membrane] GO:0035371 [microtubule plus-end] GO:0035594 [ganglioside binding] GO:0043065 [positive regulation of apoptotic process] GO:0044091 [membrane biogenesis] GO:0045121 [membrane raft] GO:0045444 [fat cell differentiation] GO:0045807 [positive regulation of endocytosis] GO:0051010 [microtubule plus-end binding] GO:0055038 [recycling endosome membrane] GO:0072321 [chaperone-mediated protein transport] GO:1903078 [positive regulation of protein localization to plasma membrane] Show all	547 aa 59.6 kDa	No	0
CLIP3-204 ENSP00000466026 ENST00000590559	K7ESF3 [Direct mapping] CAP-Gly domain-containing linker protein 3 Show all	Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Protein evidence (Ezkurdia et al 2014) Show all		133 aa 14.9 kDa	No	0
CLIP3-205 ENSP00000468689 ENST00000592017	K7ESF3 [Direct mapping] CAP-Gly domain-containing linker protein 3 Show all	Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Protein evidence (Ezkurdia et al 2014) Show all		133 aa 14.9 kDa	No	0
CLIP3-206 ENSP00000466832 ENST00000593074	Q96DZ5 [Direct mapping] CAP-Gly domain-containing linker protein 3 Show all	SPOCTOPUS predicted membrane proteins Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014) Show all	GO:0001934 [positive regulation of protein phosphorylation] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005737 [cytoplasm] GO:0005794 [Golgi apparatus] GO:0005795 [Golgi stack] GO:0005802 [trans-Golgi network] GO:0005829 [cytosol] GO:0005886 [plasma membrane] GO:0008017 [microtubule binding] GO:0010803 [regulation of tumor necrosis factor-mediated signaling pathway] GO:0010828 [positive regulation of glucose transmembrane transport] GO:0016020 [membrane] GO:0018230 [peptidyl-L-cysteine S-palmitoylation] GO:0031115 [negative regulation of microtubule polymerization] GO:0031122 [cytoplasmic microtubule organization] GO:0031901 [early endosome membrane] GO:0032588 [trans-Golgi network membrane] GO:0035371 [microtubule plus-end] GO:0035594 [ganglioside binding] GO:0043065 [positive regulation of apoptotic process] GO:0044091 [membrane biogenesis] GO:0045121 [membrane raft] GO:0045444 [fat cell differentiation] GO:0045807 [positive regulation of endocytosis] GO:0051010 [microtubule plus-end binding] GO:0055038 [recycling endosome membrane] GO:0072321 [chaperone-mediated protein transport] GO:1903078 [positive regulation of protein localization to plasma membrane] Show all	547 aa 59.6 kDa	No	0

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