Brain tissue expression of SLC30A3 - Summary - The Human Protein Atlas

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SLC30A3

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TISSUE

BRAIN

SINGLE CELL

TISSUE CELL

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IMMUNE

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METABOLIC

GENERAL INFORMATIONⁱ 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.
Human gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	SLC30A3
Mouse gene name	Slc30a3
Human gene descriptionⁱ Full gene name according to HGNC.	Solute carrier family 30 member 3
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	Membrane
Mouse gene	ENSMUSG00000029151 (version 103)
Pig gene	ENSSSCG00000021534 (version 103)
Antibodies in assayⁱ The internal antibody ID for the antibody/antibodies available for this specific target, click link for more antibody information.	HPA060505 HPA067637 CAB079044

HUMAN PROTEIN ATLAS INFORMATION
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	Group enriched (brain, epididymis, testis)
	Human brain	Pig brain	Mouse brain
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	Group enriched (amygdala, basal ganglia, cerebral cortex, hippocampal formation)	Group enriched (amygdala, cerebral cortex, hippocampal formation)	Group enriched (amygdala, basal ganglia, cerebral cortex, hippocampal formation, white matter)
Regional distributionⁱ The regional distribution category is based on mRNA expression detected above cut off or not in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. Brain expression for all species is based on data from HPA. The distribution categories include: detected in all, detected in many, detected in some, detected in single and not detected. The classification rules are the same used for the tissue distribution category. Read more	Detected in many	Detected in many	Detected in all
Cellular locationⁱ Manually selected location of the protein positivity, observed by immunofluorescence staining in mouse brain. Read more	Endfeet in astrocytes. Synapse in neurons. Circumventricular organs of ependymal cells.
Protein profileⁱ A summary of the overall protein localization across the analyzed brain tissue. The summary is based on manual annotation. Mouse brain profiles includes a more extensive summary of the protein location while summaries with only human protein profile are more limited and are based on imported data/images from the Tissue Atlas stainings that has undergone an additional brain-centric curation step. Read more	Diffuse-synaptic, neuropil-like staining pattern is noticed throughout the brain with various intensities (weak to strong). The strongest is in the granular layer of the olfactory bulb, rostral cortical regions (especially in layers I-II and IV), cingulate cortex, piriform cortex, entorhinal cortex, amygdala nuclei, hippocampus mossy fibers, arcuate nucleus and the region of median eminence, and some more caudal medullar nuclei like the hypoglossal nucleus, dorsal motor nucleus of vagus and nucleus tractus solitarii. .

BRAIN RNA EXPRESSION

HUMAN

Cerebral cortex Hippocampal formation Amygdala Basal ganglia Thalamus Hypothalamus Midbrain Cerebellum Pons Medulla oblongata Spinal cord White matter Corpus callosum Expression Detection All organs	HPA Human brain datasetⁱ Normalized RNA expression levels (nTPM) shown for the 13 brain regions. Color coding is based on brain region and the bar shows the highest expression among the subregions included. To access sample data, click on region name or bar. Read more about normalized expression levels in Assays & Annotation.
CTX HPF AMY BG TH HY MB CB P M SC WM
Cerebral cortex Hippocampal formation Amygdala Basal ganglia Thalamus Hypothalamus Midbrain Cerebellum Pons Medulla oblongata Spinal cord White matter

COMPARISON BRAIN RNA EXPRESSION

GTEX AND FANTOM HUMAN BRAIN

PIG
GTEx Human brain RNA-Seq datasetⁱ GTEx dataset RNA-seq tissue data generated by the Genotype-Tissue Expression (GTEx) project is reported as mean nTPM, corresponding to mean values of the different individual samples for respective subregion. Highest expression among the subregions represents the brain region. To access sample data, click on region name or bar. The GTEx RNA-seq assay is described in detail in Assays & Annotation.	FANTOM5 Human brain CAGE datasetⁱ FANTOM5 dataset Tissue data for RNA expression obtained through Cap Analysis of Gene Expression (CAGE) generated by the FANTOM5 project are reported as Scaled Tags Per Million. To access sample data, click on region name or bar. The CAGE method is described in detail in Assays & Annotation.
Cerebral cortex Olfactory bulb Hippocampal formation Amygdala Basal ganglia Thalamus Hypothalamus Midbrain Cerebellum Pons Medulla oblongata Spinal cord Pituitary gland Retina White matter	HPA Pig brain RNA-Seq datasetⁱ HPA Pig dataset HPA RNA-seq tissue data is reported as mean nTPM (normalized expression) for each of the brain regions analyzed in pig. The detailed pages (reached when clicking a bar or regional name) show nTPM values at the individual sample level. To access sample data, click on region name or bar. The HPA RNA-seq assay is described in detail in Assays & Annotation. The pig brain transcriptomics project is a collaborative project between human protein atlas and the Lars Bolund institute of regenerative Medicine (Dr. Yonglun Luo), BGI-Qingdao, China.
MOUSE
Cerebral cortex Olfactory bulb Hippocampal formation Amygdala Basal ganglia Thalamus Hypothalamus Midbrain Pons and medulla Cerebellum Pituitary gland Retina White matter	HPA Mouse brain RNA-Seq datasetⁱ HPA Mouse dataset HPA RNA-seq tissue data is reported as mean nTPM (normalized expression) for each of the brain regions analyzed in mouse. The detailed pages (reached when clicking a bar or regional name) show nTPM values at the individual sample level. To access sample data, click on region name or bar. The HPA RNA-seq assay is described in detail in Assays & Annotation. Allen Mouse brain ISH datasetⁱ The Allen Mouse Brain ISH The expression values based on in situ hybridization (ISH) available through the ABA API (© 2004 Allen Institute for Brain Science, Allen Mouse Brain Atlas) is imported and show regional expression grouped in the same manner as the other datasets. To access sample data and links to the ABA, click on region name or bar. Read more

HUMAN BRAIN PROTEIN LOCATIONⁱ

Location example	Hippocampus
Location summary	Distinct positivity observed in neuropil of forebrain regions.
Antibody reliability	Enhanced based on HPA060505 , HPA067637

HPA Human protein locationⁱ

MOUSE BRAIN PROTEIN LOCATIONⁱ

Protein profile	Diffuse-synaptic, neuropil-like staining pattern is noticed throughout the brain with various intensities (weak to strong). The strongest is in the granular layer of the olfactory bulb, rostral cortical regions (especially in layers I-II and IV), cingulate cortex, piriform cortex, entorhinal cortex, amygdala nuclei, hippocampus mossy fibers, arcuate nucleus and the region of median eminence, and some more caudal medullar nuclei like the hypoglossal nucleus, dorsal motor nucleus of vagus and nucleus tractus solitarii. .
Cellular location	Endfeet in astrocytes. Synapse in neurons. Circumventricular organs of ependymal cells.
Protein profile reliability	Enhanced based on CAB079044

HPA Mouse staining intesityⁱ


Selected annotations	Olfactory bulb	Pons and medulla	Hypothalamus
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