Brain tissue expression of PAX6 - Summary - The Human Protein Atlas

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PAX6

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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.	PAX6
Mouse gene name	Pax6
Human gene descriptionⁱ Full gene name according to HGNC.	Paired box 6
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,Membrane
Mouse gene	ENSMUSG00000027168 (version 92)
Pig gene	ENSSSCG00000013320 (version 92)
Antibodies in assayⁱ The internal antibody ID for the antibody/antibodies available for this specific target, click link for more antibody information.	HPA030775 CAB034143

HUMAN PROTEIN ATLAS INFORMATION
Tissue specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA, GTEX and FANTOM5. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. The Tissue classification is based on 37 human tissue types, where brain is represented by the highest expression value among the human brain regions (including spinal cord and corpus callosum that is excluded from the regional classification based on 10 main brain regions). The combination of tissue and regional classification can be found here Read more	Tissue enhanced (brain, retina)
	Human brain	Pig brain	Mouse brain
Regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analyzed brain samples, grouped into 10 main brain regions and calculated for the three different species. The human brain expression profile is based on a combination of data from GTEX and FANTOM5. 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	Region enriched (cerebellum)	Low region specificity	Group enriched (cerebellum, olfactory region)
Regional distributionⁱ The regional distribution category is based on mRNA expression detected above cut off or not in the analyzed brain samples, grouped into 10 main brain regions and calculated for the three different species. The human brain expression is based on a combination of data from GTEX and FANTOM5. 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 all	Detected in all	Detected in many
Cellular locationⁱ Manually selected location of the protein positivity, observed by immunofluorescence staining in mouse brain. Read more	Nucleus in neurons. Ventricle wall and 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	Pax6 is a transcription factor with a key regulatory role in eye and brain development. Within the mouse brain, both transcriptomic and proteomic databases show high expression in olfactory areas, where it is involved in the development of cell that process smell. However, in both human and mouse brain, PAX6 is predominantly seen in cerebellum, with a distinct distribution in cells of the granular layer. In the current immunostaining, strong neuronal nuclear staining is noticed, which is highly restricted to a limited brain areas/nuclei: In the olfactory bulb: granular and glomerular layers; In the forebrain: lateral septum, piriform cortex, hypothalamic paraventricular nucleus, multiple amygdala nuclei, zona incerta, lateral hypothalamus, habenulae, caudal part of the hippocampus, entorhinal cortex; In the brainstem: periaqueductal gray matter, dorsal raphe and raphe magnus, vestibular nucelus; In the cerebellum: the staining is highly abundant in the cerebellar molecular layer. In addition, very rare, sparse immunoreactive nuclei are noticed throughout the entire brain.

BRAIN RNA EXPRESSION

HUMAN

PIG
Cerebral cortex Olfactory region Hippocampal formation Amygdala Basal ganglia Thalamus Hypothalamus Midbrain Pons and medulla Cerebellum Corpus callosum Expression Detection All organs	Consensus Human brain datasetⁱ Consensus normalized expression (NX) levels were created for the 10 brain regions by combining the data from two transcriptomics datasets (GTEx and FANTOM5). 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 how the datasets were combined into consensus normalized expression levels in Assays & Annotation. GTEx Human brain RNA-Seq datasetⁱ GTEx dataset RNA-seq tissue data generated by the Genotype-Tissue Expression (GTEx) project is reported as mean pTPM (protein-coding transcripts per million), 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.
ACG, pregenual-dorsal ACG, pregenual-ventral ACG, subgenual IFG, triangular IFG, orbital OrG, lateral OrG, posterior Ventrolateral PFC Ventromedial PFC Dorsolateral PFC Dorsomedial PFC Frontomarginal cortex Frontopolar cortex OrG, medial Gyrus rectus Subcallosal gyrus Superior frontal gyrus Frontal cortex Parietal cortex Temporal cortex	HPA Prefrontal cortex datasetⁱ HPA Prefrontal cortex dataset This dataset is a stand-alone dataset not integrated with other human transcriptomics data presented in the brain atlas. Brain expression data obtained through RNA-seq generated by the HPA, reported as normalized expression (NX) for human prefrontal cortex samples. Color coding of the bars separates prefrontal cortex and the three reference cortex regions (frontal, parietal and temporal). Trimmed mean values are calculated for the different subregions, to access individual sample data, click on subregion name or bar. Read more about data normalization strategy and the prefrontal cortex sampling in Assays & Annotation.
Cerebral cortex Olfactory region Hippocampal formation Amygdala Basal ganglia Thalamus Hypothalamus Midbrain Pons and medulla Cerebellum Corpus callosum Spinal cord Pituitary gland Retina	HPA Pig brain RNA-Seq datasetⁱ HPA Pig dataset HPA RNA-seq tissue data is reported as mean NX (normalized expression) for the 10 brain regions. The NX calculation is based on pTPM (protein-coding transcripts per million) of the individual samples, avaliable at the detaile pages (reached when clicking a bar or regional name). 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 region Hippocampal formation Amygdala Basal ganglia Thalamus Hypothalamus Midbrain Pons and medulla Cerebellum Corpus callosum Pituitary gland Retina	HPA Mouse brain RNA-Seq datasetⁱ HPA Mouse dataset HPA RNA-seq tissue data is reported as mean NX (normalized expression) for the 10 brain regions. The NX calculation is based on pTPM (protein-coding transcripts per million) of the individual samples, avaliable at the detaile pages (reached when clicking a bar or regional name). 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	Cerebellum
Location summary	Nuclear protein was selectively detected in retina and granular layer of cerebellum.
Antibody reliability	Enhanced based on HPA030775 , CAB034143

HPA Human protein locationⁱ

MOUSE BRAIN PROTEIN LOCATIONⁱ

Protein profile	Pax6 is a transcription factor with a key regulatory role in eye and brain development. Within the mouse brain, both transcriptomic and proteomic databases show high expression in olfactory areas, where it is involved in the development of cell that process smell. However, in both human and mouse brain, PAX6 is predominantly seen in cerebellum, with a distinct distribution in cells of the granular layer. In the current immunostaining, strong neuronal nuclear staining is noticed, which is highly restricted to a limited brain areas/nuclei: In the olfactory bulb: granular and glomerular layers; In the forebrain: lateral septum, piriform cortex, hypothalamic paraventricular nucleus, multiple amygdala nuclei, zona incerta, lateral hypothalamus, habenulae, caudal part of the hippocampus, entorhinal cortex; In the brainstem: periaqueductal gray matter, dorsal raphe and raphe magnus, vestibular nucelus; In the cerebellum: the staining is highly abundant in the cerebellar molecular layer. In addition, very rare, sparse immunoreactive nuclei are noticed throughout the entire brain.
Cellular location	Nucleus in neurons. Ventricle wall and circumventricular organs of ependymal cells.
Protein profile reliability	Enhanced based on HPA030775

HPA Mouse staining intesityⁱ


Selected annotations	Thalamus	Midbrain	Cerebellum
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The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.