Single cell type - RRH - The Human Protein Atlas

RRH

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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.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	RRH
Gene descriptionⁱ Full gene name according to HGNC.	Retinal pigment epithelium-derived rhodopsin homolog
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	G-protein coupled receptors
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.	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
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.	Muller glia cells - Visual perception (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.	Cell type enriched (Muller glia cells)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.94
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Low cell type specificity
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.	Not detected in immune cells
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized single cell RNA (nTPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Single cell types RNA single cell type specificity: Cell type enriched (Muller glia cells)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Low cell type specificity

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Not detected in immune cells
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

RRH is part of cluster 10 Muller glia cells - Visual perception with confidenceⁱ 1
166 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
CLRN1	Clarin 1	0.9604	10
RGR	Retinal G protein coupled receptor	0.9567	10
RLBP1	Retinaldehyde binding protein 1	0.9551	10
WIF1	WNT inhibitory factor 1	0.9523	10
NPVF	Neuropeptide VF precursor	0.9409	10
CNMD	Chondromodulin	0.9367	10
SLITRK2	SLIT and NTRK like family member 2	0.9336	10
DIPK1C	Divergent protein kinase domain 1C	0.9292	10
CRABP1	Cellular retinoic acid binding protein 1	0.9273	10
LIX1	Limb and CNS expressed 1	0.9212	10
RAX	Retina and anterior neural fold homeobox	0.9188	10
PRSS35	Serine protease 35	0.9071	10
SEC14L3	SEC14 like lipid binding 3	0.8978	10
TRH	Thyrotropin releasing hormone	0.8855	10
GATB	Glutamyl-tRNA amidotransferase subunit B	0.8851	10

Adipocytes	0.0 nTPM
Breast	0.1 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	0.6 nTPM
Lung	0.6 nTPM

Alveolar cells type 2	0.3 nTPM
Lung	0.3 nTPM

Astrocytes	5.9 nTPM
Brain	5.9 nTPM

B-cells	0.0 nTPM
Salivary gland	0.2 nTPM
Thymus	0.2 nTPM
Lymph node	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM

Ciliated cells	0.2 nTPM
Lung	0.4 nTPM
Bronchus	0.3 nTPM
Endometrium	0.2 nTPM
Fallopian tube	0.1 nTPM

Club cells	0.2 nTPM
Lung	0.3 nTPM
Bronchus	0.1 nTPM
Prostate	0.1 nTPM

Endothelial cells	0.2 nTPM
Salivary gland	0.6 nTPM
Lung	0.4 nTPM
Thymus	0.4 nTPM
Testis	0.3 nTPM
Heart muscle	0.2 nTPM
Prostate	0.2 nTPM
Vascular	0.2 nTPM
Fallopian tube	0.2 nTPM
Ovary	0.2 nTPM
Endometrium	0.1 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Tongue	0.0 nTPM
Breast	0.0 nTPM

Enteroendocrine cells	0.6 nTPM
Rectum	1.7 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Fibroblasts	0.1 nTPM
Lung	0.3 nTPM
Salivary gland	0.3 nTPM
Thymus	0.2 nTPM
Vascular	0.2 nTPM
Breast	0.2 nTPM
Skin	0.1 nTPM
Skeletal muscle	0.1 nTPM
Esophagus	0.1 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Adipose tissue	0.0 nTPM
Stomach	0.0 nTPM
Prostate	0.0 nTPM
Fallopian tube	0.0 nTPM

Granulocytes	0.0 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM
Fallopian tube	0.0 nTPM

Intestinal goblet cells	0.3 nTPM
Rectum	0.8 nTPM
Colon	0.2 nTPM
Small intestine	0.0 nTPM

Lymphatic endothelial cells	0.0 nTPM
Fallopian tube	0.0 nTPM
Ovary	0.0 nTPM

Macrophages	0.1 nTPM
Skin	1.1 nTPM
Breast	0.3 nTPM
Skeletal muscle	0.2 nTPM
Adipose tissue	0.2 nTPM
Salivary gland	0.1 nTPM
Vascular	0.1 nTPM
Fallopian tube	0.1 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Thymus	0.0 nTPM
Tongue	0.0 nTPM

Paneth cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Bipolar cells	1.2 nTPM
Eye	1.2 nTPM

Cone photoreceptor cells	10.2 nTPM
Eye	10.2 nTPM

Excitatory neurons	8.0 nTPM
Brain	8.0 nTPM

Plasma cells	0.0 nTPM
Thymus	0.1 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM
Fallopian tube	0.0 nTPM

Schwann cells	0.3 nTPM
Vascular	1.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	0.2 nTPM
Salivary gland	0.3 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	0.1 nTPM
Endometrium	0.3 nTPM
Skeletal muscle	0.2 nTPM
Vascular	0.2 nTPM
Thymus	0.1 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM
Tongue	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM
Ovary	0.0 nTPM

T-cells	0.2 nTPM
Salivary gland	0.9 nTPM
Breast	0.5 nTPM
Skin	0.4 nTPM
Vascular	0.4 nTPM
PBMC	0.3 nTPM
Fallopian tube	0.3 nTPM
Endometrium	0.1 nTPM
Adipose tissue	0.1 nTPM
Thymus	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Tongue	0.0 nTPM

Undifferentiated cells	0.2 nTPM
Rectum	0.4 nTPM
Colon	0.2 nTPM
Small intestine	0.1 nTPM

Amygdala excitatory	11.7 nTPM
Hypothalamus	14.5 nTPM
Amygdala	12.8 nTPM
Hippocampus	12.2 nTPM
Cerebral cortex	11.4 nTPM
Basal ganglia	10.1 nTPM
Thalamus	9.1 nTPM

Astrocyte	8.6 nTPM
Hypothalamus	14.0 nTPM
Amygdala	12.3 nTPM
Spinal cord	10.2 nTPM
Medulla oblongata	9.0 nTPM
Cerebral cortex	8.9 nTPM
Hippocampus	8.6 nTPM
Thalamus	7.0 nTPM
Basal ganglia	6.9 nTPM
Pons	6.7 nTPM
Midbrain	6.5 nTPM
Cerebellum	4.7 nTPM

Bergmann glia	4.2 nTPM
Cerebellum	5.6 nTPM
Medulla oblongata	4.3 nTPM
Pons	2.9 nTPM

Central nervous system macrophage	2.3 nTPM
Amygdala	3.8 nTPM
Thalamus	3.0 nTPM
Midbrain	2.9 nTPM
Cerebral cortex	2.5 nTPM
Hypothalamus	2.5 nTPM
Spinal cord	2.4 nTPM
Hippocampus	2.1 nTPM
Basal ganglia	1.9 nTPM
Pons	1.6 nTPM
Cerebellum	1.5 nTPM
Medulla oblongata	1.2 nTPM

Cerebellar inhibitory	11.3 nTPM
Spinal cord	19.2 nTPM
Pons	10.3 nTPM
Midbrain	10.0 nTPM
Cerebellum	9.1 nTPM
Medulla oblongata	7.7 nTPM

Cge interneuron	8.5 nTPM
Amygdala	10.0 nTPM
Hypothalamus	9.6 nTPM
Hippocampus	8.5 nTPM
Thalamus	8.4 nTPM
Cerebral cortex	8.0 nTPM
Midbrain	7.8 nTPM
Basal ganglia	7.6 nTPM

Choroid plexus epithelial cell	10.7 nTPM
Hippocampus	13.9 nTPM
Thalamus	11.0 nTPM
Basal ganglia	9.5 nTPM
Medulla oblongata	8.6 nTPM

Committed oligodendrocyte precursor	4.1 nTPM
Spinal cord	7.4 nTPM
Hypothalamus	6.1 nTPM
Medulla oblongata	5.2 nTPM
Amygdala	4.5 nTPM
Thalamus	4.5 nTPM
Pons	4.4 nTPM
Hippocampus	3.9 nTPM
Basal ganglia	3.8 nTPM
Cerebral cortex	3.2 nTPM
Midbrain	2.5 nTPM
Cerebellum	0.0 nTPM

Deep-layer corticothalamic and 6b	10.1 nTPM
Amygdala	13.1 nTPM
Hippocampus	12.1 nTPM
Hypothalamus	11.1 nTPM
Cerebral cortex	10.5 nTPM
Basal ganglia	8.5 nTPM
Midbrain	5.5 nTPM

Deep-layer intratelencephalic	10.2 nTPM
Hypothalamus	11.7 nTPM
Amygdala	11.6 nTPM
Hippocampus	10.2 nTPM
Cerebral cortex	9.6 nTPM
Basal ganglia	7.9 nTPM

Deep-layer near-projecting	12.7 nTPM
Amygdala	14.5 nTPM
Hypothalamus	14.1 nTPM
Cerebral cortex	13.6 nTPM
Basal ganglia	11.1 nTPM
Hippocampus	10.1 nTPM

Eccentric medium spiny neuron	8.7 nTPM
Amygdala	10.0 nTPM
Hippocampus	9.1 nTPM
Cerebral cortex	8.8 nTPM
Basal ganglia	8.5 nTPM
Hypothalamus	8.2 nTPM
Thalamus	7.7 nTPM

Endothelial cell	1.7 nTPM
Thalamus	3.4 nTPM
Pons	3.1 nTPM
Basal ganglia	2.8 nTPM
Amygdala	2.2 nTPM
Spinal cord	1.7 nTPM
Hippocampus	1.6 nTPM
Cerebellum	1.5 nTPM
Hypothalamus	1.2 nTPM
Cerebral cortex	0.6 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM

Ependymal cell	14.8 nTPM
Amygdala	29.6 nTPM
Thalamus	16.2 nTPM
Hippocampus	16.0 nTPM
Basal ganglia	14.9 nTPM
Midbrain	14.6 nTPM
Hypothalamus	13.4 nTPM
Spinal cord	11.5 nTPM
Medulla oblongata	9.7 nTPM
Pons	7.1 nTPM