Single cell type - RDH5 - The Human Protein Atlas

RDH5

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Pathway

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.	RDH5
Gene descriptionⁱ Full gene name according to HGNC.	Retinol dehydrogenase 5
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Enzymes Human disease related genes Metabolic proteins Potential drug targets
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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	4

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.	Photoreceptor 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 enhanced (Rod photoreceptor cells, Proximal enterocytes, Cone photoreceptor 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.	0.65
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.	Cell type enhanced (Vascular associated smooth muscle cell, Ependymal cell, Pericyte)
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 enhanced (Rod photoreceptor cells, Proximal enterocytes, Cone photoreceptor 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: Cell type enhanced (Vascular associated smooth muscle cell, Ependymal cell, Pericyte)

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

RDH5 is part of cluster 66 Photoreceptor cells - Visual perception with confidenceⁱ 1
340 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.
SPHK2	Sphingosine kinase 2	0.6056	71
OR6J1	Olfactory receptor family 6 subfamily J member 1	0.5985	66
DENND2B	DENN domain containing 2B	0.5934	66
SPINT4	Serine peptidase inhibitor, Kunitz type 4	0.5930	66
OR5P3	Olfactory receptor family 5 subfamily P member 3	0.5792	66
ABHD14A-ACY1	ABHD14A-ACY1 readthrough	0.5733	38
HRNR	Hornerin	0.5721	66
PPEF2	Protein phosphatase with EF-hand domain 2	0.5549	66
SLC23A3	Solute carrier family 23 member 3	0.5501	22
OR5P2	Olfactory receptor family 5 subfamily P member 2	0.5498	66
FN3K	Fructosamine 3 kinase	0.5497	38
SYNE3	Spectrin repeat containing nuclear envelope family member 3	0.5467	66
ZNF283	Zinc finger protein 283	0.5385	66
DDC	Dopa decarboxylase	0.5350	22
ANKS3	Ankyrin repeat and sterile alpha motif domain containing 3	0.5342	66

Adipocytes	2.5 nTPM
Breast	3.3 nTPM
Adipose tissue	1.6 nTPM

Alveolar cells type 1	0.8 nTPM
Lung	0.8 nTPM

Alveolar cells type 2	1.2 nTPM
Lung	1.2 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	4.6 nTPM
PBMC	16.9 nTPM
Liver	9.7 nTPM
Skin	8.5 nTPM
Lung	6.7 nTPM
Kidney	5.2 nTPM
Salivary gland	5.1 nTPM
Thymus	3.7 nTPM
Adipose tissue	3.3 nTPM
Spleen	0.4 nTPM
Lymph node	0.2 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Ciliated cells	3.5 nTPM
Lung	6.0 nTPM
Bronchus	3.6 nTPM
Fallopian tube	3.1 nTPM
Endometrium	1.4 nTPM

Club cells	4.3 nTPM
Prostate	6.3 nTPM
Bronchus	3.4 nTPM
Lung	3.4 nTPM

Endothelial cells	3.3 nTPM
Ovary	10.4 nTPM
Testis	7.9 nTPM
Pancreas	7.8 nTPM
Prostate	4.4 nTPM
Tongue	3.7 nTPM
Breast	3.5 nTPM
Skeletal muscle	3.2 nTPM
Vascular	3.2 nTPM
Lung	2.8 nTPM
Skin	2.5 nTPM
Thymus	2.2 nTPM
Endometrium	2.0 nTPM
Salivary gland	2.0 nTPM
Liver	1.3 nTPM
Placenta	1.1 nTPM
Esophagus	0.5 nTPM
Fallopian tube	0.5 nTPM
Heart muscle	0.3 nTPM

Enteroendocrine cells	13.6 nTPM
Small intestine	17.2 nTPM
Rectum	16.8 nTPM
Colon	6.9 nTPM

Fibroblasts	4.7 nTPM
Vascular	13.2 nTPM
Salivary gland	7.9 nTPM
Thymus	7.8 nTPM
Skeletal muscle	7.4 nTPM
Skin	5.7 nTPM
Prostate	5.3 nTPM
Liver	4.7 nTPM
Breast	4.7 nTPM
Stomach	4.3 nTPM
Adipose tissue	3.3 nTPM
Esophagus	2.8 nTPM
Heart muscle	2.3 nTPM
Lung	1.8 nTPM
Placenta	1.6 nTPM
Fallopian tube	1.2 nTPM
Pancreas	0.7 nTPM

Granulocytes	1.8 nTPM
Tongue	4.9 nTPM
Fallopian tube	0.6 nTPM
Lung	0.0 nTPM

Intestinal goblet cells	6.6 nTPM
Small intestine	11.1 nTPM
Rectum	5.1 nTPM
Colon	3.7 nTPM

Lymphatic endothelial cells	3.1 nTPM
Ovary	5.5 nTPM
Fallopian tube	0.8 nTPM

Macrophages	2.3 nTPM
Kidney	6.2 nTPM
Testis	5.6 nTPM
Breast	3.9 nTPM
Tongue	3.8 nTPM
Prostate	3.4 nTPM
Salivary gland	3.0 nTPM
Skeletal muscle	2.8 nTPM
Stomach	2.6 nTPM
Lung	2.3 nTPM
Pancreas	2.1 nTPM
Fallopian tube	2.1 nTPM
Adipose tissue	1.7 nTPM
Vascular	1.5 nTPM
Esophagus	1.3 nTPM
Bone marrow	1.0 nTPM
Thymus	0.8 nTPM
Endometrium	0.0 nTPM
Skin	0.0 nTPM
Spleen	0.0 nTPM

Paneth cells	11.8 nTPM
Rectum	14.3 nTPM
Small intestine	13.8 nTPM
Colon	7.2 nTPM

Basal respiratory cells	4.1 nTPM
Bronchus	4.1 nTPM

Bipolar cells	14.5 nTPM
Eye	14.5 nTPM

Cholangiocytes	7.6 nTPM
Liver	7.6 nTPM

Collecting duct cells	1.9 nTPM
Kidney	1.9 nTPM

Plasma cells	0.5 nTPM
Salivary gland	2.2 nTPM
Liver	1.5 nTPM
Thymus	0.6 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Fallopian tube	0.0 nTPM

Schwann cells	3.0 nTPM
Vascular	7.3 nTPM
Adipose tissue	1.6 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	1.0 nTPM
Salivary gland	2.0 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	13.0 nTPM
Esophagus	39.6 nTPM
Thymus	39.5 nTPM
Vascular	20.0 nTPM
Tongue	15.6 nTPM
Endometrium	13.0 nTPM
Skin	11.6 nTPM
Breast	11.6 nTPM
Ovary	11.5 nTPM
Skeletal muscle	10.7 nTPM
Salivary gland	7.7 nTPM
Lung	7.1 nTPM
Fallopian tube	5.3 nTPM
Adipose tissue	4.5 nTPM
Placenta	4.4 nTPM
Liver	3.4 nTPM
Prostate	3.0 nTPM

T-cells	4.9 nTPM
PBMC	14.7 nTPM
Liver	10.4 nTPM
Kidney	9.8 nTPM
Skeletal muscle	9.1 nTPM
Skin	8.4 nTPM
Tongue	7.7 nTPM
Lung	6.6 nTPM
Colon	5.8 nTPM
Salivary gland	5.8 nTPM
Prostate	5.4 nTPM
Vascular	4.8 nTPM
Breast	4.5 nTPM
Thymus	3.1 nTPM
Adipose tissue	2.4 nTPM
Endometrium	1.8 nTPM
Fallopian tube	0.7 nTPM
Bone marrow	0.4 nTPM
Lymph node	0.3 nTPM
Spleen	0.3 nTPM
Stomach	0.1 nTPM
Esophagus	0.0 nTPM

Undifferentiated cells	9.0 nTPM
Small intestine	12.7 nTPM
Rectum	10.4 nTPM
Colon	4.1 nTPM

Amygdala excitatory	0.0 nTPM
Hypothalamus	0.1 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Astrocyte	1.3 nTPM
Spinal cord	2.2 nTPM
Cerebellum	2.0 nTPM
Medulla oblongata	1.9 nTPM
Hippocampus	1.5 nTPM
Pons	1.5 nTPM
Midbrain	1.3 nTPM
Thalamus	1.1 nTPM
Basal ganglia	0.8 nTPM
Cerebral cortex	0.8 nTPM
Hypothalamus	0.7 nTPM
Amygdala	0.5 nTPM

Bergmann glia	0.5 nTPM
Cerebellum	1.4 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	0.7 nTPM
Spinal cord	1.5 nTPM
Medulla oblongata	1.4 nTPM
Cerebellum	0.8 nTPM
Basal ganglia	0.7 nTPM
Midbrain	0.7 nTPM
Pons	0.7 nTPM
Hippocampus	0.6 nTPM
Cerebral cortex	0.4 nTPM
Amygdala	0.3 nTPM
Hypothalamus	0.2 nTPM
Thalamus	0.1 nTPM

Cerebellar inhibitory	0.1 nTPM
Pons	0.3 nTPM
Cerebellum	0.2 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.1 nTPM
Midbrain	0.3 nTPM
Thalamus	0.2 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hippocampus	0.1 nTPM
Hypothalamus	0.1 nTPM

Choroid plexus epithelial cell	0.6 nTPM
Medulla oblongata	1.6 nTPM
Basal ganglia	0.7 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	0.2 nTPM
Midbrain	0.8 nTPM
Hippocampus	0.5 nTPM
Thalamus	0.5 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM

Deep-layer near-projecting	0.0 nTPM
Amygdala	0.2 nTPM
Cerebral cortex	0.1 nTPM
Basal ganglia	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM

Eccentric medium spiny neuron	0.1 nTPM
Hippocampus	0.4 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.0 nTPM
Hypothalamus	0.0 nTPM
Thalamus	0.0 nTPM

Endothelial cell	0.4 nTPM
Midbrain	2.8 nTPM
Cerebral cortex	0.6 nTPM
Hippocampus	0.6 nTPM
Thalamus	0.6 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

Ependymal cell	1.5 nTPM
Spinal cord	5.7 nTPM
Pons	2.0 nTPM
Medulla oblongata	1.3 nTPM
Hippocampus	1.2 nTPM
Hypothalamus	0.9 nTPM
Thalamus	0.8 nTPM
Basal ganglia	0.6 nTPM
Midbrain	0.6 nTPM
Amygdala	0.0 nTPM