Single cell type - SLC24A4 - The Human Protein Atlas

SLC24A4

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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.	SLC24A4
Gene descriptionⁱ Full gene name according to HGNC.	Solute carrier family 24 member 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes Metabolic proteins Potential drug targets Transporters
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, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	6

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.	Bipolar 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 (Bipolar cells, Cone photoreceptor cells, Monocytes, Astrocytes, Schwann 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.	0.87
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 enriched (Choroid plexus epithelial cell)
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.	Group enriched (intermediate monocyte, non-classical monocyte, classical monocyte)
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 (Bipolar cells, Cone photoreceptor cells, Monocytes, Astrocytes, Schwann 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 enriched (Choroid plexus epithelial cell)

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: Group enriched (intermediate monocyte, non-classical monocyte, classical monocyte)
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

SLC24A4 is part of cluster 25 Bipolar cells - Visual perception with confidenceⁱ 1
152 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.
NTSR1	Neurotensin receptor 1	0.7205	25
ASIC4	Acid sensing ion channel subunit family member 4	0.6921	25
BSPH1	Binder of sperm protein homolog 1	0.6237	25
TMEM196	Transmembrane protein 196	0.6227	25
RGS8	Regulator of G protein signaling 8	0.6194	25
VSX1	Visual system homeobox 1	0.6173	25
GPR179	G protein-coupled receptor 179	0.6115	25
GABRR2	Gamma-aminobutyric acid type A receptor subunit rho2	0.6109	25
SLITRK1	SLIT and NTRK like family member 1	0.6090	25
PRDM8	PR/SET domain 8	0.6084	25
CCDC177	Coiled-coil domain containing 177	0.6083	25
GRM6	Glutamate metabotropic receptor 6	0.6073	25
TRPM1	Transient receptor potential cation channel subfamily M member 1	0.6024	25
NEUROD4	Neuronal differentiation 4	0.6024	25
LRTM1	Leucine rich repeats and transmembrane domains 1	0.6004	25

IMMUNE CELLS

SLC24A4 is part of cluster 40 Monocytes - Innate immune response with confidenceⁱ 1
228 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.
SLC31A1	Solute carrier family 31 member 1	1.0000	40
PGA5	Pepsinogen A5	1.0000	40
LIPN	Lipase family member N	1.0000	40
AP2A1	Adaptor related protein complex 2 subunit alpha 1	1.0000	40
CD300E	CD300e molecule	1.0000	40
PENK	Proenkephalin	1.0000	40
CDC42EP4	CDC42 effector protein 4	1.0000	40
FLII	FLII actin remodeling protein	1.0000	40
CXCL16	C-X-C motif chemokine ligand 16	1.0000	40
ATG3	Autophagy related 3	1.0000	40
SAT1	Spermidine/spermine N1-acetyltransferase 1	1.0000	40
CALML4	Calmodulin like 4	1.0000	40
TJP2	Tight junction protein 2	1.0000	40
LOXL3	Lysyl oxidase like 3	1.0000	40
ABHD11	Abhydrolase domain containing 11	1.0000	40

Adipocytes	0.8 nTPM
Adipose tissue	1.0 nTPM
Breast	0.5 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	0.1 nTPM
Lung	0.1 nTPM

B-cells	0.7 nTPM
Skin	6.8 nTPM
PBMC	1.5 nTPM
Spleen	0.9 nTPM
Salivary gland	0.3 nTPM
Thymus	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM

Basal keratinocytes	0.1 nTPM
Tongue	0.2 nTPM
Skin	0.0 nTPM

Ciliated cells	0.2 nTPM
Lung	0.4 nTPM
Endometrium	0.2 nTPM
Bronchus	0.1 nTPM
Fallopian tube	0.0 nTPM

Club cells	0.3 nTPM
Lung	0.8 nTPM
Bronchus	0.0 nTPM
Prostate	0.0 nTPM

Endothelial cells	0.8 nTPM
Liver	3.8 nTPM
Breast	2.6 nTPM
Heart muscle	1.9 nTPM
Skeletal muscle	1.4 nTPM
Placenta	1.1 nTPM
Prostate	1.0 nTPM
Lung	0.7 nTPM
Esophagus	0.5 nTPM
Skin	0.4 nTPM
Salivary gland	0.4 nTPM
Endometrium	0.3 nTPM
Vascular	0.3 nTPM
Thymus	0.2 nTPM
Fallopian tube	0.1 nTPM
Ovary	0.1 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Tongue	0.0 nTPM

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

Fibroblasts	0.4 nTPM
Heart muscle	2.0 nTPM
Liver	1.2 nTPM
Lung	1.2 nTPM
Prostate	0.7 nTPM
Skeletal muscle	0.5 nTPM
Breast	0.4 nTPM
Thymus	0.3 nTPM
Adipose tissue	0.2 nTPM
Vascular	0.2 nTPM
Skin	0.1 nTPM
Salivary gland	0.1 nTPM
Fallopian tube	0.1 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM

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

Intestinal goblet cells	0.1 nTPM
Colon	0.2 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Lymphatic endothelial cells	0.5 nTPM
Fallopian tube	1.0 nTPM
Ovary	0.0 nTPM

Macrophages	15.1 nTPM
Skeletal muscle	47.4 nTPM
Kidney	38.1 nTPM
Fallopian tube	29.9 nTPM
Stomach	28.3 nTPM
Spleen	25.1 nTPM
Endometrium	22.1 nTPM
Bone marrow	18.2 nTPM
Adipose tissue	16.4 nTPM
Esophagus	10.3 nTPM
Lung	8.2 nTPM
Vascular	8.2 nTPM
Salivary gland	7.0 nTPM
Testis	6.8 nTPM
Thymus	5.6 nTPM
Prostate	4.4 nTPM
Breast	4.3 nTPM
Tongue	2.3 nTPM
Skin	2.2 nTPM
Pancreas	2.1 nTPM

Paneth cells	0.1 nTPM
Rectum	0.2 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Astrocytes	44.6 nTPM
Brain	44.6 nTPM

Plasma cells	0.1 nTPM
Liver	0.5 nTPM
Fallopian tube	0.3 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM

Schwann cells	42.2 nTPM
Adipose tissue	81.6 nTPM
Vascular	44.9 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	0.4 nTPM
Salivary gland	0.7 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	0.3 nTPM
Lung	1.2 nTPM
Adipose tissue	0.9 nTPM
Skeletal muscle	0.6 nTPM
Ovary	0.5 nTPM
Liver	0.4 nTPM
Vascular	0.4 nTPM
Placenta	0.3 nTPM
Tongue	0.3 nTPM
Thymus	0.1 nTPM
Endometrium	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM

T-cells	0.2 nTPM
PBMC	1.8 nTPM
Liver	0.5 nTPM
Skin	0.4 nTPM
Vascular	0.4 nTPM
Fallopian tube	0.2 nTPM
Adipose tissue	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Endometrium	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
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Tongue	0.0 nTPM
Breast	0.0 nTPM

Undifferentiated cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Amygdala excitatory	88.9 nTPM
Amygdala	150.6 nTPM
Thalamus	116.2 nTPM
Hippocampus	84.4 nTPM
Basal ganglia	77.6 nTPM
Cerebral cortex	71.0 nTPM
Hypothalamus	33.9 nTPM

Astrocyte	225.3 nTPM
Cerebellum	504.8 nTPM
Pons	363.7 nTPM
Medulla oblongata	325.6 nTPM
Midbrain	285.0 nTPM
Spinal cord	272.1 nTPM
Thalamus	269.3 nTPM
Hypothalamus	163.1 nTPM
Basal ganglia	149.6 nTPM
Hippocampus	65.8 nTPM
Amygdala	42.8 nTPM
Cerebral cortex	36.7 nTPM

Bergmann glia	6.5 nTPM
Pons	12.9 nTPM
Medulla oblongata	4.3 nTPM
Cerebellum	2.2 nTPM

Central nervous system macrophage	13.0 nTPM
Amygdala	18.0 nTPM
Cerebral cortex	16.2 nTPM
Cerebellum	14.6 nTPM
Midbrain	14.3 nTPM
Thalamus	13.0 nTPM
Pons	12.7 nTPM
Basal ganglia	12.0 nTPM
Hippocampus	11.5 nTPM
Hypothalamus	10.9 nTPM
Medulla oblongata	10.9 nTPM
Spinal cord	9.4 nTPM

Cerebellar inhibitory	2.3 nTPM
Spinal cord	5.5 nTPM
Medulla oblongata	2.8 nTPM
Pons	1.7 nTPM
Cerebellum	0.8 nTPM
Midbrain	0.6 nTPM

Cge interneuron	32.7 nTPM
Hypothalamus	40.6 nTPM
Cerebral cortex	40.1 nTPM
Hippocampus	36.1 nTPM
Amygdala	31.3 nTPM
Basal ganglia	31.3 nTPM
Midbrain	27.2 nTPM
Thalamus	21.9 nTPM

Choroid plexus epithelial cell	1029.6 nTPM
Basal ganglia	1716.9 nTPM
Medulla oblongata	888.7 nTPM
Thalamus	811.1 nTPM
Hippocampus	701.6 nTPM

Committed oligodendrocyte precursor	27.8 nTPM
Medulla oblongata	123.9 nTPM
Basal ganglia	70.6 nTPM
Pons	36.3 nTPM
Cerebellum	19.0 nTPM
Amygdala	10.7 nTPM
Thalamus	9.5 nTPM
Midbrain	8.4 nTPM
Hypothalamus	8.2 nTPM
Spinal cord	7.4 nTPM
Cerebral cortex	6.3 nTPM
Hippocampus	5.4 nTPM

Deep-layer corticothalamic and 6b	1.4 nTPM
Hypothalamus	2.9 nTPM
Amygdala	1.7 nTPM
Basal ganglia	1.4 nTPM
Cerebral cortex	1.4 nTPM
Hippocampus	1.0 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	34.6 nTPM
Amygdala	50.4 nTPM
Hypothalamus	41.0 nTPM
Basal ganglia	32.3 nTPM
Cerebral cortex	28.8 nTPM
Hippocampus	20.6 nTPM

Deep-layer near-projecting	1.5 nTPM
Hypothalamus	2.8 nTPM
Hippocampus	1.6 nTPM
Cerebral cortex	1.5 nTPM
Amygdala	1.2 nTPM
Basal ganglia	0.5 nTPM

Eccentric medium spiny neuron	26.9 nTPM
Amygdala	48.0 nTPM
Hippocampus	39.4 nTPM
Cerebral cortex	24.0 nTPM
Thalamus	20.2 nTPM
Hypothalamus	19.3 nTPM
Basal ganglia	10.3 nTPM

Endothelial cell	2.9 nTPM
Basal ganglia	17.7 nTPM
Spinal cord	3.5 nTPM
Medulla oblongata	2.1 nTPM
Pons	1.9 nTPM
Cerebellum	1.5 nTPM
Hypothalamus	1.2 nTPM
Amygdala	1.1 nTPM
Hippocampus	1.0 nTPM
Midbrain	0.9 nTPM
Cerebral cortex	0.6 nTPM
Thalamus	0.6 nTPM

Ependymal cell	27.6 nTPM
Midbrain	36.2 nTPM
Thalamus	34.4 nTPM
Pons	33.4 nTPM
Medulla oblongata	32.9 nTPM
Spinal cord	28.7 nTPM
Basal ganglia	22.3 nTPM
Hippocampus	21.4 nTPM
Amygdala	19.9 nTPM
Hypothalamus	18.7 nTPM