Single cell type - SLC19A3 - The Human Protein Atlas

SLC19A3

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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.	SLC19A3
Gene descriptionⁱ Full gene name according to HGNC.	Solute carrier family 19 member 3
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
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	7

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.	Syncytiotrophoblasts - Pregnancy (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.	Group enriched (Syncytiotrophoblasts, Cytotrophoblasts)
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.	0.86
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 (Endothelial 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.	Immune cell enhanced (basophil)
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: Group enriched (Syncytiotrophoblasts, Cytotrophoblasts)

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 (Endothelial 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: Immune cell enhanced (basophil)
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

SLC19A3 is part of cluster 27 Syncytiotrophoblasts - Pregnancy with confidenceⁱ 1
142 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.
SLC22A11	Solute carrier family 22 member 11	0.8938	27
CALHM4	Calcium homeostasis modulator family member 4	0.8884	27
SLC19A1	Solute carrier family 19 member 1	0.8562	24
GSTA3	Glutathione S-transferase alpha 3	0.8456	27
ERVW-1	Endogenous retrovirus group W member 1, envelope	0.8430	27
SLC52A1	Solute carrier family 52 member 1	0.8409	27
SLC13A4	Solute carrier family 13 member 4	0.8403	27
NFE2L3	NFE2 like bZIP transcription factor 3	0.8329	24
HSD17B1	Hydroxysteroid 17-beta dehydrogenase 1	0.8210	27
DACT2	Dishevelled binding antagonist of beta catenin 2	0.8042	27
PHLDA2	Pleckstrin homology like domain family A member 2	0.8010	24
MLLT1	MLLT1 super elongation complex subunit	0.7951	24
DUSP9	Dual specificity phosphatase 9	0.7796	24
INSL4	Insulin like 4	0.7706	27
KCNN4	Potassium calcium-activated channel subfamily N member 4	0.7649	27

IMMUNE CELLS

SLC19A3 is part of cluster 20 Non-specific - DNA binding with confidenceⁱ 1
266 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.
C2orf80	Chromosome 2 open reading frame 80	1.0000	20
CWC25	CWC25 spliceosome associated protein homolog	0.9762	20
CCDC194	Coiled-coil domain containing 194	0.9762	20
PAEP	Progestagen associated endometrial protein	0.9762	20
H2BC18	H2B clustered histone 18	0.9762	20
TBX6	T-box transcription factor 6	0.9762	20
RNF111	Ring finger protein 111	0.9762	20
RSBN1L	Round spermatid basic protein 1 like	0.9762	20
OR4D9	Olfactory receptor family 4 subfamily D member 9	0.9762	20
COX6B2	Cytochrome c oxidase subunit 6B2	0.9524	20
CDK12	Cyclin dependent kinase 12	0.9524	20
ANKRD40CL	ANKRD40 C-terminal like	0.9524	20
FBLIM1	Filamin binding LIM protein 1	0.9524	20
CAPN15	Calpain 15	0.9524	20
NCF1	Neutrophil cytosolic factor 1	0.9524	20

Adipocytes	0.1 nTPM
Breast	0.2 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	4.5 nTPM
Lung	4.5 nTPM

Alveolar cells type 2	5.1 nTPM
Lung	5.1 nTPM

Astrocytes	2.2 nTPM
Brain	2.2 nTPM

B-cells	0.1 nTPM
Lung	1.3 nTPM
Thymus	0.2 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
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM

Ciliated cells	0.3 nTPM
Lung	0.9 nTPM
Endometrium	0.1 nTPM
Bronchus	0.0 nTPM
Fallopian tube	0.0 nTPM

Club cells	0.3 nTPM
Lung	0.8 nTPM
Bronchus	0.1 nTPM
Prostate	0.0 nTPM

Endothelial cells	0.9 nTPM
Pancreas	5.2 nTPM
Fallopian tube	3.2 nTPM
Placenta	1.7 nTPM
Esophagus	1.3 nTPM
Skeletal muscle	1.0 nTPM
Skin	0.9 nTPM
Lung	0.8 nTPM
Endometrium	0.5 nTPM
Prostate	0.5 nTPM
Tongue	0.5 nTPM
Heart muscle	0.3 nTPM
Ovary	0.3 nTPM
Salivary gland	0.2 nTPM
Vascular	0.2 nTPM
Thymus	0.1 nTPM
Testis	0.0 nTPM
Liver	0.0 nTPM
Breast	0.0 nTPM

Enteroendocrine cells	2.5 nTPM
Colon	4.2 nTPM
Rectum	3.4 nTPM
Small intestine	0.0 nTPM

Fibroblasts	2.4 nTPM
Lung	7.3 nTPM
Salivary gland	7.3 nTPM
Placenta	5.4 nTPM
Adipose tissue	4.5 nTPM
Vascular	3.7 nTPM
Thymus	3.3 nTPM
Liver	1.2 nTPM
Esophagus	1.2 nTPM
Skeletal muscle	1.1 nTPM
Breast	1.0 nTPM
Skin	0.6 nTPM
Heart muscle	0.5 nTPM
Pancreas	0.4 nTPM
Fallopian tube	0.3 nTPM
Stomach	0.0 nTPM
Prostate	0.0 nTPM

Granulocytes	0.3 nTPM
Lung	1.0 nTPM
Tongue	0.0 nTPM
Fallopian tube	0.0 nTPM

Intestinal goblet cells	2.0 nTPM
Rectum	3.4 nTPM
Colon	1.5 nTPM
Small intestine	1.1 nTPM

Lymphatic endothelial cells	0.1 nTPM
Fallopian tube	0.2 nTPM
Ovary	0.0 nTPM

Macrophages	2.0 nTPM
Lung	33.2 nTPM
Skeletal muscle	1.6 nTPM
Kidney	0.9 nTPM
Thymus	0.4 nTPM
Salivary gland	0.3 nTPM
Vascular	0.3 nTPM
Prostate	0.2 nTPM
Tongue	0.2 nTPM
Testis	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	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
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM

Paneth cells	2.1 nTPM
Small intestine	3.5 nTPM
Rectum	2.9 nTPM
Colon	0.0 nTPM

Bipolar cells	6.0 nTPM
Eye	6.0 nTPM

Cholangiocytes	5.7 nTPM
Liver	5.7 nTPM

Collecting duct cells	1.9 nTPM
Kidney	1.9 nTPM

Cytotrophoblasts	66.3 nTPM
Placenta	66.3 nTPM

Plasma cells	0.1 nTPM
Liver	0.5 nTPM
Thymus	0.1 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	0.2 nTPM
Vascular	0.5 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	0.1 nTPM
Salivary gland	0.1 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	2.0 nTPM
Placenta	13.4 nTPM
Adipose tissue	4.0 nTPM
Lung	2.4 nTPM
Tongue	2.4 nTPM
Thymus	1.7 nTPM
Vascular	1.5 nTPM
Skeletal muscle	1.2 nTPM
Esophagus	1.2 nTPM
Prostate	1.2 nTPM
Breast	1.1 nTPM
Ovary	0.8 nTPM
Skin	0.6 nTPM
Salivary gland	0.5 nTPM
Fallopian tube	0.3 nTPM
Endometrium	0.2 nTPM
Liver	0.0 nTPM

T-cells	0.2 nTPM
Kidney	0.9 nTPM
Skeletal muscle	0.8 nTPM
Lung	0.8 nTPM
Salivary gland	0.4 nTPM
Tongue	0.4 nTPM
Vascular	0.4 nTPM
Liver	0.3 nTPM
PBMC	0.3 nTPM
Prostate	0.2 nTPM
Endometrium	0.1 nTPM
Thymus	0.1 nTPM
Colon	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	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
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM

Undifferentiated cells	6.9 nTPM
Rectum	12.4 nTPM
Small intestine	5.8 nTPM
Colon	2.6 nTPM

Amygdala excitatory	2.7 nTPM
Thalamus	4.1 nTPM
Amygdala	3.5 nTPM
Cerebral cortex	2.8 nTPM
Basal ganglia	2.4 nTPM
Hippocampus	2.1 nTPM
Hypothalamus	1.2 nTPM

Astrocyte	7.6 nTPM
Spinal cord	15.9 nTPM
Midbrain	10.3 nTPM
Cerebellum	9.3 nTPM
Medulla oblongata	9.0 nTPM
Pons	8.3 nTPM
Thalamus	7.7 nTPM
Amygdala	5.6 nTPM
Hypothalamus	5.2 nTPM
Hippocampus	4.7 nTPM
Cerebral cortex	4.3 nTPM
Basal ganglia	3.0 nTPM

Bergmann glia	5.5 nTPM
Cerebellum	9.5 nTPM
Medulla oblongata	4.3 nTPM
Pons	2.9 nTPM

Central nervous system macrophage	0.3 nTPM
Spinal cord	0.9 nTPM
Cerebellum	0.6 nTPM
Hippocampus	0.4 nTPM
Basal ganglia	0.3 nTPM
Hypothalamus	0.3 nTPM
Pons	0.3 nTPM
Amygdala	0.2 nTPM
Cerebral cortex	0.2 nTPM
Thalamus	0.2 nTPM
Midbrain	0.1 nTPM
Medulla oblongata	0.0 nTPM

Cerebellar inhibitory	2.0 nTPM
Pons	4.4 nTPM
Cerebellum	2.8 nTPM
Medulla oblongata	1.5 nTPM
Midbrain	1.2 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	2.1 nTPM
Hypothalamus	3.0 nTPM
Hippocampus	2.4 nTPM
Amygdala	2.3 nTPM
Basal ganglia	2.1 nTPM
Cerebral cortex	2.1 nTPM
Midbrain	1.5 nTPM
Thalamus	1.1 nTPM

Choroid plexus epithelial cell	1.1 nTPM
Hippocampus	2.8 nTPM
Basal ganglia	1.6 nTPM
Medulla oblongata	0.1 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	4.0 nTPM
Spinal cord	22.1 nTPM
Cerebral cortex	5.1 nTPM
Amygdala	4.5 nTPM
Hippocampus	3.6 nTPM
Pons	2.7 nTPM
Cerebellum	1.6 nTPM
Hypothalamus	1.4 nTPM
Medulla oblongata	1.3 nTPM
Thalamus	0.9 nTPM
Midbrain	0.8 nTPM
Basal ganglia	0.5 nTPM

Deep-layer corticothalamic and 6b	1.4 nTPM
Hypothalamus	2.0 nTPM
Hippocampus	1.7 nTPM
Amygdala	1.6 nTPM
Basal ganglia	1.2 nTPM
Midbrain	1.1 nTPM
Cerebral cortex	0.7 nTPM

Deep-layer intratelencephalic	2.2 nTPM
Amygdala	3.2 nTPM
Hypothalamus	2.3 nTPM
Hippocampus	2.0 nTPM
Basal ganglia	1.8 nTPM
Cerebral cortex	1.6 nTPM

Deep-layer near-projecting	2.7 nTPM
Amygdala	3.4 nTPM
Hippocampus	3.3 nTPM
Basal ganglia	2.6 nTPM
Hypothalamus	2.1 nTPM
Cerebral cortex	2.0 nTPM

Eccentric medium spiny neuron	1.6 nTPM
Hippocampus	2.5 nTPM
Amygdala	1.9 nTPM
Cerebral cortex	1.5 nTPM
Basal ganglia	1.1 nTPM
Hypothalamus	1.1 nTPM
Thalamus	1.1 nTPM

Endothelial cell	265.3 nTPM
Midbrain	327.9 nTPM
Amygdala	307.4 nTPM
Hippocampus	306.8 nTPM
Spinal cord	303.8 nTPM
Pons	283.4 nTPM
Thalamus	281.8 nTPM
Cerebral cortex	278.7 nTPM
Cerebellum	254.0 nTPM
Basal ganglia	210.7 nTPM
Medulla oblongata	203.1 nTPM
Hypothalamus	161.3 nTPM

Ependymal cell	1.3 nTPM
Hypothalamus	3.6 nTPM
Thalamus	1.6 nTPM
Medulla oblongata	1.5 nTPM
Hippocampus	1.4 nTPM
Midbrain	1.3 nTPM
Pons	1.2 nTPM
Basal ganglia	0.9 nTPM
Amygdala	0.6 nTPM
Spinal cord	0.0 nTPM