Single cell type - SLC31A1 - The Human Protein Atlas

SLC31A1

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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.	SLC31A1
Gene descriptionⁱ Full gene name according to HGNC.	Solute carrier family 31 member 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Metabolic proteins 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.	1

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.	Macrophages - Innate immune response (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 (Serous glandular cells, Prostatic glandular cells, Hepatocytes)
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.	0.40
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 (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.	Group enriched (non-classical monocyte, intermediate monocyte, classical monocyte, myeloid DC, neutrophil)
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 (Serous glandular cells, Prostatic glandular cells, Hepatocytes)

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 (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: Group enriched (non-classical monocyte, intermediate monocyte, classical monocyte, myeloid DC, neutrophil)
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

SLC31A1 is part of cluster 58 Macrophages - Innate immune response with confidenceⁱ 1
420 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.
ATP6AP1	ATPase H+ transporting accessory protein 1	0.7410	58
DNASE2B	Deoxyribonuclease 2 beta	0.7058	75
RMDN3	Regulator of microtubule dynamics 3	0.6920	58
CTSD	Cathepsin D	0.6745	58
FKBP15	FKBP prolyl isomerase family member 15	0.6628	58
LAMP2	Lysosomal associated membrane protein 2	0.6617	58
SOAT1	Sterol O-acyltransferase 1	0.6551	58
GRN	Granulin precursor	0.6495	58
CYP27A1	Cytochrome P450 family 27 subfamily A member 1	0.6403	58
INHBA	Inhibin subunit beta A	0.6311	58
SLC31A2	Solute carrier family 31 member 2	0.6298	75
RRAGD	Ras related GTP binding D	0.6229	75
HEXB	Hexosaminidase subunit beta	0.6222	58
ACP5	Acid phosphatase 5, tartrate resistant	0.6121	58
DCSTAMP	Dendrocyte expressed seven transmembrane protein	0.6118	58

IMMUNE CELLS

SLC31A1 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.
SLC24A4	Solute carrier family 24 member 4	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	7.8 nTPM
Breast	8.2 nTPM
Adipose tissue	7.5 nTPM

Alveolar cells type 1	15.2 nTPM
Lung	15.2 nTPM

Alveolar cells type 2	41.1 nTPM
Lung	41.1 nTPM

Astrocytes	7.1 nTPM
Brain	7.1 nTPM

B-cells	6.1 nTPM
Salivary gland	11.9 nTPM
Esophagus	11.8 nTPM
Lung	10.7 nTPM
Skin	8.5 nTPM
Adipose tissue	5.8 nTPM
Stomach	5.5 nTPM
Kidney	5.2 nTPM
Liver	4.8 nTPM
Thymus	3.9 nTPM
Spleen	3.7 nTPM
Lymph node	3.4 nTPM
PBMC	3.1 nTPM
Bone marrow	1.6 nTPM

Ciliated cells	22.2 nTPM
Lung	33.7 nTPM
Bronchus	28.0 nTPM
Endometrium	15.8 nTPM
Fallopian tube	11.3 nTPM

Club cells	55.9 nTPM
Lung	88.5 nTPM
Bronchus	49.5 nTPM
Prostate	29.5 nTPM

Endothelial cells	11.8 nTPM
Liver	32.8 nTPM
Endometrium	26.6 nTPM
Placenta	20.4 nTPM
Lung	14.2 nTPM
Salivary gland	13.3 nTPM
Pancreas	12.9 nTPM
Heart muscle	12.8 nTPM
Prostate	10.3 nTPM
Vascular	9.8 nTPM
Thymus	8.8 nTPM
Fallopian tube	8.7 nTPM
Tongue	8.6 nTPM
Skin	7.4 nTPM
Esophagus	7.3 nTPM
Skeletal muscle	5.9 nTPM
Ovary	5.2 nTPM
Breast	4.4 nTPM
Testis	3.4 nTPM

Enteroendocrine cells	11.1 nTPM
Colon	23.1 nTPM
Rectum	6.7 nTPM
Small intestine	3.4 nTPM

Fibroblasts	15.6 nTPM
Pancreas	39.1 nTPM
Salivary gland	18.7 nTPM
Lung	18.1 nTPM
Stomach	17.3 nTPM
Vascular	16.7 nTPM
Heart muscle	16.0 nTPM
Liver	15.4 nTPM
Fallopian tube	15.4 nTPM
Thymus	15.1 nTPM
Placenta	14.4 nTPM
Adipose tissue	13.6 nTPM
Skeletal muscle	10.6 nTPM
Prostate	10.6 nTPM
Skin	10.3 nTPM
Breast	10.3 nTPM
Esophagus	8.4 nTPM

Granulocytes	9.7 nTPM
Tongue	19.4 nTPM
Lung	5.0 nTPM
Fallopian tube	4.8 nTPM

Intestinal goblet cells	18.8 nTPM
Colon	25.3 nTPM
Small intestine	17.5 nTPM
Rectum	13.7 nTPM

Lymphatic endothelial cells	3.1 nTPM
Fallopian tube	6.1 nTPM
Ovary	0.0 nTPM

Macrophages	46.9 nTPM
Lung	169.8 nTPM
Pancreas	113.1 nTPM
Vascular	78.2 nTPM
Salivary gland	62.7 nTPM
Thymus	62.6 nTPM
Prostate	58.8 nTPM
Fallopian tube	39.4 nTPM
Spleen	37.1 nTPM
Stomach	36.0 nTPM
Tongue	32.7 nTPM
Bone marrow	29.4 nTPM
Skin	26.7 nTPM
Adipose tissue	25.4 nTPM
Testis	23.6 nTPM
Kidney	22.1 nTPM
Skeletal muscle	21.9 nTPM
Endometrium	19.7 nTPM
Breast	17.5 nTPM
Esophagus	14.1 nTPM

Paneth cells	7.1 nTPM
Rectum	10.7 nTPM
Colon	7.2 nTPM
Small intestine	3.5 nTPM

Basal keratinocytes	18.4 nTPM
Tongue	19.1 nTPM
Skin	17.8 nTPM

Basal squamous epithelial cells	11.7 nTPM
Esophagus	11.7 nTPM

Bipolar cells	7.9 nTPM
Eye	7.9 nTPM

Cholangiocytes	24.8 nTPM
Liver	24.8 nTPM

Plasma cells	22.9 nTPM
Thymus	35.0 nTPM
Spleen	32.5 nTPM
Liver	31.0 nTPM
Salivary gland	29.1 nTPM
Stomach	15.5 nTPM
Bone marrow	15.1 nTPM
Fallopian tube	14.8 nTPM
Esophagus	10.4 nTPM

Schwann cells	10.2 nTPM
Adipose tissue	19.1 nTPM
Vascular	11.5 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	102.7 nTPM
Salivary gland	143.5 nTPM
Tongue	61.9 nTPM

Smooth muscle cells	14.1 nTPM
Salivary gland	56.3 nTPM
Placenta	28.2 nTPM
Vascular	14.8 nTPM
Prostate	12.8 nTPM
Thymus	12.7 nTPM
Endometrium	12.3 nTPM
Fallopian tube	11.8 nTPM
Liver	11.5 nTPM
Lung	10.6 nTPM
Tongue	9.6 nTPM
Skin	9.1 nTPM
Adipose tissue	8.9 nTPM
Esophagus	7.2 nTPM
Breast	7.2 nTPM
Skeletal muscle	6.9 nTPM
Ovary	6.1 nTPM

Suprabasal keratinocytes	26.0 nTPM
Tongue	36.5 nTPM
Skin	15.5 nTPM

T-cells	6.3 nTPM
Salivary gland	12.7 nTPM
Prostate	11.7 nTPM
Vascular	10.1 nTPM
Colon	9.7 nTPM
Tongue	9.5 nTPM
Stomach	8.3 nTPM
Kidney	7.1 nTPM
Endometrium	6.4 nTPM
Spleen	5.9 nTPM
Skin	5.6 nTPM
Fallopian tube	5.6 nTPM
Lung	5.0 nTPM
Esophagus	4.9 nTPM
Liver	4.7 nTPM
Breast	4.7 nTPM
Adipose tissue	4.0 nTPM
PBMC	3.8 nTPM
Bone marrow	3.7 nTPM
Skeletal muscle	3.4 nTPM
Thymus	3.4 nTPM
Lymph node	2.3 nTPM

Undifferentiated cells	19.0 nTPM
Colon	21.1 nTPM
Small intestine	20.6 nTPM
Rectum	15.4 nTPM

Amygdala excitatory	18.8 nTPM
Hypothalamus	20.4 nTPM
Amygdala	19.8 nTPM
Cerebral cortex	19.7 nTPM
Hippocampus	19.5 nTPM
Basal ganglia	18.0 nTPM
Thalamus	15.4 nTPM

Astrocyte	16.8 nTPM
Amygdala	18.6 nTPM
Thalamus	18.3 nTPM
Cerebral cortex	17.8 nTPM
Hypothalamus	17.7 nTPM
Basal ganglia	17.3 nTPM
Hippocampus	17.3 nTPM
Spinal cord	17.2 nTPM
Midbrain	16.5 nTPM
Medulla oblongata	15.8 nTPM
Pons	15.5 nTPM
Cerebellum	13.2 nTPM

Bergmann glia	19.0 nTPM
Medulla oblongata	23.4 nTPM
Pons	17.3 nTPM
Cerebellum	16.4 nTPM

Central nervous system macrophage	43.3 nTPM
Spinal cord	53.6 nTPM
Pons	48.7 nTPM
Cerebellum	46.8 nTPM
Hypothalamus	45.9 nTPM
Basal ganglia	45.0 nTPM
Medulla oblongata	43.9 nTPM
Midbrain	42.5 nTPM
Amygdala	39.5 nTPM
Hippocampus	39.0 nTPM
Thalamus	38.4 nTPM
Cerebral cortex	32.5 nTPM

Cerebellar inhibitory	28.5 nTPM
Medulla oblongata	36.1 nTPM
Pons	33.1 nTPM
Midbrain	31.7 nTPM
Cerebellum	30.6 nTPM
Spinal cord	11.0 nTPM

Cge interneuron	21.9 nTPM
Thalamus	25.1 nTPM
Hippocampus	22.7 nTPM
Cerebral cortex	22.3 nTPM
Amygdala	22.1 nTPM
Midbrain	22.1 nTPM
Basal ganglia	21.8 nTPM
Hypothalamus	17.3 nTPM

Choroid plexus epithelial cell	65.8 nTPM
Basal ganglia	78.5 nTPM
Hippocampus	63.8 nTPM
Medulla oblongata	60.5 nTPM
Thalamus	60.3 nTPM

Committed oligodendrocyte precursor	17.3 nTPM
Medulla oblongata	29.7 nTPM
Cerebellum	23.8 nTPM
Basal ganglia	22.4 nTPM
Hippocampus	20.4 nTPM
Amygdala	16.4 nTPM
Thalamus	14.9 nTPM
Hypothalamus	13.7 nTPM
Pons	13.3 nTPM
Midbrain	12.6 nTPM
Cerebral cortex	12.0 nTPM
Spinal cord	11.0 nTPM

Deep-layer corticothalamic and 6b	21.6 nTPM
Midbrain	32.2 nTPM
Cerebral cortex	21.4 nTPM
Hippocampus	20.1 nTPM
Hypothalamus	19.1 nTPM
Amygdala	18.4 nTPM
Basal ganglia	18.4 nTPM

Deep-layer intratelencephalic	20.8 nTPM
Hippocampus	23.1 nTPM
Cerebral cortex	22.7 nTPM
Basal ganglia	20.5 nTPM
Amygdala	20.3 nTPM
Hypothalamus	17.6 nTPM

Deep-layer near-projecting	19.6 nTPM
Hippocampus	24.4 nTPM
Cerebral cortex	22.7 nTPM
Amygdala	18.7 nTPM
Basal ganglia	18.7 nTPM
Hypothalamus	13.5 nTPM

Eccentric medium spiny neuron	21.8 nTPM
Hippocampus	23.6 nTPM
Amygdala	22.7 nTPM
Basal ganglia	22.0 nTPM
Thalamus	22.0 nTPM
Cerebral cortex	20.8 nTPM
Hypothalamus	19.8 nTPM

Endothelial cell	111.6 nTPM
Cerebellum	148.7 nTPM
Pons	129.8 nTPM
Hippocampus	123.7 nTPM
Cerebral cortex	122.7 nTPM
Thalamus	119.7 nTPM
Spinal cord	119.1 nTPM
Medulla oblongata	112.8 nTPM
Midbrain	107.7 nTPM
Amygdala	96.1 nTPM
Basal ganglia	76.4 nTPM
Hypothalamus	70.7 nTPM