Single cell type - PGRMC2 - The Human Protein Atlas

PGRMC2

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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.	PGRMC2
Gene descriptionⁱ Full gene name according to HGNC.	Progesterone receptor membrane component 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	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.	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.	Plasma cells - Protein processing (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 (Syncytiotrophoblasts)
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.	0.34
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.	Low immune cell specificity
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 (Syncytiotrophoblasts)

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: Low immune cell specificity
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

PGRMC2 is part of cluster 77 Plasma cells - Protein processing with confidenceⁱ 1
324 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.
SDF4	Stromal cell derived factor 4	0.5559	77
NFYB	Nuclear transcription factor Y subunit beta	0.5166	3
TOR1AIP2	Torsin 1A interacting protein 2	0.5145	43
SLC39A7	Solute carrier family 39 member 7	0.4615	77
SEC31A	SEC31 homolog A, COPII coat complex component	0.4570	77
SEC22B	SEC22 homolog B, vesicle trafficking protein	0.4565	77
KDELR3	KDEL endoplasmic reticulum protein retention receptor 3	0.4515	50
GPR146	G protein-coupled receptor 146	0.4513	4
EIF4EBP2	Eukaryotic translation initiation factor 4E binding protein 2	0.4484	3
C1orf115	Chromosome 1 open reading frame 115	0.4373	5
TGFBR3	Transforming growth factor beta receptor 3	0.4263	53
SLC37A4	Solute carrier family 37 member 4	0.4263	22
FLT1	Fms related receptor tyrosine kinase 1	0.4249	4
B4GALT7	Beta-1,4-galactosyltransferase 7	0.4225	77
FBLN1	Fibulin 1	0.4221	53

IMMUNE CELLS

PGRMC2 is part of cluster 41 Basophils - Unknown function with confidenceⁱ 0.91
293 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.
RITA1	RBPJ interacting and tubulin associated 1	1.0000	41
FPGT-TNNI3K	FPGT-TNNI3K readthrough	0.9762	41
PPIL3	Peptidylprolyl isomerase like 3	0.9762	41
GPATCH2	G-patch domain containing 2	0.9762	41
JRK	Jrk helix-turn-helix protein	0.9762	41
NSMCE1	NSE1 homolog, SMC5-SMC6 complex component	0.9762	41
SPICE1	Spindle and centriole associated protein 1	0.9762	41
BBOF1	Basal body orientation factor 1	0.9762	41
MAPK9	Mitogen-activated protein kinase 9	0.9762	41
CHD1L	Chromodomain helicase DNA binding protein 1 like	0.9524	41
AHI1	Abelson helper integration site 1	0.9524	41
AP4B1	Adaptor related protein complex 4 subunit beta 1	0.9524	41
ZMYM5	Zinc finger MYM-type containing 5	0.9524	41
DLST	Dihydrolipoamide S-succinyltransferase	0.9524	41
DHCR24	24-dehydrocholesterol reductase	0.9524	41

Adipocytes	89.4 nTPM
Adipose tissue	107.0 nTPM
Breast	71.9 nTPM

Alveolar cells type 1	62.5 nTPM
Lung	62.5 nTPM

Alveolar cells type 2	47.1 nTPM
Lung	47.1 nTPM

Astrocytes	15.8 nTPM
Brain	15.8 nTPM

B-cells	25.0 nTPM
Skin	54.2 nTPM
Kidney	41.6 nTPM
Salivary gland	36.7 nTPM
Adipose tissue	33.3 nTPM
Thymus	25.7 nTPM
Lung	24.1 nTPM
Spleen	22.8 nTPM
Stomach	21.1 nTPM
Lymph node	18.6 nTPM
Liver	14.5 nTPM
Bone marrow	14.5 nTPM
PBMC	12.3 nTPM
Esophagus	5.9 nTPM

Ciliated cells	31.6 nTPM
Endometrium	42.2 nTPM
Fallopian tube	32.3 nTPM
Bronchus	27.3 nTPM
Lung	24.5 nTPM

Club cells	40.7 nTPM
Prostate	62.1 nTPM
Lung	34.9 nTPM
Bronchus	25.1 nTPM

Dendritic cells	22.4 nTPM
Adipose tissue	26.8 nTPM
PBMC	18.0 nTPM

Endothelial cells	53.4 nTPM
Vascular	81.8 nTPM
Lung	77.4 nTPM
Thymus	68.9 nTPM
Liver	63.0 nTPM
Salivary gland	60.6 nTPM
Heart muscle	58.9 nTPM
Prostate	57.4 nTPM
Fallopian tube	55.2 nTPM
Placenta	53.9 nTPM
Skin	50.3 nTPM
Pancreas	49.1 nTPM
Skeletal muscle	48.1 nTPM
Breast	46.6 nTPM
Tongue	45.4 nTPM
Testis	37.2 nTPM
Endometrium	37.2 nTPM
Esophagus	36.7 nTPM
Ovary	33.9 nTPM

Enteroendocrine cells	53.0 nTPM
Colon	60.7 nTPM
Rectum	57.0 nTPM
Small intestine	41.2 nTPM

Fibroblasts	75.9 nTPM
Adipose tissue	123.9 nTPM
Skin	99.9 nTPM
Salivary gland	91.4 nTPM
Skeletal muscle	90.8 nTPM
Pancreas	90.7 nTPM
Placenta	87.9 nTPM
Vascular	82.0 nTPM
Esophagus	74.5 nTPM
Lung	70.9 nTPM
Prostate	70.6 nTPM
Thymus	65.2 nTPM
Breast	64.3 nTPM
Fallopian tube	62.9 nTPM
Heart muscle	56.8 nTPM
Stomach	51.9 nTPM
Liver	30.8 nTPM

Granulocytes	32.5 nTPM
Lung	42.4 nTPM
Fallopian tube	35.9 nTPM
Tongue	19.4 nTPM

Intestinal goblet cells	81.8 nTPM
Small intestine	93.2 nTPM
Rectum	76.7 nTPM
Colon	75.5 nTPM

Lymphatic endothelial cells	41.4 nTPM
Fallopian tube	55.6 nTPM
Ovary	27.3 nTPM

Macrophages	23.6 nTPM
Pancreas	41.1 nTPM
Prostate	37.6 nTPM
Skin	36.8 nTPM
Salivary gland	33.3 nTPM
Kidney	31.9 nTPM
Vascular	28.0 nTPM
Tongue	27.9 nTPM
Lung	26.9 nTPM
Thymus	23.9 nTPM
Endometrium	20.3 nTPM
Fallopian tube	19.9 nTPM
Skeletal muscle	19.8 nTPM
Esophagus	18.0 nTPM
Testis	17.4 nTPM
Breast	16.5 nTPM
Adipose tissue	16.2 nTPM
Stomach	12.9 nTPM
Spleen	12.0 nTPM
Bone marrow	8.1 nTPM

Bipolar cells	23.0 nTPM
Eye	23.0 nTPM

Cholangiocytes	59.1 nTPM
Liver	59.1 nTPM

Collecting duct cells	42.8 nTPM
Kidney	42.8 nTPM

Cone photoreceptor cells	6.8 nTPM
Eye	6.8 nTPM

Paneth cells	58.5 nTPM
Rectum	69.5 nTPM
Colon	54.3 nTPM
Small intestine	51.8 nTPM

Plasma cells	71.3 nTPM
Fallopian tube	168.2 nTPM
Salivary gland	88.6 nTPM
Liver	71.6 nTPM
Esophagus	67.6 nTPM
Stomach	55.7 nTPM
Thymus	54.1 nTPM
Spleen	35.6 nTPM
Bone marrow	28.7 nTPM

Schwann cells	37.3 nTPM
Esophagus	47.9 nTPM
Vascular	46.0 nTPM
Adipose tissue	18.0 nTPM

Serous glandular cells	63.9 nTPM
Salivary gland	70.4 nTPM
Tongue	57.4 nTPM

Smooth muscle cells	53.7 nTPM
Tongue	76.6 nTPM
Skin	70.3 nTPM
Prostate	63.3 nTPM
Vascular	63.2 nTPM
Placenta	59.2 nTPM
Liver	59.0 nTPM
Skeletal muscle	57.6 nTPM
Fallopian tube	53.3 nTPM
Adipose tissue	51.2 nTPM
Ovary	51.1 nTPM
Salivary gland	46.3 nTPM
Thymus	44.5 nTPM
Lung	43.5 nTPM
Endometrium	40.4 nTPM
Breast	39.7 nTPM
Esophagus	39.6 nTPM

Suprabasal keratinocytes	94.4 nTPM
Skin	106.4 nTPM
Tongue	82.4 nTPM

T-cells	36.0 nTPM
Salivary gland	56.8 nTPM
Adipose tissue	54.7 nTPM
Prostate	54.3 nTPM
Fallopian tube	49.8 nTPM
Thymus	47.8 nTPM
Endometrium	47.1 nTPM
Skin	44.9 nTPM
Kidney	40.8 nTPM
Lung	39.2 nTPM
Tongue	38.4 nTPM
Vascular	37.8 nTPM
Skeletal muscle	36.7 nTPM
Colon	32.2 nTPM
Lymph node	28.1 nTPM
Breast	26.0 nTPM
Liver	25.3 nTPM
Spleen	23.8 nTPM
PBMC	22.2 nTPM
Stomach	19.9 nTPM
Bone marrow	16.2 nTPM
Esophagus	14.6 nTPM

Undifferentiated cells	54.5 nTPM
Small intestine	64.3 nTPM
Rectum	52.2 nTPM
Colon	47.0 nTPM

Amygdala excitatory	30.0 nTPM
Hippocampus	32.6 nTPM
Amygdala	32.0 nTPM
Hypothalamus	29.6 nTPM
Thalamus	29.5 nTPM
Cerebral cortex	28.7 nTPM
Basal ganglia	27.5 nTPM

Astrocyte	27.8 nTPM
Spinal cord	38.7 nTPM
Medulla oblongata	30.8 nTPM
Cerebellum	29.3 nTPM
Hippocampus	28.6 nTPM
Hypothalamus	28.5 nTPM
Amygdala	27.1 nTPM
Midbrain	25.3 nTPM
Thalamus	25.0 nTPM
Cerebral cortex	24.7 nTPM
Basal ganglia	24.4 nTPM
Pons	23.3 nTPM

Bergmann glia	27.6 nTPM
Pons	30.2 nTPM
Cerebellum	27.0 nTPM
Medulla oblongata	25.6 nTPM

Central nervous system macrophage	30.6 nTPM
Amygdala	35.8 nTPM
Medulla oblongata	33.7 nTPM
Pons	31.7 nTPM
Basal ganglia	31.1 nTPM
Hippocampus	30.8 nTPM
Midbrain	30.4 nTPM
Thalamus	30.1 nTPM
Cerebellum	29.4 nTPM
Cerebral cortex	29.1 nTPM
Hypothalamus	27.6 nTPM
Spinal cord	26.8 nTPM

Cerebellar inhibitory	24.4 nTPM
Pons	26.1 nTPM
Midbrain	25.5 nTPM
Medulla oblongata	24.7 nTPM
Cerebellum	24.0 nTPM
Spinal cord	22.0 nTPM

Cge interneuron	32.9 nTPM
Basal ganglia	36.5 nTPM
Midbrain	35.5 nTPM
Thalamus	33.7 nTPM
Hippocampus	33.0 nTPM
Amygdala	32.9 nTPM
Cerebral cortex	32.0 nTPM
Hypothalamus	26.8 nTPM

Choroid plexus epithelial cell	38.1 nTPM
Basal ganglia	42.3 nTPM
Medulla oblongata	41.1 nTPM
Thalamus	41.1 nTPM
Hippocampus	27.7 nTPM

Committed oligodendrocyte precursor	30.8 nTPM
Pons	46.0 nTPM
Midbrain	41.2 nTPM
Amygdala	32.7 nTPM
Thalamus	32.2 nTPM
Basal ganglia	31.2 nTPM
Medulla oblongata	31.0 nTPM
Hypothalamus	30.7 nTPM
Hippocampus	29.5 nTPM
Spinal cord	25.8 nTPM
Cerebral cortex	21.5 nTPM
Cerebellum	17.4 nTPM

Deep-layer corticothalamic and 6b	29.5 nTPM
Midbrain	36.6 nTPM
Amygdala	29.3 nTPM
Cerebral cortex	28.6 nTPM
Hippocampus	28.3 nTPM
Basal ganglia	27.1 nTPM
Hypothalamus	26.9 nTPM

Deep-layer intratelencephalic	29.5 nTPM
Amygdala	31.8 nTPM
Hippocampus	31.4 nTPM
Cerebral cortex	29.0 nTPM
Basal ganglia	28.7 nTPM
Hypothalamus	26.6 nTPM

Deep-layer near-projecting	31.0 nTPM
Hippocampus	37.4 nTPM
Basal ganglia	32.7 nTPM
Cerebral cortex	30.9 nTPM
Amygdala	27.5 nTPM
Hypothalamus	26.3 nTPM

Eccentric medium spiny neuron	32.0 nTPM
Hippocampus	39.0 nTPM
Thalamus	33.2 nTPM
Hypothalamus	31.9 nTPM
Amygdala	30.6 nTPM
Basal ganglia	29.3 nTPM
Cerebral cortex	27.9 nTPM