Single cell type - RCN3 - The Human Protein Atlas

RCN3

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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.	RCN3
Gene descriptionⁱ Full gene name according to HGNC.	Reticulocalbin 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Plasma proteins
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.	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.	Connective tissue cells - ECM organization (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 (Fibroblasts, Pancreatic endocrine cells, Endometrial stromal cells, Ovarian stromal cells, Peritubular cells, Leydig 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.	0.68
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.	Group enriched (Fibroblast, Central nervous system macrophage, Vascular associated smooth muscle cell, Astrocyte)
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 (naive CD4 T-cell)
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 (Fibroblasts, Pancreatic endocrine cells, Endometrial stromal cells, Ovarian stromal cells, Peritubular cells, Leydig 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: Group enriched (Fibroblast, Central nervous system macrophage, Vascular associated smooth muscle cell, Astrocyte)

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 (naive CD4 T-cell)
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

RCN3 is part of cluster 50 Connective tissue cells - ECM organization with confidenceⁱ 1
176 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.
COL1A1	Collagen type I alpha 1 chain	0.9218	50
FKBP10	FKBP prolyl isomerase 10	0.8999	50
COL3A1	Collagen type III alpha 1 chain	0.8982	50
COL5A1	Collagen type V alpha 1 chain	0.8976	50
CTHRC1	Collagen triple helix repeat containing 1	0.8662	50
LUM	Lumican	0.8656	50
OLFML3	Olfactomedin like 3	0.8584	50
COL1A2	Collagen type I alpha 2 chain	0.8515	50
P3H1	Prolyl 3-hydroxylase 1	0.8214	50
SPARC	Secreted protein acidic and cysteine rich	0.8165	50
SERPINH1	Serpin family H member 1	0.8116	50
GPX8	Glutathione peroxidase 8 (putative)	0.8001	50
P3H4	Prolyl 3-hydroxylase family member 4 (inactive)	0.7910	50
GPX7	Glutathione peroxidase 7	0.7853	50
COL6A1	Collagen type VI alpha 1 chain	0.7784	53

IMMUNE CELLS

RCN3 is part of cluster 43 Non-specific - Transcription & Translation with confidenceⁱ 1
433 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.
DHDH	Dihydrodiol dehydrogenase	1.0000	43
GGT7	Gamma-glutamyltransferase 7	0.9762	43
FBXO48	F-box protein 48	0.9762	43
NPM1	Nucleophosmin 1	0.9762	43
ZNF771	Zinc finger protein 771	0.9762	43
B3GNT3	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	0.9762	39
TNK1	Tyrosine kinase non receptor 1	0.9762	43
LCLAT1	Lysocardiolipin acyltransferase 1	0.9762	43
APBB1	Amyloid beta precursor protein binding family B member 1	0.9762	39
ABRAXAS1	Abraxas 1, BRCA1 A complex subunit	0.9762	43
RPS15A	Ribosomal protein S15a	0.9762	43
HAVCR1	Hepatitis A virus cellular receptor 1	0.9762	43
ENO2	Enolase 2	0.9762	43
PLEK2	Pleckstrin 2	0.9762	43
AKR1B1	Aldo-keto reductase family 1 member B	0.9762	39

Adipocytes	7.9 nTPM
Breast	10.6 nTPM
Adipose tissue	5.1 nTPM

Alveolar cells type 1	0.3 nTPM
Lung	0.3 nTPM

Alveolar cells type 2	1.2 nTPM
Lung	1.2 nTPM

Astrocytes	4.3 nTPM
Brain	4.3 nTPM

B-cells	2.5 nTPM
Skin	13.6 nTPM
Kidney	5.2 nTPM
Liver	4.8 nTPM
Thymus	2.4 nTPM
Salivary gland	2.1 nTPM
Adipose tissue	1.6 nTPM
Stomach	1.3 nTPM
Lung	1.3 nTPM
Lymph node	0.1 nTPM
Spleen	0.1 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Ciliated cells	1.8 nTPM
Fallopian tube	3.6 nTPM
Endometrium	2.0 nTPM
Lung	1.3 nTPM
Bronchus	0.3 nTPM

Club cells	1.8 nTPM
Lung	3.4 nTPM
Bronchus	1.8 nTPM
Prostate	0.1 nTPM

Endothelial cells	8.0 nTPM
Pancreas	31.0 nTPM
Liver	23.9 nTPM
Ovary	13.2 nTPM
Endometrium	9.1 nTPM
Placenta	8.5 nTPM
Vascular	7.5 nTPM
Skin	7.3 nTPM
Tongue	6.2 nTPM
Thymus	6.1 nTPM
Fallopian tube	4.8 nTPM
Prostate	4.4 nTPM
Esophagus	4.3 nTPM
Skeletal muscle	3.9 nTPM
Testis	3.4 nTPM
Lung	3.0 nTPM
Salivary gland	2.8 nTPM
Breast	2.6 nTPM
Heart muscle	2.2 nTPM

Enteroendocrine cells	4.0 nTPM
Colon	5.2 nTPM
Small intestine	3.4 nTPM
Rectum	3.4 nTPM

Fibroblasts	110.5 nTPM
Pancreas	456.6 nTPM
Adipose tissue	160.5 nTPM
Stomach	141.2 nTPM
Skin	138.9 nTPM
Breast	133.5 nTPM
Skeletal muscle	109.0 nTPM
Esophagus	107.0 nTPM
Vascular	100.3 nTPM
Placenta	90.9 nTPM
Fallopian tube	89.3 nTPM
Thymus	78.2 nTPM
Salivary gland	65.6 nTPM
Lung	34.7 nTPM
Liver	24.9 nTPM
Prostate	19.8 nTPM
Heart muscle	17.7 nTPM

Granulocytes	2.4 nTPM
Fallopian tube	4.8 nTPM
Lung	2.5 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	5.8 nTPM
Rectum	6.6 nTPM
Small intestine	6.3 nTPM
Colon	4.7 nTPM

Lymphatic endothelial cells	2.3 nTPM
Fallopian tube	4.7 nTPM
Ovary	0.0 nTPM

Macrophages	12.2 nTPM
Esophagus	43.7 nTPM
Thymus	27.0 nTPM
Skin	24.5 nTPM
Vascular	18.9 nTPM
Spleen	15.0 nTPM
Breast	14.5 nTPM
Adipose tissue	13.2 nTPM
Endometrium	9.2 nTPM
Bone marrow	9.1 nTPM
Fallopian tube	9.1 nTPM
Skeletal muscle	8.4 nTPM
Salivary gland	6.9 nTPM
Prostate	6.7 nTPM
Testis	6.2 nTPM
Lung	5.6 nTPM
Tongue	5.4 nTPM
Kidney	3.5 nTPM
Stomach	2.6 nTPM
Pancreas	2.1 nTPM

Paneth cells	6.3 nTPM
Small intestine	10.4 nTPM
Rectum	4.9 nTPM
Colon	3.6 nTPM

Basal prostatic cells	0.8 nTPM
Prostate	0.8 nTPM

Bipolar cells	0.7 nTPM
Eye	0.7 nTPM

Cholangiocytes	1.9 nTPM
Liver	1.9 nTPM

Collecting duct cells	1.9 nTPM
Kidney	1.9 nTPM

Plasma cells	9.7 nTPM
Fallopian tube	30.2 nTPM
Salivary gland	15.7 nTPM
Stomach	9.6 nTPM
Liver	7.0 nTPM
Thymus	7.0 nTPM
Esophagus	5.2 nTPM
Spleen	3.1 nTPM
Bone marrow	0.0 nTPM

Schwann cells	3.1 nTPM
Vascular	5.7 nTPM
Adipose tissue	3.5 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	7.5 nTPM
Tongue	8.8 nTPM
Salivary gland	6.1 nTPM

Smooth muscle cells	32.2 nTPM
Placenta	155.7 nTPM
Endometrium	52.0 nTPM
Vascular	45.7 nTPM
Tongue	39.8 nTPM
Adipose tissue	32.3 nTPM
Lung	31.7 nTPM
Thymus	29.6 nTPM
Ovary	25.1 nTPM
Breast	21.1 nTPM
Esophagus	18.0 nTPM
Fallopian tube	17.7 nTPM
Skin	17.1 nTPM
Liver	15.7 nTPM
Skeletal muscle	10.3 nTPM
Salivary gland	2.3 nTPM
Prostate	1.2 nTPM

T-cells	2.0 nTPM
Vascular	8.4 nTPM
Skin	8.1 nTPM
Endometrium	6.1 nTPM
Kidney	2.7 nTPM
Salivary gland	2.3 nTPM
Colon	1.9 nTPM
PBMC	1.9 nTPM
Breast	1.8 nTPM
Skeletal muscle	1.5 nTPM
Lymph node	1.3 nTPM
Thymus	1.3 nTPM
Spleen	1.1 nTPM
Fallopian tube	1.0 nTPM
Lung	0.8 nTPM
Bone marrow	0.7 nTPM
Liver	0.6 nTPM
Adipose tissue	0.3 nTPM
Stomach	0.1 nTPM
Prostate	0.1 nTPM
Tongue	0.1 nTPM
Esophagus	0.0 nTPM

Undifferentiated cells	5.7 nTPM
Small intestine	9.5 nTPM
Rectum	5.2 nTPM
Colon	2.4 nTPM

Amygdala excitatory	0.6 nTPM
Thalamus	0.9 nTPM
Basal ganglia	0.6 nTPM
Amygdala	0.5 nTPM
Cerebral cortex	0.5 nTPM
Hypothalamus	0.5 nTPM
Hippocampus	0.4 nTPM

Astrocyte	6.4 nTPM
Cerebellum	12.2 nTPM
Pons	8.4 nTPM
Spinal cord	7.5 nTPM
Medulla oblongata	6.6 nTPM
Midbrain	6.4 nTPM
Thalamus	6.2 nTPM
Basal ganglia	5.8 nTPM
Hippocampus	5.8 nTPM
Cerebral cortex	5.0 nTPM
Amygdala	3.3 nTPM
Hypothalamus	3.1 nTPM

Bergmann glia	2.7 nTPM
Pons	4.3 nTPM
Cerebellum	3.7 nTPM
Medulla oblongata	0.0 nTPM

Central nervous system macrophage	21.7 nTPM
Hippocampus	29.2 nTPM
Basal ganglia	28.8 nTPM
Cerebral cortex	28.5 nTPM
Cerebellum	25.8 nTPM
Midbrain	24.5 nTPM
Pons	19.1 nTPM
Amygdala	19.0 nTPM
Thalamus	18.1 nTPM
Medulla oblongata	17.3 nTPM
Spinal cord	15.6 nTPM
Hypothalamus	12.6 nTPM

Cerebellar inhibitory	1.6 nTPM
Spinal cord	2.7 nTPM
Pons	2.5 nTPM
Cerebellum	1.0 nTPM
Medulla oblongata	0.9 nTPM
Midbrain	0.6 nTPM

Cge interneuron	1.6 nTPM
Cerebral cortex	2.3 nTPM
Basal ganglia	1.9 nTPM
Thalamus	1.7 nTPM
Hypothalamus	1.6 nTPM
Hippocampus	1.5 nTPM
Amygdala	1.4 nTPM
Midbrain	0.7 nTPM

Choroid plexus epithelial cell	1.9 nTPM
Basal ganglia	4.8 nTPM
Medulla oblongata	3.0 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	2.6 nTPM
Hippocampus	4.7 nTPM
Medulla oblongata	3.9 nTPM
Cerebral cortex	3.8 nTPM
Amygdala	3.4 nTPM
Cerebellum	3.2 nTPM
Midbrain	2.5 nTPM
Basal ganglia	2.2 nTPM
Hypothalamus	2.0 nTPM
Pons	1.8 nTPM
Thalamus	0.7 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	1.1 nTPM
Hypothalamus	1.9 nTPM
Basal ganglia	1.7 nTPM
Amygdala	1.0 nTPM
Cerebral cortex	1.0 nTPM
Hippocampus	0.8 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	1.3 nTPM
Cerebral cortex	1.8 nTPM
Hypothalamus	1.7 nTPM
Basal ganglia	1.4 nTPM
Hippocampus	1.0 nTPM
Amygdala	0.8 nTPM

Deep-layer near-projecting	1.9 nTPM
Hippocampus	3.6 nTPM
Hypothalamus	1.9 nTPM
Amygdala	1.6 nTPM
Basal ganglia	1.5 nTPM
Cerebral cortex	1.0 nTPM

Eccentric medium spiny neuron	1.0 nTPM
Hippocampus	1.2 nTPM
Cerebral cortex	1.1 nTPM
Hypothalamus	1.0 nTPM
Amygdala	0.9 nTPM
Thalamus	0.9 nTPM
Basal ganglia	0.8 nTPM

Endothelial cell	3.6 nTPM
Basal ganglia	7.5 nTPM
Medulla oblongata	6.2 nTPM
Spinal cord	5.2 nTPM
Midbrain	3.8 nTPM
Hypothalamus	3.7 nTPM
Cerebral cortex	3.2 nTPM
Pons	3.1 nTPM
Thalamus	2.8 nTPM
Cerebellum	2.3 nTPM
Hippocampus	1.9 nTPM
Amygdala	0.0 nTPM

Ependymal cell	1.6 nTPM
Amygdala	2.8 nTPM
Basal ganglia	2.6 nTPM
Hippocampus	2.3 nTPM
Midbrain	1.9 nTPM
Pons	1.6 nTPM
Thalamus	1.6 nTPM
Medulla oblongata	1.1 nTPM
Hypothalamus	0.9 nTPM
Spinal cord	0.0 nTPM