Single cell type - RFC3 - The Human Protein Atlas

RFC3

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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.	RFC3
Gene descriptionⁱ Full gene name according to HGNC.	Replication factor C subunit 3
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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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.	Non-specific - Mixed function (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 (Oocytes, Spermatocytes)
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.	0.49
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 (Oocytes, Spermatocytes)

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

RFC3 is part of cluster 15 Non-specific - Mixed function with confidenceⁱ 1
295 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.
POLE2	DNA polymerase epsilon 2, accessory subunit	0.7579	52
NDC1	NDC1 transmembrane nucleoporin	0.6849	15
RAD54L	RAD54 like	0.6351	52
SMC2	Structural maintenance of chromosomes 2	0.6261	52
PSMD1	Proteasome 26S subunit, non-ATPase 1	0.5985	15
PPT2	Palmitoyl-protein thioesterase 2	0.5920	15
WDR12	WD repeat domain 12	0.5841	15
ZNF90	Zinc finger protein 90	0.5840	15
BDNF	Brain derived neurotrophic factor	0.5757	15
CDC45	Cell division cycle 45	0.5646	52
GNG5B	G protein subunit gamma 5B	0.5637	15
CPSF6	Cleavage and polyadenylation specific factor 6	0.5634	15
HNRNPCL1	Heterogeneous nuclear ribonucleoprotein C like 1	0.5620	15
ANP32D	Acidic nuclear phosphoprotein 32 family member D	0.5559	15
GSTA5	Glutathione S-transferase alpha 5	0.5551	15

IMMUNE CELLS

RFC3 is part of cluster 12 Non-specific - Mitochondrial translation with confidenceⁱ 0.99
566 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.
TRAF3	TNF receptor associated factor 3	0.9524	12
GEMIN5	Gem nuclear organelle associated protein 5	0.9286	43
DNAJC30	DnaJ heat shock protein family (Hsp40) member C30	0.9286	12
IFRD2	Interferon related developmental regulator 2	0.9048	12
ING2	Inhibitor of growth family member 2	0.9048	12
FBXO25	F-box protein 25	0.9048	12
C2orf49	Chromosome 2 open reading frame 49	0.9048	14
HSPBP1	HSPA (Hsp70) binding protein 1	0.9048	12
CCDC77	Coiled-coil domain containing 77	0.9048	12
IFT57	Intraflagellar transport 57	0.9048	12
NAT9	N-acetyltransferase 9 (putative)	0.9048	12
USP21	Ubiquitin specific peptidase 21	0.8810	43
METTL25B	Methyltransferase like 25B	0.8810	12
FARS2	Phenylalanyl-tRNA synthetase 2, mitochondrial	0.8810	12
HDGFL2	HDGF like 2	0.8810	43

Adipocytes	8.5 nTPM
Adipose tissue	10.7 nTPM
Breast	6.4 nTPM

Alveolar cells type 1	6.1 nTPM
Lung	6.1 nTPM

Alveolar cells type 2	26.0 nTPM
Lung	26.0 nTPM

Astrocytes	5.6 nTPM
Brain	5.6 nTPM

B-cells	8.4 nTPM
Kidney	15.6 nTPM
Bone marrow	13.4 nTPM
PBMC	12.3 nTPM
Lymph node	11.9 nTPM
Salivary gland	9.9 nTPM
Spleen	8.1 nTPM
Stomach	7.2 nTPM
Adipose tissue	7.0 nTPM
Skin	6.8 nTPM
Thymus	6.6 nTPM
Esophagus	5.9 nTPM
Lung	4.0 nTPM
Liver	0.0 nTPM

Ciliated cells	6.7 nTPM
Fallopian tube	11.3 nTPM
Endometrium	7.6 nTPM
Lung	4.8 nTPM
Bronchus	3.0 nTPM

Club cells	5.8 nTPM
Lung	6.4 nTPM
Bronchus	5.7 nTPM
Prostate	5.2 nTPM

Endothelial cells	11.3 nTPM
Fallopian tube	23.2 nTPM
Vascular	17.7 nTPM
Testis	15.9 nTPM
Esophagus	15.9 nTPM
Thymus	12.5 nTPM
Skin	12.3 nTPM
Salivary gland	12.3 nTPM
Tongue	11.5 nTPM
Liver	11.3 nTPM
Lung	10.7 nTPM
Placenta	9.7 nTPM
Ovary	9.5 nTPM
Endometrium	8.9 nTPM
Skeletal muscle	8.8 nTPM
Prostate	8.5 nTPM
Heart muscle	7.5 nTPM
Breast	4.4 nTPM
Pancreas	2.6 nTPM

Enteroendocrine cells	7.2 nTPM
Rectum	10.1 nTPM
Small intestine	6.9 nTPM
Colon	4.6 nTPM

Fibroblasts	7.7 nTPM
Pancreas	18.9 nTPM
Placenta	16.4 nTPM
Adipose tissue	9.0 nTPM
Fallopian tube	8.7 nTPM
Liver	8.3 nTPM
Vascular	8.2 nTPM
Lung	7.9 nTPM
Esophagus	7.5 nTPM
Prostate	7.3 nTPM
Skin	6.5 nTPM
Breast	5.5 nTPM
Salivary gland	5.0 nTPM
Thymus	4.7 nTPM
Skeletal muscle	4.0 nTPM
Stomach	2.9 nTPM
Heart muscle	2.7 nTPM

Granulocytes	4.3 nTPM
Fallopian tube	8.3 nTPM
Lung	4.5 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	5.3 nTPM
Colon	7.9 nTPM
Rectum	5.4 nTPM
Small intestine	2.7 nTPM

Lymphatic endothelial cells	6.4 nTPM
Fallopian tube	7.4 nTPM
Ovary	5.5 nTPM

Macrophages	6.5 nTPM
Bone marrow	17.2 nTPM
Endometrium	10.5 nTPM
Stomach	10.3 nTPM
Testis	9.9 nTPM
Esophagus	9.0 nTPM
Vascular	7.6 nTPM
Adipose tissue	6.7 nTPM
Prostate	6.7 nTPM
Tongue	6.6 nTPM
Fallopian tube	5.6 nTPM
Breast	4.4 nTPM
Pancreas	4.1 nTPM
Salivary gland	4.1 nTPM
Thymus	4.1 nTPM
Spleen	4.0 nTPM
Skeletal muscle	3.6 nTPM
Kidney	3.5 nTPM
Skin	3.3 nTPM
Lung	2.7 nTPM

Paneth cells	1.4 nTPM
Rectum	4.1 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Bipolar cells	14.3 nTPM
Eye	14.3 nTPM

Cholangiocytes	1.9 nTPM
Liver	1.9 nTPM

Cytotrophoblasts	31.2 nTPM
Placenta	31.2 nTPM

Early spermatids	8.6 nTPM
Testis	8.6 nTPM

Plasma cells	21.3 nTPM
Bone marrow	54.4 nTPM
Spleen	34.6 nTPM
Liver	31.5 nTPM
Thymus	30.9 nTPM
Salivary gland	9.0 nTPM
Fallopian tube	5.5 nTPM
Stomach	4.6 nTPM
Esophagus	0.0 nTPM

Schwann cells	7.0 nTPM
Vascular	16.2 nTPM
Adipose tissue	4.7 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	5.0 nTPM
Salivary gland	5.5 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	7.2 nTPM
Endometrium	12.3 nTPM
Adipose tissue	11.1 nTPM
Esophagus	10.8 nTPM
Placenta	10.6 nTPM
Ovary	9.5 nTPM
Liver	8.1 nTPM
Fallopian tube	7.9 nTPM
Skin	7.3 nTPM
Prostate	6.1 nTPM
Breast	6.1 nTPM
Skeletal muscle	5.5 nTPM
Vascular	5.4 nTPM
Salivary gland	4.9 nTPM
Thymus	4.0 nTPM
Tongue	3.9 nTPM
Lung	2.4 nTPM

T-cells	5.8 nTPM
Kidney	11.5 nTPM
Bone marrow	10.1 nTPM
Esophagus	9.7 nTPM
Lymph node	9.6 nTPM
Endometrium	8.8 nTPM
Vascular	7.2 nTPM
Spleen	6.6 nTPM
Fallopian tube	6.6 nTPM
Adipose tissue	5.7 nTPM
Thymus	5.5 nTPM
Salivary gland	5.2 nTPM
Tongue	4.9 nTPM
Stomach	4.8 nTPM
Prostate	4.6 nTPM
Liver	4.3 nTPM
Skin	4.2 nTPM
PBMC	3.8 nTPM
Lung	2.4 nTPM
Breast	2.1 nTPM
Colon	1.9 nTPM
Skeletal muscle	1.9 nTPM

Undifferentiated cells	19.7 nTPM
Colon	28.6 nTPM
Small intestine	17.0 nTPM
Rectum	13.7 nTPM

Amygdala excitatory	104.1 nTPM
Hypothalamus	139.9 nTPM
Amygdala	128.9 nTPM
Basal ganglia	91.0 nTPM
Hippocampus	89.6 nTPM
Thalamus	88.9 nTPM
Cerebral cortex	86.2 nTPM

Astrocyte	14.2 nTPM
Amygdala	18.4 nTPM
Basal ganglia	17.1 nTPM
Hypothalamus	16.6 nTPM
Medulla oblongata	15.3 nTPM
Hippocampus	14.8 nTPM
Pons	13.6 nTPM
Cerebral cortex	12.9 nTPM
Thalamus	12.9 nTPM
Midbrain	12.5 nTPM
Cerebellum	11.3 nTPM
Spinal cord	11.0 nTPM

Bergmann glia	17.5 nTPM
Cerebellum	24.1 nTPM
Medulla oblongata	21.3 nTPM
Pons	7.2 nTPM

Central nervous system macrophage	72.1 nTPM
Amygdala	118.1 nTPM
Hypothalamus	85.1 nTPM
Basal ganglia	76.1 nTPM
Thalamus	75.5 nTPM
Hippocampus	74.1 nTPM
Midbrain	74.0 nTPM
Cerebral cortex	64.4 nTPM
Pons	59.8 nTPM
Medulla oblongata	56.6 nTPM
Cerebellum	56.2 nTPM
Spinal cord	53.3 nTPM

Cerebellar inhibitory	87.6 nTPM
Spinal cord	151.2 nTPM
Cerebellum	87.9 nTPM
Medulla oblongata	77.3 nTPM
Pons	61.4 nTPM
Midbrain	60.3 nTPM

Cge interneuron	47.8 nTPM
Amygdala	60.0 nTPM
Hypothalamus	59.7 nTPM
Basal ganglia	49.8 nTPM
Hippocampus	46.8 nTPM
Midbrain	41.8 nTPM
Cerebral cortex	38.5 nTPM
Thalamus	38.2 nTPM

Choroid plexus epithelial cell	16.7 nTPM
Basal ganglia	22.0 nTPM
Medulla oblongata	19.8 nTPM
Hippocampus	13.9 nTPM
Thalamus	11.0 nTPM

Committed oligodendrocyte precursor	23.4 nTPM
Amygdala	38.9 nTPM
Medulla oblongata	29.7 nTPM
Basal ganglia	26.8 nTPM
Hippocampus	26.1 nTPM
Hypothalamus	24.6 nTPM
Thalamus	23.6 nTPM
Midbrain	23.5 nTPM
Cerebellum	22.2 nTPM
Cerebral cortex	20.9 nTPM
Pons	17.7 nTPM
Spinal cord	3.7 nTPM

Deep-layer corticothalamic and 6b	63.0 nTPM
Hippocampus	81.1 nTPM
Amygdala	76.2 nTPM
Hypothalamus	69.7 nTPM
Basal ganglia	54.0 nTPM
Midbrain	53.3 nTPM
Cerebral cortex	43.9 nTPM

Deep-layer intratelencephalic	84.5 nTPM
Hippocampus	107.5 nTPM
Amygdala	100.9 nTPM
Hypothalamus	82.0 nTPM
Basal ganglia	78.2 nTPM
Cerebral cortex	53.9 nTPM

Deep-layer near-projecting	126.0 nTPM
Hypothalamus	162.9 nTPM
Amygdala	133.8 nTPM
Basal ganglia	126.1 nTPM
Cerebral cortex	104.9 nTPM
Hippocampus	102.4 nTPM

Eccentric medium spiny neuron	88.3 nTPM
Hippocampus	103.2 nTPM
Basal ganglia	99.8 nTPM
Thalamus	86.9 nTPM
Amygdala	84.0 nTPM
Hypothalamus	82.2 nTPM
Cerebral cortex	73.5 nTPM

Endothelial cell	80.5 nTPM
Basal ganglia	117.4 nTPM
Cerebellum	92.1 nTPM
Cerebral cortex	91.4 nTPM
Hippocampus	89.1 nTPM
Hypothalamus	80.6 nTPM
Spinal cord	77.7 nTPM
Amygdala	71.5 nTPM
Pons	70.5 nTPM
Medulla oblongata	69.7 nTPM
Midbrain	65.2 nTPM
Thalamus	60.4 nTPM

Ependymal cell	39.6 nTPM
Spinal cord	55.6 nTPM
Basal ganglia	52.6 nTPM
Hypothalamus	50.0 nTPM
Medulla oblongata	38.2 nTPM
Thalamus	35.2 nTPM
Midbrain	34.3 nTPM
Hippocampus	32.1 nTPM
Pons	31.4 nTPM
Amygdala	26.7 nTPM