Single cell type - R3HCC1L - The Human Protein Atlas

R3HCC1L

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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.	R3HCC1L
Gene descriptionⁱ Full gene name according to HGNC.	R3H domain and coiled-coil containing 1 like
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.	6

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 - Transcription (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 (Oligodendrocytes)
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.	0.41
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 (Oligodendrocytes)

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

R3HCC1L is part of cluster 55 Non-specific - Transcription with confidenceⁱ 1
709 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.
ESCO1	Establishment of sister chromatid cohesion N-acetyltransferase 1	0.5063	55
INO80	INO80 complex ATPase subunit	0.5042	55
THOC1	THO complex subunit 1	0.4959	39
CCDC77	Coiled-coil domain containing 77	0.4958	70
RBM48	RNA binding motif protein 48	0.4709	55
ZNF407	Zinc finger protein 407	0.4652	76
VPS50	VPS50 subunit of EARP/GARPII complex	0.4636	8
AP4E1	Adaptor related protein complex 4 subunit epsilon 1	0.4579	55
TTI1	TELO2 interacting protein 1	0.4393	30
MCM9	Minichromosome maintenance 9 homologous recombination repair factor	0.4367	76
ICE1	Interactor of little elongation complex ELL subunit 1	0.4303	55
MCPH1	Microcephalin 1	0.4300	55
VIRMA	Vir like m6A methyltransferase associated	0.4214	55
SETD2	SET domain containing 2, histone lysine methyltransferase	0.4050	55
CWC22	CWC22 spliceosome associated protein homolog	0.4046	55

IMMUNE CELLS

R3HCC1L is part of cluster 16 Non-specific - Cell proliferation with confidenceⁱ 1
161 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.
HERC5	HECT and RLD domain containing E3 ubiquitin protein ligase 5	0.9762	33
WBP11	WW domain binding protein 11	0.9524	16
CTNNAL1	Catenin alpha like 1	0.9524	16
ZNF76	Zinc finger protein 76	0.9286	16
ESCO2	Establishment of sister chromatid cohesion N-acetyltransferase 2	0.9286	9
RIBC1	RIB43A domain with coiled-coils 1	0.9286	33
TMC6	Transmembrane channel like 6	0.9286	33
EML4	EMAP like 4	0.9286	9
KIF11	Kinesin family member 11	0.9048	16
SMIM35	Small integral membrane protein 35	0.9048	16
NSUN6	NOP2/Sun RNA methyltransferase 6	0.9048	16
GEMIN4	Gem nuclear organelle associated protein 4	0.9048	16
CCNF	Cyclin F	0.9048	33
CDCA8	Cell division cycle associated 8	0.9048	16
MCM10	Minichromosome maintenance 10 replication initiation factor	0.9048	16

Adipocytes	11.2 nTPM
Breast	11.5 nTPM
Adipose tissue	10.9 nTPM

Alveolar cells type 1	6.7 nTPM
Lung	6.7 nTPM

Alveolar cells type 2	8.0 nTPM
Lung	8.0 nTPM

Astrocytes	28.5 nTPM
Brain	28.5 nTPM

B-cells	15.2 nTPM
Esophagus	29.5 nTPM
Salivary gland	23.5 nTPM
Thymus	20.5 nTPM
Lymph node	19.9 nTPM
Lung	18.8 nTPM
Stomach	18.1 nTPM
Adipose tissue	16.5 nTPM
Spleen	16.3 nTPM
Bone marrow	14.8 nTPM
Skin	6.8 nTPM
Kidney	5.2 nTPM
Liver	4.8 nTPM
PBMC	3.1 nTPM

Ciliated cells	9.4 nTPM
Endometrium	10.9 nTPM
Fallopian tube	10.5 nTPM
Lung	8.6 nTPM
Bronchus	7.5 nTPM

Club cells	9.8 nTPM
Prostate	16.1 nTPM
Lung	8.7 nTPM
Bronchus	4.7 nTPM

Endothelial cells	10.3 nTPM
Prostate	17.3 nTPM
Heart muscle	16.4 nTPM
Pancreas	15.5 nTPM
Salivary gland	15.1 nTPM
Breast	14.9 nTPM
Vascular	14.0 nTPM
Esophagus	10.8 nTPM
Thymus	10.4 nTPM
Tongue	9.9 nTPM
Fallopian tube	9.4 nTPM
Endometrium	9.3 nTPM
Skeletal muscle	9.2 nTPM
Lung	9.1 nTPM
Ovary	6.7 nTPM
Skin	6.2 nTPM
Testis	5.5 nTPM
Placenta	4.5 nTPM
Liver	1.3 nTPM

Enteroendocrine cells	8.9 nTPM
Colon	13.0 nTPM
Small intestine	6.9 nTPM
Rectum	6.7 nTPM

Fibroblasts	8.3 nTPM
Heart muscle	29.8 nTPM
Adipose tissue	10.8 nTPM
Salivary gland	10.7 nTPM
Prostate	10.6 nTPM
Vascular	9.6 nTPM
Breast	8.9 nTPM
Esophagus	7.6 nTPM
Fallopian tube	7.5 nTPM
Thymus	6.7 nTPM
Skeletal muscle	6.6 nTPM
Skin	5.4 nTPM
Pancreas	5.2 nTPM
Placenta	5.0 nTPM
Lung	5.0 nTPM
Liver	2.4 nTPM
Stomach	1.4 nTPM

Granulocytes	14.5 nTPM
Fallopian tube	19.2 nTPM
Lung	14.6 nTPM
Tongue	9.7 nTPM

Intestinal goblet cells	12.7 nTPM
Colon	16.2 nTPM
Small intestine	11.0 nTPM
Rectum	10.8 nTPM

Lymphatic endothelial cells	13.5 nTPM
Fallopian tube	16.1 nTPM
Ovary	10.9 nTPM

Macrophages	13.8 nTPM
Prostate	20.2 nTPM
Fallopian tube	19.7 nTPM
Bone marrow	19.3 nTPM
Salivary gland	18.4 nTPM
Lung	17.3 nTPM
Stomach	15.4 nTPM
Adipose tissue	15.0 nTPM
Vascular	14.8 nTPM
Breast	14.0 nTPM
Testis	13.6 nTPM
Thymus	13.6 nTPM
Spleen	13.0 nTPM
Endometrium	12.9 nTPM
Skeletal muscle	11.8 nTPM
Tongue	10.1 nTPM
Kidney	9.7 nTPM
Pancreas	8.2 nTPM
Esophagus	7.7 nTPM
Skin	6.7 nTPM

Paneth cells	6.5 nTPM
Colon	10.9 nTPM
Rectum	8.7 nTPM
Small intestine	0.0 nTPM

Basal keratinocytes	6.1 nTPM
Tongue	7.8 nTPM
Skin	4.3 nTPM

Basal respiratory cells	4.3 nTPM
Bronchus	4.3 nTPM

Basal squamous epithelial cells	6.4 nTPM
Esophagus	6.4 nTPM

Cholangiocytes	13.4 nTPM
Liver	13.4 nTPM

Plasma cells	9.9 nTPM
Fallopian tube	16.4 nTPM
Stomach	12.6 nTPM
Thymus	11.9 nTPM
Salivary gland	10.7 nTPM
Bone marrow	10.6 nTPM
Spleen	9.4 nTPM
Liver	7.5 nTPM
Esophagus	0.0 nTPM

Schwann cells	17.1 nTPM
Esophagus	24.0 nTPM
Vascular	15.7 nTPM
Adipose tissue	11.7 nTPM

Serous glandular cells	16.1 nTPM
Tongue	22.1 nTPM
Salivary gland	10.0 nTPM

Smooth muscle cells	7.5 nTPM
Salivary gland	11.1 nTPM
Prostate	9.7 nTPM
Vascular	9.7 nTPM
Adipose tissue	8.9 nTPM
Breast	8.6 nTPM
Endometrium	8.4 nTPM
Esophagus	8.4 nTPM
Tongue	8.4 nTPM
Thymus	8.1 nTPM
Ovary	7.4 nTPM
Fallopian tube	6.4 nTPM
Skeletal muscle	5.9 nTPM
Skin	5.8 nTPM
Liver	5.5 nTPM
Lung	4.7 nTPM
Placenta	3.4 nTPM

T-cells	16.5 nTPM
Vascular	25.3 nTPM
Prostate	24.5 nTPM
Adipose tissue	21.5 nTPM
Fallopian tube	21.3 nTPM
Salivary gland	20.3 nTPM
Skeletal muscle	20.0 nTPM
Lymph node	19.3 nTPM
Tongue	18.5 nTPM
Lung	18.3 nTPM
Thymus	16.8 nTPM
Breast	15.8 nTPM
Colon	15.6 nTPM
Kidney	15.1 nTPM
Endometrium	14.8 nTPM
Esophagus	14.6 nTPM
Bone marrow	14.3 nTPM
Spleen	12.1 nTPM
Liver	11.4 nTPM
Stomach	11.0 nTPM
Skin	8.1 nTPM
PBMC	7.0 nTPM

Undifferentiated cells	7.3 nTPM
Colon	7.7 nTPM
Rectum	7.4 nTPM
Small intestine	6.9 nTPM

Amygdala excitatory	60.7 nTPM
Hypothalamus	69.8 nTPM
Basal ganglia	62.1 nTPM
Amygdala	59.8 nTPM
Hippocampus	58.7 nTPM
Cerebral cortex	57.4 nTPM
Thalamus	56.7 nTPM

Astrocyte	59.7 nTPM
Amygdala	82.1 nTPM
Cerebral cortex	67.8 nTPM
Hypothalamus	67.2 nTPM
Hippocampus	67.0 nTPM
Basal ganglia	61.4 nTPM
Medulla oblongata	54.7 nTPM
Spinal cord	53.5 nTPM
Midbrain	52.7 nTPM
Thalamus	52.0 nTPM
Pons	51.9 nTPM
Cerebellum	46.5 nTPM

Bergmann glia	69.3 nTPM
Medulla oblongata	89.5 nTPM
Cerebellum	65.3 nTPM
Pons	53.2 nTPM

Central nervous system macrophage	162.9 nTPM
Amygdala	209.4 nTPM
Hypothalamus	200.0 nTPM
Basal ganglia	170.7 nTPM
Midbrain	164.1 nTPM
Cerebellum	159.4 nTPM
Pons	158.7 nTPM
Thalamus	158.3 nTPM
Hippocampus	151.5 nTPM
Medulla oblongata	146.0 nTPM
Spinal cord	137.2 nTPM
Cerebral cortex	136.2 nTPM

Cerebellar inhibitory	34.4 nTPM
Spinal cord	38.5 nTPM
Medulla oblongata	38.1 nTPM
Pons	34.0 nTPM
Cerebellum	33.5 nTPM
Midbrain	28.0 nTPM

Cge interneuron	42.1 nTPM
Hypothalamus	46.4 nTPM
Amygdala	45.6 nTPM
Midbrain	43.1 nTPM
Thalamus	41.6 nTPM
Hippocampus	40.9 nTPM
Basal ganglia	38.5 nTPM
Cerebral cortex	38.3 nTPM

Choroid plexus epithelial cell	86.4 nTPM
Basal ganglia	109.3 nTPM
Hippocampus	97.1 nTPM
Medulla oblongata	76.1 nTPM
Thalamus	63.0 nTPM

Committed oligodendrocyte precursor	55.0 nTPM
Basal ganglia	67.9 nTPM
Hippocampus	59.8 nTPM
Hypothalamus	59.4 nTPM
Amygdala	59.2 nTPM
Pons	57.5 nTPM
Thalamus	56.7 nTPM
Midbrain	55.4 nTPM
Medulla oblongata	52.9 nTPM
Cerebral cortex	50.0 nTPM
Spinal cord	47.8 nTPM
Cerebellum	38.1 nTPM

Deep-layer corticothalamic and 6b	65.9 nTPM
Amygdala	77.4 nTPM
Hypothalamus	70.8 nTPM
Hippocampus	66.3 nTPM
Cerebral cortex	61.9 nTPM
Basal ganglia	61.5 nTPM
Midbrain	57.7 nTPM

Deep-layer intratelencephalic	63.6 nTPM
Amygdala	79.3 nTPM
Hypothalamus	63.4 nTPM
Basal ganglia	59.6 nTPM
Cerebral cortex	57.9 nTPM
Hippocampus	57.8 nTPM

Deep-layer near-projecting	52.0 nTPM
Hypothalamus	62.1 nTPM
Basal ganglia	54.6 nTPM
Amygdala	53.7 nTPM
Cerebral cortex	49.4 nTPM
Hippocampus	40.0 nTPM

Eccentric medium spiny neuron	65.4 nTPM
Basal ganglia	68.1 nTPM
Amygdala	67.8 nTPM
Thalamus	67.1 nTPM
Cerebral cortex	64.4 nTPM
Hypothalamus	64.3 nTPM
Hippocampus	60.9 nTPM

Endothelial cell	93.6 nTPM
Basal ganglia	110.9 nTPM
Midbrain	107.7 nTPM
Amygdala	102.8 nTPM
Hippocampus	99.4 nTPM
Cerebellum	99.1 nTPM
Thalamus	94.9 nTPM
Pons	90.5 nTPM
Hypothalamus	88.1 nTPM
Cerebral cortex	84.4 nTPM
Medulla oblongata	75.9 nTPM
Spinal cord	75.9 nTPM

Ependymal cell	71.0 nTPM
Hypothalamus	81.2 nTPM
Amygdala	80.8 nTPM
Midbrain	80.6 nTPM
Hippocampus	77.4 nTPM
Basal ganglia	75.9 nTPM
Thalamus	73.7 nTPM
Pons	62.9 nTPM
Medulla oblongata	54.9 nTPM
Spinal cord	51.7 nTPM