Single cell type - RC3H1 - The Human Protein Atlas

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.	RC3H1
Gene descriptionⁱ Full gene name according to HGNC.	Ring finger and CCCH-type domains 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes
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. Read more	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. Read more	Endometrium - 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. Read more	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. Read more	Low immune cell specificity
Immune cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in many
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Low cell line specificity
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in all
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of 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 Group Expression Alphabetical RNA single cell type specificity: Low cell type specificity

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

RC3H1 is part of cluster 44 Endometrium - Transcription with confidenceⁱ 1
491 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type 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. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
NUP153	Nucleoporin 153	0.7109	44
CRTC2	CREB regulated transcription coactivator 2	0.7060	44
ZBTB11	Zinc finger and BTB domain containing 11	0.6358	44
KMT2C	Lysine methyltransferase 2C	0.6352	44
GPR75	G protein-coupled receptor 75	0.6328	44
SPEN	Spen family transcriptional repressor	0.6277	44
ATXN2L	Ataxin 2 like	0.6180	44
NFAT5	Nuclear factor of activated T cells 5	0.6089	44
SNIP1	Smad nuclear interacting protein 1	0.6010	44
TSC22D2	TSC22 domain family member 2	0.6003	44
ZNF592	Zinc finger protein 592	0.6001	44
WDFY1	WD repeat and FYVE domain containing 1	0.5923	44
HNRNPL	Heterogeneous nuclear ribonucleoprotein L	0.5852	59
UBXN7	UBX domain protein 7	0.5720	44
SMG1	SMG1 nonsense mediated mRNA decay associated PI3K related kinase	0.5673	44

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	39.8 nTPM
Adipose tissue	58.2 nTPM
Breast	21.5 nTPM

Alveolar cells type 1	41.7 nTPM
Lung	41.7 nTPM

Alveolar cells type 2	34.5 nTPM
Lung	34.5 nTPM

Astrocytes	32.0 nTPM
Brain	32.0 nTPM

B-cells	49.4 nTPM
Adipose tissue	88.2 nTPM
Lymph node	84.8 nTPM
Spleen	65.4 nTPM
Stomach	63.6 nTPM
Bone marrow	62.1 nTPM
Colon	35.1 nTPM
Breast	30.7 nTPM
PBMC	24.3 nTPM
Liver	21.1 nTPM
Kidney	19.0 nTPM

Dendritic cells	70.2 nTPM
Adipose tissue	147.1 nTPM
PBMC	31.8 nTPM
Breast	31.7 nTPM

Endothelial cells	32.0 nTPM
Skin	50.0 nTPM
Endometrium	48.5 nTPM
Heart muscle	47.5 nTPM
Esophagus	47.1 nTPM
Breast	39.7 nTPM
Skeletal muscle	35.8 nTPM
Liver	34.8 nTPM
Prostate	30.4 nTPM
Ovary	25.9 nTPM
Eye	21.8 nTPM
Placenta	21.6 nTPM
Testis	17.7 nTPM
Lung	15.6 nTPM
Pancreas	11.6 nTPM

Fibroblasts	34.9 nTPM
Adipose tissue	47.2 nTPM
Skin	44.7 nTPM
Prostate	44.5 nTPM
Heart muscle	43.2 nTPM
Esophagus	40.7 nTPM
Lung	40.2 nTPM
Stomach	37.1 nTPM
Skeletal muscle	32.9 nTPM
Breast	29.9 nTPM
Ovary	13.2 nTPM
Placenta	9.8 nTPM

Intestinal goblet cells	28.9 nTPM
Small intestine	30.3 nTPM
Rectum	30.0 nTPM
Colon	26.4 nTPM

Macrophages	38.5 nTPM
Adipose tissue	105.7 nTPM
Stomach	67.4 nTPM
Spleen	59.1 nTPM
Esophagus	50.4 nTPM
Endometrium	42.7 nTPM
Skeletal muscle	42.4 nTPM
Prostate	42.3 nTPM
Bone marrow	30.0 nTPM
Lung	26.8 nTPM
Breast	24.2 nTPM
Ovary	23.9 nTPM
Pancreas	17.8 nTPM
Kidney	16.6 nTPM
Testis	14.0 nTPM
PBMC	13.6 nTPM

Paneth cells	22.1 nTPM
Rectum	27.8 nTPM
Colon	19.7 nTPM
Small intestine	18.8 nTPM

Plasma cells	52.2 nTPM
Adipose tissue	85.8 nTPM
Esophagus	67.8 nTPM
Spleen	43.2 nTPM
Stomach	42.8 nTPM
Bone marrow	21.4 nTPM

Respiratory ciliated cells	30.2 nTPM
Bronchus	32.8 nTPM
Lung	27.7 nTPM

Smooth muscle cells	31.5 nTPM
Adipose tissue	57.5 nTPM
Heart muscle	45.8 nTPM
Endometrium	44.2 nTPM
Esophagus	38.8 nTPM
Skin	33.5 nTPM
Skeletal muscle	32.2 nTPM
Prostate	25.6 nTPM
Ovary	19.1 nTPM
Breast	18.6 nTPM
Bronchus	18.0 nTPM
Pancreas	13.2 nTPM

T-cells	41.4 nTPM
Adipose tissue	93.9 nTPM
Endometrium	65.9 nTPM
Spleen	64.0 nTPM
Lymph node	58.5 nTPM
Stomach	53.2 nTPM
Skeletal muscle	48.6 nTPM
Liver	47.6 nTPM
Esophagus	45.9 nTPM
Colon	39.9 nTPM
Bone marrow	39.8 nTPM
Skin	30.4 nTPM
PBMC	27.9 nTPM
Breast	27.1 nTPM
Lung	25.8 nTPM
Ovary	17.8 nTPM
Prostate	9.5 nTPM
Kidney	8.2 nTPM

Basal keratinocytes	34.4 nTPM
Skin	34.4 nTPM

Basal prostatic cells	17.3 nTPM
Prostate	17.3 nTPM

Basal respiratory cells	14.1 nTPM
Bronchus	14.1 nTPM

Basal squamous epithelial cells	60.9 nTPM
Esophagus	60.9 nTPM

Undifferentiated cells	25.9 nTPM
Colon	26.6 nTPM
Rectum	26.6 nTPM
Small intestine	24.4 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC