Single cell type - PCGF3 - 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.	PCGF3
Gene descriptionⁱ Full gene name according to HGNC.	Polycomb group ring finger 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. Read more	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. Read more	Spermatids - Unknown 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. 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 all
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

PCGF3 is part of cluster 34 Spermatids - Unknown function with confidenceⁱ 1
366 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
PCDHGB1	Protocadherin gamma subfamily B, 1	0.6119	34
CTDSPL2	CTD small phosphatase like 2	0.5842	34
KCNJ18	Potassium inwardly rectifying channel subfamily J member 18	0.5800	43
LYPLA1	Lysophospholipase 1	0.5775	34
SMR3B	Submaxillary gland androgen regulated protein 3B	0.5710	34
IZUMO1	Izumo sperm-egg fusion 1	0.5534	34
RNF141	Ring finger protein 141	0.5430	34
HSFY1	Heat shock transcription factor Y-linked 1	0.5428	34
AGAP6	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	0.5306	29
ZNF677	Zinc finger protein 677	0.5296	34
PSME3	Proteasome activator subunit 3	0.5143	34
SSX7	SSX family member 7	0.5136	34
PITRM1	Pitrilysin metallopeptidase 1	0.5080	34
TSKS	Testis specific serine kinase substrate	0.5077	34
KIF2B	Kinesin family member 2B	0.5071	34

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	29.5 nTPM
Adipose tissue	32.1 nTPM
Breast	26.9 nTPM

Alveolar cells type 1	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	28.8 nTPM
Lung	28.8 nTPM

Astrocytes	19.6 nTPM
Brain	19.6 nTPM

B-cells	12.5 nTPM
Breast	20.0 nTPM
Kidney	19.0 nTPM
Liver	16.7 nTPM
Colon	14.4 nTPM
Adipose tissue	14.1 nTPM
Lymph node	12.8 nTPM
Bone marrow	10.6 nTPM
Stomach	5.9 nTPM
PBMC	5.7 nTPM
Spleen	5.5 nTPM

Dendritic cells	13.5 nTPM
Adipose tissue	21.6 nTPM
Breast	14.9 nTPM
PBMC	4.0 nTPM

Endothelial cells	27.8 nTPM
Heart muscle	63.6 nTPM
Ovary	32.3 nTPM
Endometrium	31.6 nTPM
Prostate	28.8 nTPM
Skeletal muscle	27.3 nTPM
Liver	25.7 nTPM
Esophagus	25.7 nTPM
Testis	25.5 nTPM
Lung	24.9 nTPM
Breast	24.6 nTPM
Skin	22.8 nTPM
Placenta	20.5 nTPM
Pancreas	19.3 nTPM
Eye	17.0 nTPM

Fibroblasts	17.8 nTPM
Heart muscle	34.7 nTPM
Prostate	21.1 nTPM
Skin	19.7 nTPM
Skeletal muscle	17.7 nTPM
Breast	17.7 nTPM
Adipose tissue	17.6 nTPM
Placenta	16.5 nTPM
Esophagus	15.0 nTPM
Lung	14.5 nTPM
Ovary	13.9 nTPM
Stomach	7.4 nTPM

Intestinal goblet cells	21.7 nTPM
Rectum	25.2 nTPM
Small intestine	23.5 nTPM
Colon	16.5 nTPM

Macrophages	20.1 nTPM
Bone marrow	27.5 nTPM
Spleen	27.0 nTPM
Esophagus	26.8 nTPM
Adipose tissue	26.7 nTPM
Lung	23.5 nTPM
Stomach	23.5 nTPM
Skeletal muscle	22.3 nTPM
Prostate	19.5 nTPM
Breast	18.0 nTPM
Pancreas	15.3 nTPM
Kidney	15.2 nTPM
Endometrium	14.7 nTPM
Ovary	14.2 nTPM
Testis	14.0 nTPM
PBMC	13.6 nTPM

Paneth cells	19.3 nTPM
Rectum	26.6 nTPM
Colon	16.5 nTPM
Small intestine	15.0 nTPM

Plasma cells	22.9 nTPM
Esophagus	30.7 nTPM
Adipose tissue	27.1 nTPM
Stomach	20.2 nTPM
Spleen	18.5 nTPM
Bone marrow	18.2 nTPM

Respiratory ciliated cells	14.0 nTPM
Bronchus	17.7 nTPM
Lung	10.2 nTPM

Smooth muscle cells	18.8 nTPM
Ovary	27.5 nTPM
Endometrium	25.8 nTPM
Adipose tissue	24.3 nTPM
Pancreas	19.5 nTPM
Heart muscle	19.4 nTPM
Breast	15.9 nTPM
Skin	15.7 nTPM
Esophagus	15.5 nTPM
Skeletal muscle	15.4 nTPM
Bronchus	15.0 nTPM
Prostate	12.5 nTPM

T-cells	13.3 nTPM
Skin	19.8 nTPM
Endometrium	19.7 nTPM
Adipose tissue	18.5 nTPM
Lung	18.2 nTPM
Breast	15.6 nTPM
Colon	15.2 nTPM
Prostate	14.2 nTPM
Skeletal muscle	13.4 nTPM
Esophagus	13.1 nTPM
Liver	12.8 nTPM
Ovary	11.1 nTPM
Bone marrow	10.9 nTPM
Spleen	10.7 nTPM
Stomach	9.7 nTPM
Lymph node	8.5 nTPM
Kidney	8.2 nTPM
PBMC	6.0 nTPM

Basal keratinocytes	25.4 nTPM
Skin	25.4 nTPM

Basal prostatic cells	17.3 nTPM
Prostate	17.3 nTPM

Basal respiratory cells	17.2 nTPM
Bronchus	17.2 nTPM

Basal squamous epithelial cells	25.0 nTPM
Esophagus	25.0 nTPM

Undifferentiated cells	20.2 nTPM
Rectum	24.2 nTPM
Small intestine	21.6 nTPM
Colon	14.8 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