Single cell type - APOBEC3A - 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.	APOBEC3A
Gene descriptionⁱ Full gene name according to HGNC.	Apolipoprotein B mRNA editing enzyme catalytic subunit 3A
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	Monocytes & Neutrophils - Innate immune response (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	Cell type enriched (Urothelial cells)
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	Immune cell enhanced (intermediate monocyte)
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	Not detected
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	Not detected
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: Cell type enriched (Urothelial cells)

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

APOBEC3A is part of cluster 19 Monocytes & Neutrophils - Innate immune response with confidenceⁱ 1
175 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
CD300E	CD300e molecule	0.7426	19
AC008982.1	Novel protein	0.6928	11
FPR1	Formyl peptide receptor 1	0.6892	19
PLAUR	Plasminogen activator, urokinase receptor	0.6875	41
FFAR2	Free fatty acid receptor 2	0.6745	19
SLC11A1	Solute carrier family 11 member 1	0.6643	19
NLRP12	NLR family pyrin domain containing 12	0.6476	19
AL645941.2	Novel protein	0.6376	11
AC018755.2	Novel transcript, sense intronic to AC018755.18	0.6376	11
AC005833.1	Novel protein	0.6335	11
AL133500.1	Novel protein	0.6323	11
IFI30	IFI30 lysosomal thiol reductase	0.6290	19
PADI3	Peptidyl arginine deiminase 3	0.6266	22
CLEC4D	C-type lectin domain family 4 member D	0.6243	19
ADGRE2	Adhesion G protein-coupled receptor E2	0.6219	19

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	0.7 nTPM
Breast	1.3 nTPM
Adipose tissue	0.3 nTPM

Alveolar cells type 1	28.9 nTPM
Lung	28.9 nTPM

Alveolar cells type 2	33.6 nTPM
Lung	33.6 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	0.5 nTPM
Breast	2.6 nTPM
Liver	2.0 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Dendritic cells	0.2 nTPM
Adipose tissue	0.7 nTPM
PBMC	0.0 nTPM
Breast	0.0 nTPM

Endothelial cells	1.4 nTPM
Lung	15.6 nTPM
Placenta	1.1 nTPM
Skin	0.9 nTPM
Skeletal muscle	0.8 nTPM
Breast	0.5 nTPM
Prostate	0.4 nTPM
Heart muscle	0.2 nTPM
Ovary	0.2 nTPM
Endometrium	0.1 nTPM
Eye	0.0 nTPM
Liver	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM

Fibroblasts	6.3 nTPM
Lung	63.7 nTPM
Placenta	1.0 nTPM
Prostate	1.0 nTPM
Breast	0.9 nTPM
Skin	0.8 nTPM
Skeletal muscle	0.7 nTPM
Heart muscle	0.2 nTPM
Adipose tissue	0.2 nTPM
Esophagus	0.2 nTPM
Ovary	0.1 nTPM
Stomach	0.0 nTPM

Intestinal goblet cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Macrophages	91.3 nTPM
Lung	437.8 nTPM
Stomach	372.2 nTPM
Skeletal muscle	182.5 nTPM
Kidney	110.4 nTPM
Adipose tissue	104.1 nTPM
Bone marrow	63.7 nTPM
Spleen	40.4 nTPM
Esophagus	15.8 nTPM
Breast	12.8 nTPM
Prostate	11.5 nTPM
Endometrium	7.2 nTPM
Ovary	6.5 nTPM
Testis	4.6 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM

Paneth cells	27.4 nTPM
Colon	82.3 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Plasma cells	15.6 nTPM
Esophagus	55.5 nTPM
Adipose tissue	13.6 nTPM
Stomach	8.1 nTPM
Spleen	0.6 nTPM
Bone marrow	0.0 nTPM

Respiratory ciliated cells	10.7 nTPM
Lung	16.0 nTPM
Bronchus	5.3 nTPM

Smooth muscle cells	1.2 nTPM
Prostate	10.3 nTPM
Skin	1.4 nTPM
Skeletal muscle	1.0 nTPM
Adipose tissue	0.4 nTPM
Heart muscle	0.2 nTPM
Ovary	0.2 nTPM
Endometrium	0.1 nTPM
Pancreas	0.0 nTPM
Bronchus	0.0 nTPM
Esophagus	0.0 nTPM
Breast	0.0 nTPM

T-cells	3.1 nTPM
Lung	31.9 nTPM
Prostate	9.5 nTPM
Skin	3.3 nTPM
PBMC	1.5 nTPM
Liver	1.3 nTPM
Skeletal muscle	1.3 nTPM
Colon	1.0 nTPM
Kidney	0.7 nTPM
Breast	0.7 nTPM
Adipose tissue	0.6 nTPM
Spleen	0.4 nTPM
Endometrium	0.3 nTPM
Bone marrow	0.1 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Stomach	0.0 nTPM

Basal respiratory cells	1.8 nTPM
Bronchus	1.8 nTPM

Collecting duct cells	1.8 nTPM
Kidney	1.8 nTPM

Cone photoreceptor cells	4.2 nTPM
Eye	4.2 nTPM

Undifferentiated cells	1.7 nTPM
Colon	4.6 nTPM
Small intestine	0.5 nTPM
Rectum	0.0 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