Single cell type - PLXNA3 - 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.	PLXNA3
Gene descriptionⁱ Full gene name according to HGNC.	Plexin A3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Plasma proteins
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	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	1

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	Non-specific - Mitochondria (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	Not detected in immune cells
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	Not detected
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	Cell line enhanced (HeLa)
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 many
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

PLXNA3 is part of cluster 7 Non-specific - Mitochondria with confidenceⁱ 1
481 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
YME1L1	YME1 like 1 ATPase	0.5638	7
AC013394.1	Novel protein	0.5519	7
SMAD7	SMAD family member 7	0.5420	24
BCL9L	BCL9 like	0.5366	44
INTS13	Integrator complex subunit 13	0.5304	7
TSPOAP1	TSPO associated protein 1	0.5168	7
PPP1R2C	PPP1R2C family member C	0.5039	7
TMEM238	Transmembrane protein 238	0.4943	35
IER5L	Immediate early response 5 like	0.4929	7
NUMA1	Nuclear mitotic apparatus protein 1	0.4926	44
CARMIL2	Capping protein regulator and myosin 1 linker 2	0.4897	7
AL158151.3	Novel protein	0.4841	7
PCNX2	Pecanex 2	0.4836	7
MMP11	Matrix metallopeptidase 11	0.4824	36
AP003108.2	Novel transcript	0.4786	40

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	5.2 nTPM
Breast	5.8 nTPM
Adipose tissue	4.6 nTPM

Alveolar cells type 1	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	7.7 nTPM
Lung	7.7 nTPM

Astrocytes	13.4 nTPM
Brain	13.4 nTPM

B-cells	9.8 nTPM
Adipose tissue	28.5 nTPM
Breast	20.0 nTPM
PBMC	11.5 nTPM
Lymph node	9.8 nTPM
Spleen	6.9 nTPM
Colon	6.4 nTPM
Stomach	6.4 nTPM
Bone marrow	5.7 nTPM
Liver	2.5 nTPM
Kidney	0.0 nTPM

Dendritic cells	10.3 nTPM
Breast	17.8 nTPM
Adipose tissue	13.1 nTPM
PBMC	0.0 nTPM

Endothelial cells	3.9 nTPM
Endometrium	8.9 nTPM
Lung	6.2 nTPM
Skeletal muscle	5.0 nTPM
Breast	4.9 nTPM
Heart muscle	4.7 nTPM
Skin	4.7 nTPM
Placenta	4.0 nTPM
Liver	3.7 nTPM
Eye	3.3 nTPM
Prostate	3.2 nTPM
Testis	3.0 nTPM
Esophagus	2.1 nTPM
Ovary	1.1 nTPM
Pancreas	0.0 nTPM

Fibroblasts	11.0 nTPM
Placenta	20.0 nTPM
Skeletal muscle	15.7 nTPM
Ovary	13.5 nTPM
Breast	12.4 nTPM
Skin	10.6 nTPM
Esophagus	10.0 nTPM
Adipose tissue	9.5 nTPM
Stomach	8.9 nTPM
Lung	7.8 nTPM
Prostate	7.0 nTPM
Heart muscle	6.1 nTPM

Intestinal goblet cells	15.1 nTPM
Colon	19.3 nTPM
Rectum	15.9 nTPM
Small intestine	10.0 nTPM

Macrophages	10.5 nTPM
Breast	22.7 nTPM
Lung	20.1 nTPM
Ovary	19.9 nTPM
Esophagus	17.3 nTPM
Adipose tissue	12.9 nTPM
Skeletal muscle	12.6 nTPM
Stomach	11.7 nTPM
Endometrium	11.6 nTPM
Testis	8.1 nTPM
Kidney	6.1 nTPM
Spleen	5.2 nTPM
Bone marrow	5.0 nTPM
Prostate	4.6 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM

Paneth cells	11.4 nTPM
Colon	13.2 nTPM
Small intestine	11.3 nTPM
Rectum	9.7 nTPM

Plasma cells	8.5 nTPM
Adipose tissue	32.2 nTPM
Stomach	5.4 nTPM
Bone marrow	3.3 nTPM
Spleen	1.6 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	10.9 nTPM
Lung	11.7 nTPM
Bronchus	10.2 nTPM

Smooth muscle cells	9.4 nTPM
Ovary	20.0 nTPM
Breast	13.8 nTPM
Endometrium	12.7 nTPM
Skeletal muscle	11.3 nTPM
Adipose tissue	8.9 nTPM
Skin	8.7 nTPM
Pancreas	7.5 nTPM
Esophagus	6.2 nTPM
Heart muscle	5.7 nTPM
Prostate	4.7 nTPM
Bronchus	3.6 nTPM

T-cells	13.2 nTPM
Breast	40.0 nTPM
Skeletal muscle	37.1 nTPM
Adipose tissue	28.4 nTPM
Endometrium	24.5 nTPM
Ovary	15.6 nTPM
Liver	11.4 nTPM
Skin	11.1 nTPM
PBMC	10.2 nTPM
Lymph node	7.4 nTPM
Kidney	6.9 nTPM
Colon	6.6 nTPM
Esophagus	6.6 nTPM
Stomach	5.4 nTPM
Spleen	5.1 nTPM
Lung	4.5 nTPM
Bone marrow	4.2 nTPM
Prostate	0.0 nTPM

Basal prostatic cells	9.0 nTPM
Prostate	9.0 nTPM

Basal respiratory cells	7.3 nTPM
Bronchus	7.3 nTPM

Basal squamous epithelial cells	9.6 nTPM
Esophagus	9.6 nTPM

Cholangiocytes	2.8 nTPM
Liver	2.8 nTPM

Undifferentiated cells	9.6 nTPM
Rectum	11.9 nTPM
Colon	10.3 nTPM
Small intestine	6.5 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