Single cell type - ATP13A1 - 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.	ATP13A1
Gene descriptionⁱ Full gene name according to HGNC.	ATPase 13A1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Plasma proteins Transporters
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,Membrane
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	Intestinal epithelial cells - 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 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

ATP13A1 is part of cluster 53 Intestinal epithelial cells - Unknown function with confidenceⁱ 1
611 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
NCLN	Nicalin	0.6759	53
SLC52A2	Solute carrier family 52 member 2	0.6199	53
APEH	Acylaminoacyl-peptide hydrolase	0.6081	53
SEC61A1	SEC61 translocon subunit alpha 1	0.5951	53
RABL6	RAB, member RAS oncogene family like 6	0.5910	53
MED16	Mediator complex subunit 16	0.5786	53
E4F1	E4F transcription factor 1	0.5693	53
LONP1	Lon peptidase 1, mitochondrial	0.5692	39
ATAD3B	ATPase family AAA domain containing 3B	0.5601	39
SMG5	SMG5 nonsense mediated mRNA decay factor	0.5459	53
PRRC2A	Proline rich coiled-coil 2A	0.5411	59
ATAD3A	ATPase family AAA domain containing 3A	0.5396	39
SKIV2L	Ski2 like RNA helicase	0.5381	59
ERCC2	ERCC excision repair 2, TFIIH core complex helicase subunit	0.5338	40
CCAR2	Cell cycle and apoptosis regulator 2	0.5334	58

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	11.3 nTPM
Adipose tissue	11.8 nTPM
Breast	10.6 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	5.8 nTPM
Lung	5.8 nTPM

Astrocytes	12.1 nTPM
Brain	12.1 nTPM

B-cells	22.7 nTPM
Liver	40.2 nTPM
Bone marrow	29.4 nTPM
Kidney	28.5 nTPM
Stomach	26.3 nTPM
Lymph node	23.4 nTPM
Spleen	22.9 nTPM
Breast	20.0 nTPM
PBMC	14.3 nTPM
Colon	12.8 nTPM
Adipose tissue	9.6 nTPM

Dendritic cells	12.5 nTPM
PBMC	16.0 nTPM
Breast	14.9 nTPM
Adipose tissue	6.6 nTPM

Endothelial cells	9.0 nTPM
Ovary	17.9 nTPM
Placenta	14.2 nTPM
Liver	13.7 nTPM
Endometrium	12.3 nTPM
Esophagus	9.7 nTPM
Breast	8.8 nTPM
Testis	8.6 nTPM
Skeletal muscle	8.6 nTPM
Pancreas	7.7 nTPM
Eye	7.3 nTPM
Skin	6.7 nTPM
Prostate	6.6 nTPM
Heart muscle	4.5 nTPM
Lung	0.0 nTPM

Fibroblasts	10.2 nTPM
Ovary	17.1 nTPM
Placenta	13.4 nTPM
Stomach	13.4 nTPM
Adipose tissue	11.4 nTPM
Esophagus	10.4 nTPM
Skeletal muscle	10.1 nTPM
Lung	8.9 nTPM
Skin	8.9 nTPM
Breast	8.2 nTPM
Prostate	7.2 nTPM
Heart muscle	3.1 nTPM

Intestinal goblet cells	22.9 nTPM
Colon	27.1 nTPM
Small intestine	22.5 nTPM
Rectum	19.1 nTPM

Macrophages	18.3 nTPM
Stomach	38.1 nTPM
Spleen	35.3 nTPM
Ovary	29.2 nTPM
Esophagus	22.0 nTPM
Breast	18.2 nTPM
Bone marrow	17.5 nTPM
Kidney	15.8 nTPM
Adipose tissue	15.6 nTPM
Endometrium	15.3 nTPM
Skeletal muscle	15.0 nTPM
PBMC	13.6 nTPM
Lung	11.7 nTPM
Testis	11.7 nTPM
Prostate	8.1 nTPM
Pancreas	7.7 nTPM

Paneth cells	22.4 nTPM
Colon	29.6 nTPM
Rectum	22.6 nTPM
Small intestine	15.0 nTPM

Plasma cells	50.4 nTPM
Esophagus	67.8 nTPM
Spleen	57.9 nTPM
Stomach	55.8 nTPM
Bone marrow	54.4 nTPM
Adipose tissue	16.1 nTPM

Respiratory ciliated cells	12.8 nTPM
Bronchus	22.6 nTPM
Lung	2.9 nTPM

Smooth muscle cells	11.4 nTPM
Bronchus	21.5 nTPM
Pancreas	19.8 nTPM
Esophagus	17.0 nTPM
Ovary	13.1 nTPM
Adipose tissue	11.0 nTPM
Skeletal muscle	9.8 nTPM
Breast	8.8 nTPM
Endometrium	7.7 nTPM
Skin	6.3 nTPM
Heart muscle	5.9 nTPM
Prostate	5.0 nTPM

T-cells	13.9 nTPM
Esophagus	32.8 nTPM
Lymph node	24.2 nTPM
Spleen	22.5 nTPM
Bone marrow	20.8 nTPM
Stomach	19.0 nTPM
Kidney	15.8 nTPM
Breast	14.4 nTPM
Liver	14.1 nTPM
Colon	11.4 nTPM
PBMC	11.4 nTPM
Skin	10.2 nTPM
Endometrium	8.9 nTPM
Ovary	8.9 nTPM
Skeletal muscle	8.7 nTPM
Adipose tissue	8.7 nTPM
Lung	4.5 nTPM
Prostate	0.0 nTPM

Basal prostatic cells	7.4 nTPM
Prostate	7.4 nTPM

Cholangiocytes	11.5 nTPM
Liver	11.5 nTPM

Collecting duct cells	14.7 nTPM
Kidney	14.7 nTPM

Cone photoreceptor cells	18.8 nTPM
Eye	18.8 nTPM

Undifferentiated cells	22.2 nTPM
Colon	27.8 nTPM
Rectum	21.1 nTPM
Small intestine	17.7 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