Single cell type - CLTA - 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.	CLTA
Gene descriptionⁱ Full gene name according to HGNC.	Clathrin light chain A
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
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	8

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 - 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	Cell type enhanced (Syncytiotrophoblasts)
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: Cell type enhanced (Syncytiotrophoblasts)

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

CLTA is part of cluster 10 Non-specific - Unknown function with confidenceⁱ 1
482 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
PPP1R2B	PPP1R2 family member B	0.7636	10
ACTBL2	Actin beta like 2	0.7560	10
ANP32D	Acidic nuclear phosphoprotein 32 family member D	0.7440	10
SNX6	Sorting nexin 6	0.7389	10
PF4V1	Platelet factor 4 variant 1	0.7346	10
POTEE	POTE ankyrin domain family member E	0.7318	10
PITPNA	Phosphatidylinositol transfer protein alpha	0.7033	10
SMIM35	Small integral membrane protein 35	0.7002	10
RBM42	RNA binding motif protein 42	0.6991	18
DCAF8L2	DDB1 and CUL4 associated factor 8 like 2	0.6855	10
MED12	Mediator complex subunit 12	0.6673	10
FES	FES proto-oncogene, tyrosine kinase	0.6626	10
ETV3L	ETS variant transcription factor 3 like	0.6560	10
PSEN2	Presenilin 2	0.6529	10
POTEF	POTE ankyrin domain family member F	0.6484	10

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	291.5 nTPM
Breast	394.7 nTPM
Adipose tissue	188.3 nTPM

Alveolar cells type 1	128.2 nTPM
Lung	128.2 nTPM

Alveolar cells type 2	143.9 nTPM
Lung	143.9 nTPM

Astrocytes	14.4 nTPM
Brain	14.4 nTPM

B-cells	105.9 nTPM
Liver	157.4 nTPM
PBMC	147.0 nTPM
Colon	132.6 nTPM
Kidney	109.5 nTPM
Spleen	101.8 nTPM
Breast	96.4 nTPM
Bone marrow	94.8 nTPM
Stomach	79.1 nTPM
Adipose tissue	77.7 nTPM
Lymph node	62.5 nTPM

Basal squamous epithelial cells	169.0 nTPM
Esophagus	169.0 nTPM

Dendritic cells	140.1 nTPM
PBMC	183.3 nTPM
Breast	133.7 nTPM
Adipose tissue	103.3 nTPM

Endothelial cells	244.0 nTPM
Liver	425.6 nTPM
Placenta	326.2 nTPM
Testis	313.2 nTPM
Breast	309.0 nTPM
Pancreas	305.0 nTPM
Ovary	294.2 nTPM
Prostate	274.5 nTPM
Skin	225.7 nTPM
Esophagus	192.4 nTPM
Endometrium	184.9 nTPM
Skeletal muscle	181.4 nTPM
Eye	178.0 nTPM
Lung	137.3 nTPM
Heart muscle	68.0 nTPM

Enteroendocrine cells	183.8 nTPM
Colon	202.5 nTPM
Rectum	165.1 nTPM

Erythroid cells	154.8 nTPM
Liver	155.0 nTPM
Bone marrow	154.7 nTPM

Fibroblasts	187.5 nTPM
Placenta	282.0 nTPM
Ovary	278.0 nTPM
Prostate	241.2 nTPM
Breast	217.4 nTPM
Skin	203.4 nTPM
Adipose tissue	197.4 nTPM
Esophagus	184.0 nTPM
Stomach	154.4 nTPM
Skeletal muscle	140.0 nTPM
Heart muscle	87.8 nTPM
Lung	77.1 nTPM

Intestinal goblet cells	350.5 nTPM
Colon	486.7 nTPM
Rectum	300.1 nTPM
Small intestine	264.8 nTPM

Macrophages	249.3 nTPM
Ovary	521.0 nTPM
Pancreas	387.9 nTPM
Kidney	348.6 nTPM
Prostate	285.4 nTPM
Testis	260.9 nTPM
Spleen	231.2 nTPM
Bone marrow	229.9 nTPM
Breast	229.2 nTPM
Stomach	199.3 nTPM
Lung	192.8 nTPM
PBMC	177.3 nTPM
Adipose tissue	174.1 nTPM
Skeletal muscle	173.1 nTPM
Esophagus	166.8 nTPM
Endometrium	162.6 nTPM

Paneth cells	426.4 nTPM
Colon	592.9 nTPM
Small intestine	345.4 nTPM
Rectum	340.8 nTPM

Plasma cells	97.7 nTPM
Spleen	147.3 nTPM
Bone marrow	115.3 nTPM
Esophagus	104.7 nTPM
Stomach	77.9 nTPM
Adipose tissue	43.2 nTPM

Cholangiocytes	217.3 nTPM
Liver	217.3 nTPM

Collecting duct cells	180.3 nTPM
Kidney	180.3 nTPM

Cone photoreceptor cells	60.5 nTPM
Eye	60.5 nTPM

Cytotrophoblasts	958.0 nTPM
Placenta	958.0 nTPM

Respiratory ciliated cells	304.7 nTPM
Bronchus	396.5 nTPM
Lung	212.8 nTPM

Smooth muscle cells	310.4 nTPM
Bronchus	1179.4 nTPM
Pancreas	462.4 nTPM
Ovary	401.9 nTPM
Breast	251.3 nTPM
Prostate	240.3 nTPM
Skin	189.7 nTPM
Endometrium	159.6 nTPM
Skeletal muscle	153.6 nTPM
Esophagus	152.0 nTPM
Adipose tissue	143.5 nTPM
Heart muscle	80.3 nTPM

T-cells	103.7 nTPM
Kidney	157.4 nTPM
Ovary	146.8 nTPM
Liver	144.6 nTPM
Colon	126.4 nTPM
Breast	125.4 nTPM
Skin	118.8 nTPM
PBMC	114.5 nTPM
Adipose tissue	107.7 nTPM
Esophagus	98.3 nTPM
Stomach	95.2 nTPM
Bone marrow	91.8 nTPM
Prostate	89.9 nTPM
Endometrium	85.7 nTPM
Skeletal muscle	78.4 nTPM
Spleen	71.7 nTPM
Lymph node	58.6 nTPM
Lung	51.6 nTPM

Undifferentiated cells	380.0 nTPM
Colon	479.7 nTPM
Small intestine	337.8 nTPM
Rectum	322.6 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