Single cell type - CLN6 - 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.	CLN6
Gene descriptionⁱ Full gene name according to HGNC.	CLN6 transmembrane ER protein
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes Potential drug targets 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.	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	Bipolar cells - Visual perception (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 (Bipolar cells, Hofbauer 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	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: Cell type enhanced (Bipolar cells, Hofbauer 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

CLN6 is part of cluster 56 Bipolar cells - Visual perception with confidenceⁱ 1
199 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
GRM6	Glutamate metabotropic receptor 6	0.7428	56
CABP2	Calcium binding protein 2	0.7423	56
GNG13	G protein subunit gamma 13	0.7407	56
TRPM1	Transient receptor potential cation channel subfamily M member 1	0.7380	56
KCNG4	Potassium voltage-gated channel modifier subfamily G member 4	0.7380	56
VSX1	Visual system homeobox 1	0.7378	56
NEUROD4	Neuronal differentiation 4	0.7370	56
NYX	Nyctalopin	0.7369	56
NIF3L1	NGG1 interacting factor 3 like 1	0.7359	56
MC4R	Melanocortin 4 receptor	0.7311	56
TRNP1	TMF1 regulated nuclear protein 1	0.7306	56
HR	HR lysine demethylase and nuclear receptor corepressor	0.7260	56
ISL1	ISL LIM homeobox 1	0.7259	56
LACTBL1	Lactamase beta like 1	0.7247	56
GABRR2	Gamma-aminobutyric acid type A receptor subunit rho2	0.7228	56

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	1.4 nTPM
Adipose tissue	1.8 nTPM
Breast	1.1 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	6.9 nTPM
Lung	6.9 nTPM

Astrocytes	7.2 nTPM
Brain	7.2 nTPM

B-cells	13.4 nTPM
Liver	40.6 nTPM
Colon	22.3 nTPM
Spleen	17.3 nTPM
Stomach	11.8 nTPM
PBMC	11.5 nTPM
Lymph node	10.1 nTPM
Bone marrow	9.8 nTPM
Kidney	4.8 nTPM
Adipose tissue	3.5 nTPM
Breast	2.6 nTPM

Dendritic cells	7.1 nTPM
PBMC	16.0 nTPM
Adipose tissue	3.2 nTPM
Breast	2.2 nTPM

Endothelial cells	9.7 nTPM
Heart muscle	26.0 nTPM
Placenta	21.6 nTPM
Prostate	16.7 nTPM
Skin	14.3 nTPM
Testis	11.9 nTPM
Esophagus	10.9 nTPM
Skeletal muscle	7.4 nTPM
Liver	7.3 nTPM
Lung	6.2 nTPM
Ovary	6.2 nTPM
Eye	3.3 nTPM
Endometrium	2.9 nTPM
Breast	1.6 nTPM
Pancreas	0.0 nTPM

Fibroblasts	9.1 nTPM
Heart muscle	26.3 nTPM
Placenta	22.6 nTPM
Skin	12.5 nTPM
Ovary	10.1 nTPM
Esophagus	8.6 nTPM
Prostate	7.4 nTPM
Skeletal muscle	6.4 nTPM
Breast	2.1 nTPM
Adipose tissue	1.9 nTPM
Stomach	1.5 nTPM
Lung	1.2 nTPM

Intestinal goblet cells	20.5 nTPM
Small intestine	23.4 nTPM
Colon	21.5 nTPM
Rectum	16.5 nTPM

Macrophages	11.3 nTPM
Prostate	37.9 nTPM
Spleen	20.7 nTPM
Skeletal muscle	20.4 nTPM
Bone marrow	17.5 nTPM
Esophagus	15.8 nTPM
Testis	14.0 nTPM
Lung	10.2 nTPM
Ovary	7.8 nTPM
Pancreas	7.7 nTPM
Kidney	4.6 nTPM
Breast	4.4 nTPM
Endometrium	3.0 nTPM
Stomach	2.9 nTPM
Adipose tissue	2.3 nTPM
PBMC	0.0 nTPM

Paneth cells	26.0 nTPM
Small intestine	45.0 nTPM
Rectum	23.1 nTPM
Colon	9.9 nTPM

Plasma cells	33.4 nTPM
Esophagus	49.4 nTPM
Spleen	40.0 nTPM
Bone marrow	39.5 nTPM
Stomach	33.5 nTPM
Adipose tissue	4.5 nTPM

Respiratory ciliated cells	3.3 nTPM
Bronchus	6.6 nTPM
Lung	0.0 nTPM

Smooth muscle cells	5.6 nTPM
Heart muscle	13.9 nTPM
Skin	9.1 nTPM
Prostate	8.8 nTPM
Skeletal muscle	6.0 nTPM
Pancreas	4.9 nTPM
Ovary	4.9 nTPM
Bronchus	4.8 nTPM
Esophagus	3.1 nTPM
Endometrium	3.0 nTPM
Adipose tissue	1.6 nTPM
Breast	1.3 nTPM

T-cells	9.5 nTPM
Colon	21.9 nTPM
PBMC	15.6 nTPM
Stomach	14.9 nTPM
Esophagus	13.1 nTPM
Liver	13.0 nTPM
Skin	12.9 nTPM
Kidney	11.6 nTPM
Spleen	9.6 nTPM
Bone marrow	9.5 nTPM
Lymph node	8.2 nTPM
Skeletal muscle	8.0 nTPM
Lung	6.1 nTPM
Prostate	4.7 nTPM
Ovary	4.5 nTPM
Endometrium	2.6 nTPM
Adipose tissue	2.4 nTPM
Breast	2.2 nTPM

Basal keratinocytes	20.1 nTPM
Skin	20.1 nTPM

Basal prostatic cells	22.0 nTPM
Prostate	22.0 nTPM

Basal squamous epithelial cells	14.8 nTPM
Esophagus	14.8 nTPM

Cholangiocytes	10.0 nTPM
Liver	10.0 nTPM

Undifferentiated cells	35.6 nTPM
Colon	45.5 nTPM
Small intestine	34.3 nTPM
Rectum	26.8 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