Single cell type - CLPTM1L - 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.	CLPTM1L
Gene descriptionⁱ Full gene name according to HGNC.	CLPTM1 like
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.	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	Plasma cells - Humoral 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	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 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	Cell line enhanced (U-266/84)
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

CLPTM1L is part of cluster 55 Plasma cells - Humoral immune response with confidenceⁱ 1
379 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
IGKV6D-41	Immunoglobulin kappa variable 6D-41 (non-functional)	0.6248	55
IGHG2	Immunoglobulin heavy constant gamma 2 (G2m marker)	0.5950	55
IGLC2	Immunoglobulin lambda constant 2	0.5871	55
SSR3	Signal sequence receptor subunit 3	0.5591	55
IGHV3-35	Immunoglobulin heavy variable 3-35 (non-functional)	0.5536	55
MIXL1	Mix paired-like homeobox	0.5512	55
SEC11C	SEC11 homolog C, signal peptidase complex subunit	0.5508	55
IGLC3	Immunoglobulin lambda constant 3 (Kern-Oz+ marker)	0.5479	55
IGKC	Immunoglobulin kappa constant	0.5429	55
IGHG1	Immunoglobulin heavy constant gamma 1 (G1m marker)	0.5422	55
IGHG3	Immunoglobulin heavy constant gamma 3 (G3m marker)	0.5352	55
NUGGC	Nuclear GTPase, germinal center associated	0.5324	55
IGLV1-36	Immunoglobulin lambda variable 1-36	0.5322	55
IGKV1D-16	Immunoglobulin kappa variable 1D-16	0.5238	55
IGHV3-53	Immunoglobulin heavy variable 3-53	0.5232	55

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	33.4 nTPM
Breast	37.1 nTPM
Adipose tissue	29.7 nTPM

Alveolar cells type 1	57.7 nTPM
Lung	57.7 nTPM

Alveolar cells type 2	64.7 nTPM
Lung	64.7 nTPM

Astrocytes	7.2 nTPM
Brain	7.2 nTPM

B-cells	50.2 nTPM
Liver	217.5 nTPM
Breast	160.5 nTPM
Adipose tissue	38.6 nTPM
Kidney	19.0 nTPM
Colon	17.6 nTPM
PBMC	15.7 nTPM
Spleen	10.4 nTPM
Lymph node	9.7 nTPM
Bone marrow	6.6 nTPM
Stomach	6.4 nTPM

Dendritic cells	35.1 nTPM
Adipose tissue	41.5 nTPM
Breast	39.8 nTPM
PBMC	23.9 nTPM

Endothelial cells	25.4 nTPM
Ovary	54.4 nTPM
Endometrium	36.8 nTPM
Liver	31.2 nTPM
Eye	29.1 nTPM
Breast	28.5 nTPM
Prostate	28.4 nTPM
Lung	24.9 nTPM
Skeletal muscle	23.7 nTPM
Pancreas	23.1 nTPM
Placenta	21.0 nTPM
Testis	14.5 nTPM
Skin	14.4 nTPM
Heart muscle	13.2 nTPM
Esophagus	11.9 nTPM

Fibroblasts	23.2 nTPM
Ovary	43.0 nTPM
Adipose tissue	38.0 nTPM
Skeletal muscle	28.9 nTPM
Breast	27.8 nTPM
Lung	24.6 nTPM
Prostate	23.7 nTPM
Placenta	18.0 nTPM
Skin	17.4 nTPM
Stomach	13.4 nTPM
Esophagus	10.7 nTPM
Heart muscle	9.5 nTPM

Intestinal goblet cells	52.2 nTPM
Colon	60.8 nTPM
Rectum	56.1 nTPM
Small intestine	39.6 nTPM

Macrophages	27.9 nTPM
Ovary	65.5 nTPM
Lung	46.9 nTPM
Adipose tissue	37.9 nTPM
Breast	37.1 nTPM
Endometrium	35.8 nTPM
Skeletal muscle	32.2 nTPM
Kidney	30.3 nTPM
Spleen	22.8 nTPM
Stomach	20.5 nTPM
Bone marrow	20.0 nTPM
Testis	19.2 nTPM
Pancreas	17.8 nTPM
Esophagus	17.3 nTPM
Prostate	15.0 nTPM
PBMC	0.0 nTPM

Paneth cells	29.0 nTPM
Colon	32.9 nTPM
Rectum	31.4 nTPM
Small intestine	22.5 nTPM

Plasma cells	95.6 nTPM
Spleen	163.2 nTPM
Bone marrow	90.6 nTPM
Stomach	85.2 nTPM
Adipose tissue	83.2 nTPM
Esophagus	55.5 nTPM

Respiratory ciliated cells	31.0 nTPM
Lung	35.0 nTPM
Bronchus	27.0 nTPM

Smooth muscle cells	21.3 nTPM
Ovary	50.2 nTPM
Breast	35.0 nTPM
Adipose tissue	27.2 nTPM
Prostate	24.1 nTPM
Endometrium	24.0 nTPM
Pancreas	19.8 nTPM
Skeletal muscle	17.1 nTPM
Heart muscle	12.6 nTPM
Skin	12.6 nTPM
Bronchus	8.4 nTPM
Esophagus	3.1 nTPM

T-cells	24.4 nTPM
Ovary	86.7 nTPM
Breast	45.7 nTPM
Skeletal muscle	37.3 nTPM
Adipose tissue	33.1 nTPM
Lung	30.4 nTPM
Endometrium	29.2 nTPM
Liver	23.6 nTPM
Colon	21.4 nTPM
PBMC	20.1 nTPM
Kidney	17.8 nTPM
Spleen	12.9 nTPM
Skin	12.4 nTPM
Stomach	9.8 nTPM
Prostate	9.5 nTPM
Lymph node	8.9 nTPM
Bone marrow	8.8 nTPM
Esophagus	6.6 nTPM

Basal keratinocytes	22.3 nTPM
Skin	22.3 nTPM

Basal prostatic cells	23.3 nTPM
Prostate	23.3 nTPM

Basal respiratory cells	24.3 nTPM
Bronchus	24.3 nTPM

Basal squamous epithelial cells	8.0 nTPM
Esophagus	8.0 nTPM

Undifferentiated cells	39.8 nTPM
Colon	43.9 nTPM
Rectum	43.8 nTPM
Small intestine	31.7 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