Single cell type - CLHC1 - 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.	CLHC1
Gene descriptionⁱ Full gene name according to HGNC.	Clathrin heavy chain linker domain containing 1
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.	6

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	Ciliated cells - Cilium organization (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 (Early spermatids, Oligodendrocyte precursor cells, Respiratory ciliated cells, Oligodendrocytes, Late spermatids, Astrocytes)
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 single
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 (Early spermatids, Oligodendrocyte precursor cells, Respiratory ciliated cells, Oligodendrocytes, Late spermatids, Astrocytes)

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

CLHC1 is part of cluster 49 Ciliated cells - Cilium organization with confidenceⁱ 1
457 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
TTC26	Tetratricopeptide repeat domain 26	0.6187	49
STK33	Serine/threonine kinase 33	0.6018	49
CCDC39	Coiled-coil domain containing 39	0.5815	49
MROH9	Maestro heat like repeat family member 9	0.5753	68
NME9	NME/NM23 family member 9	0.5753	49
CHST9	Carbohydrate sulfotransferase 9	0.5736	49
EFCAB2	EF-hand calcium binding domain 2	0.5694	49
NSUN7	NOP2/Sun RNA methyltransferase family member 7	0.5686	25
IQUB	IQ motif and ubiquitin domain containing	0.5587	49
CCDC40	Coiled-coil domain containing 40	0.5573	49
TTC21A	Tetratricopeptide repeat domain 21A	0.5494	49
ERMARD	ER membrane associated RNA degradation	0.5468	66
FBXO36	F-box protein 36	0.5416	49
SPAG8	Sperm associated antigen 8	0.5408	49
LRRIQ1	Leucine rich repeats and IQ motif containing 1	0.5405	49

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	3.0 nTPM
Adipose tissue	3.3 nTPM
Breast	2.8 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	4.1 nTPM
Lung	4.1 nTPM

B-cells	2.7 nTPM
Lymph node	6.2 nTPM
Kidney	4.8 nTPM
Colon	3.2 nTPM
PBMC	2.8 nTPM
Spleen	2.8 nTPM
Stomach	2.7 nTPM
Liver	1.8 nTPM
Bone marrow	1.7 nTPM
Adipose tissue	1.0 nTPM
Breast	0.0 nTPM

Basal keratinocytes	1.9 nTPM
Skin	1.9 nTPM

Dendritic cells	1.0 nTPM
Adipose tissue	1.5 nTPM
Breast	1.5 nTPM
PBMC	0.0 nTPM

Endothelial cells	3.0 nTPM
Placenta	5.1 nTPM
Liver	4.6 nTPM
Testis	4.4 nTPM
Ovary	4.0 nTPM
Skeletal muscle	3.7 nTPM
Esophagus	3.7 nTPM
Endometrium	3.6 nTPM
Lung	3.1 nTPM
Eye	2.4 nTPM
Skin	2.0 nTPM
Breast	2.0 nTPM
Heart muscle	1.8 nTPM
Prostate	1.1 nTPM
Pancreas	0.0 nTPM

Fibroblasts	5.1 nTPM
Lung	15.7 nTPM
Stomach	10.4 nTPM
Ovary	7.2 nTPM
Esophagus	4.5 nTPM
Prostate	3.6 nTPM
Placenta	3.5 nTPM
Skeletal muscle	3.3 nTPM
Breast	2.9 nTPM
Adipose tissue	2.4 nTPM
Skin	1.2 nTPM
Heart muscle	1.0 nTPM

Intestinal goblet cells	1.7 nTPM
Rectum	2.6 nTPM
Small intestine	1.8 nTPM
Colon	0.7 nTPM

Macrophages	3.1 nTPM
Ovary	7.3 nTPM
Esophagus	6.3 nTPM
Prostate	5.7 nTPM
Testis	4.6 nTPM
Breast	3.9 nTPM
Kidney	3.8 nTPM
Lung	3.5 nTPM
Pancreas	2.5 nTPM
Endometrium	2.4 nTPM
Adipose tissue	2.2 nTPM
Spleen	2.1 nTPM
Skeletal muscle	1.6 nTPM
Bone marrow	1.2 nTPM
PBMC	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	1.2 nTPM
Rectum	3.6 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	1.6 nTPM
Adipose tissue	3.3 nTPM
Spleen	1.9 nTPM
Bone marrow	1.7 nTPM
Stomach	0.9 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	44.9 nTPM
Lung	48.1 nTPM
Bronchus	41.7 nTPM

Smooth muscle cells	3.7 nTPM
Endometrium	6.8 nTPM
Prostate	6.5 nTPM
Esophagus	6.2 nTPM
Ovary	6.1 nTPM
Skeletal muscle	3.8 nTPM
Adipose tissue	2.7 nTPM
Heart muscle	2.5 nTPM
Pancreas	2.0 nTPM
Bronchus	1.8 nTPM
Breast	1.7 nTPM
Skin	0.7 nTPM

T-cells	2.2 nTPM
Kidney	6.2 nTPM
Lymph node	5.1 nTPM
Skeletal muscle	3.3 nTPM
Lung	3.0 nTPM
Bone marrow	2.7 nTPM
Endometrium	2.6 nTPM
Spleen	2.5 nTPM
PBMC	2.4 nTPM
Ovary	2.2 nTPM
Breast	2.0 nTPM
Stomach	1.9 nTPM
Adipose tissue	1.4 nTPM
Liver	0.8 nTPM
Colon	0.5 nTPM
Skin	0.5 nTPM
Prostate	0.0 nTPM
Esophagus	0.0 nTPM

Astrocytes	35.6 nTPM
Brain	35.6 nTPM

Cone photoreceptor cells	16.7 nTPM
Eye	16.7 nTPM

Cytotrophoblasts	3.4 nTPM
Placenta	3.4 nTPM

Distal tubular cells	5.9 nTPM
Kidney	5.9 nTPM

Undifferentiated cells	2.9 nTPM
Rectum	4.0 nTPM
Small intestine	2.7 nTPM
Colon	2.2 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