Single cell type - CSNK1D - 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.	CSNK1D
Gene descriptionⁱ Full gene name according to HGNC.	Casein kinase 1 delta
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Human disease related genes Metabolic proteins Plasma proteins Potential drug targets
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.	4

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	Spermatids - Spermatogenesis (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	Group enriched (Late spermatids, Early spermatids)
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: Group enriched (Late spermatids, Early spermatids)

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

CSNK1D is part of cluster 25 Spermatids - Spermatogenesis with confidenceⁱ 1
458 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
PCYT2	Phosphate cytidylyltransferase 2, ethanolamine	0.6926	25
SRP54	Signal recognition particle 54	0.6753	25
FSCB	Fibrous sheath CABYR binding protein	0.6733	25
ODF1	Outer dense fiber of sperm tails 1	0.6690	25
TSSK3	Testis specific serine kinase 3	0.6630	25
PHKG2	Phosphorylase kinase catalytic subunit gamma 2	0.6620	25
TSSK6	Testis specific serine kinase 6	0.6590	25
KLHL10	Kelch like family member 10	0.6573	25
LPIN1	Lipin 1	0.6502	25
BOD1L2	Biorientation of chromosomes in cell division 1 like 2	0.6474	25
TEX38	Testis expressed 38	0.6452	25
UBQLN3	Ubiquilin 3	0.6425	25
LELP1	Late cornified envelope like proline rich 1	0.6389	25
LSMEM2	Leucine rich single-pass membrane protein 2	0.6377	25
DNAJB8	DnaJ heat shock protein family (Hsp40) member B8	0.6369	25

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	65.8 nTPM
Adipose tissue	81.2 nTPM
Breast	50.4 nTPM

Alveolar cells type 1	48.1 nTPM
Lung	48.1 nTPM

Alveolar cells type 2	54.3 nTPM
Lung	54.3 nTPM

Astrocytes	36.6 nTPM
Brain	36.6 nTPM

B-cells	81.1 nTPM
Adipose tissue	155.4 nTPM
Lymph node	111.4 nTPM
Colon	103.8 nTPM
Stomach	103.1 nTPM
Breast	88.2 nTPM
Spleen	82.3 nTPM
PBMC	55.7 nTPM
Liver	46.0 nTPM
Kidney	38.1 nTPM
Bone marrow	27.0 nTPM

Dendritic cells	101.0 nTPM
Adipose tissue	191.6 nTPM
Breast	99.5 nTPM
PBMC	12.0 nTPM

Endothelial cells	54.2 nTPM
Prostate	97.0 nTPM
Eye	74.4 nTPM
Skeletal muscle	69.8 nTPM
Skin	67.7 nTPM
Endometrium	56.2 nTPM
Breast	55.3 nTPM
Ovary	51.0 nTPM
Placenta	50.1 nTPM
Liver	48.6 nTPM
Esophagus	46.5 nTPM
Pancreas	42.5 nTPM
Testis	38.2 nTPM
Lung	34.3 nTPM
Heart muscle	27.9 nTPM

Fibroblasts	42.8 nTPM
Prostate	78.5 nTPM
Stomach	53.4 nTPM
Skeletal muscle	52.3 nTPM
Lung	47.0 nTPM
Skin	43.1 nTPM
Placenta	42.6 nTPM
Ovary	39.9 nTPM
Breast	35.6 nTPM
Esophagus	33.7 nTPM
Adipose tissue	30.0 nTPM
Heart muscle	14.5 nTPM

Intestinal goblet cells	62.8 nTPM
Colon	76.5 nTPM
Small intestine	66.1 nTPM
Rectum	45.9 nTPM

Macrophages	75.7 nTPM
Adipose tissue	168.7 nTPM
Prostate	113.4 nTPM
Stomach	105.5 nTPM
Skeletal muscle	98.4 nTPM
Breast	83.6 nTPM
Endometrium	77.2 nTPM
Ovary	73.8 nTPM
Pancreas	66.4 nTPM
Lung	61.5 nTPM
Spleen	61.1 nTPM
Kidney	57.5 nTPM
Bone marrow	53.7 nTPM
Esophagus	53.5 nTPM
Testis	48.3 nTPM
PBMC	13.6 nTPM

Paneth cells	83.2 nTPM
Colon	151.5 nTPM
Rectum	53.1 nTPM
Small intestine	45.0 nTPM

Plasma cells	80.9 nTPM
Adipose tissue	227.0 nTPM
Stomach	51.2 nTPM
Esophagus	49.4 nTPM
Bone marrow	39.5 nTPM
Spleen	37.4 nTPM

Respiratory ciliated cells	66.6 nTPM
Lung	69.9 nTPM
Bronchus	63.2 nTPM

Smooth muscle cells	57.5 nTPM
Prostate	91.9 nTPM
Skeletal muscle	85.9 nTPM
Bronchus	82.8 nTPM
Skin	72.2 nTPM
Pancreas	68.0 nTPM
Ovary	52.7 nTPM
Adipose tissue	46.0 nTPM
Endometrium	43.7 nTPM
Breast	37.8 nTPM
Esophagus	26.4 nTPM
Heart muscle	25.3 nTPM

T-cells	87.6 nTPM
Adipose tissue	153.6 nTPM
Colon	140.7 nTPM
Skin	132.1 nTPM
Skeletal muscle	107.2 nTPM
Breast	106.8 nTPM
Lymph node	98.3 nTPM
Stomach	96.4 nTPM
Endometrium	95.1 nTPM
Spleen	82.7 nTPM
Liver	75.6 nTPM
Ovary	71.2 nTPM
Prostate	71.1 nTPM
Lung	68.4 nTPM
Esophagus	52.4 nTPM
PBMC	47.6 nTPM
Bone marrow	45.8 nTPM
Kidney	44.5 nTPM

Basal keratinocytes	56.6 nTPM
Skin	56.6 nTPM

Basal prostatic cells	116.0 nTPM
Prostate	116.0 nTPM

Basal respiratory cells	58.3 nTPM
Bronchus	58.3 nTPM

Basal squamous epithelial cells	52.9 nTPM
Esophagus	52.9 nTPM

Undifferentiated cells	56.7 nTPM
Colon	85.1 nTPM
Small intestine	42.8 nTPM
Rectum	42.1 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