Single cell type - CDKN3 - 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.	CDKN3
Gene descriptionⁱ Full gene name according to HGNC.	Cyclin dependent kinase inhibitor 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Metabolic 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.	9

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	Early 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	Cell type enhanced (Early spermatids, Late spermatids, Spermatocytes)
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	Immune cell enhanced (T-reg)
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 (Early spermatids, Late spermatids, Spermatocytes)

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

CDKN3 is part of cluster 29 Early spermatids - Spermatogenesis with confidenceⁱ 1
337 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
GOLGA6L1	Golgin A6 family like 1	0.8283	29
C1orf94	Chromosome 1 open reading frame 94	0.7850	66
SPAG5	Sperm associated antigen 5	0.7772	12
ACTL7B	Actin like 7B	0.7674	29
SPATA31A6	SPATA31 subfamily A member 6	0.7552	29
SOX30	SRY-box transcription factor 30	0.7472	29
CALR3	Calreticulin 3	0.7444	29
MS4A6E	Membrane spanning 4-domains A6E	0.7426	29
MOS	MOS proto-oncogene, serine/threonine kinase	0.7367	66
FAM209A	Family with sequence similarity 209 member A	0.7344	29
GK2	Glycerol kinase 2	0.7318	66
C2orf78	Chromosome 2 open reading frame 78	0.7282	29
TEX33	Testis expressed 33	0.7253	29
ARHGEF39	Rho guanine nucleotide exchange factor 39	0.7227	29
ZNF829	Zinc finger protein 829	0.7138	29

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
Breast	1.9 nTPM
Adipose tissue	0.9 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	0.0 nTPM
Lung	0.0 nTPM

Astrocytes	0.7 nTPM
Brain	0.7 nTPM

B-cells	10.5 nTPM
Liver	93.2 nTPM
PBMC	2.8 nTPM
Breast	2.6 nTPM
Spleen	1.7 nTPM
Colon	1.6 nTPM
Adipose tissue	1.5 nTPM
Lymph node	0.8 nTPM
Stomach	0.5 nTPM
Kidney	0.0 nTPM
Bone marrow	0.0 nTPM

Dendritic cells	2.7 nTPM
Breast	4.7 nTPM
Adipose tissue	3.4 nTPM
PBMC	0.0 nTPM

Endothelial cells	6.8 nTPM
Placenta	20.5 nTPM
Ovary	20.0 nTPM
Testis	12.8 nTPM
Endometrium	12.6 nTPM
Esophagus	9.3 nTPM
Prostate	8.9 nTPM
Skin	3.8 nTPM
Breast	2.9 nTPM
Skeletal muscle	2.3 nTPM
Heart muscle	1.6 nTPM
Liver	0.9 nTPM
Eye	0.0 nTPM
Lung	0.0 nTPM
Pancreas	0.0 nTPM

Erythroid cells	125.5 nTPM
Liver	213.9 nTPM
Bone marrow	37.0 nTPM

Fibroblasts	10.2 nTPM
Ovary	60.4 nTPM
Placenta	21.6 nTPM
Heart muscle	11.0 nTPM
Skeletal muscle	4.5 nTPM
Skin	3.8 nTPM
Esophagus	2.6 nTPM
Breast	2.5 nTPM
Lung	2.2 nTPM
Stomach	1.5 nTPM
Prostate	1.2 nTPM
Adipose tissue	0.9 nTPM

Intestinal goblet cells	17.9 nTPM
Small intestine	30.1 nTPM
Colon	17.9 nTPM
Rectum	5.9 nTPM

Macrophages	8.9 nTPM
Testis	28.4 nTPM
Pancreas	28.0 nTPM
Endometrium	17.5 nTPM
Esophagus	17.3 nTPM
Prostate	11.5 nTPM
Bone marrow	7.5 nTPM
Breast	6.1 nTPM
Stomach	5.9 nTPM
Ovary	2.7 nTPM
Skeletal muscle	2.3 nTPM
Adipose tissue	1.8 nTPM
Lung	1.6 nTPM
Kidney	1.5 nTPM
Spleen	1.0 nTPM
PBMC	0.0 nTPM

Paneth cells	7.2 nTPM
Small intestine	11.3 nTPM
Rectum	7.0 nTPM
Colon	3.3 nTPM

Plasma cells	41.0 nTPM
Spleen	128.4 nTPM
Bone marrow	64.2 nTPM
Stomach	12.5 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	0.2 nTPM
Bronchus	0.4 nTPM
Lung	0.0 nTPM

Smooth muscle cells	20.5 nTPM
Bronchus	104.5 nTPM
Pancreas	66.2 nTPM
Ovary	21.1 nTPM
Endometrium	17.7 nTPM
Heart muscle	5.2 nTPM
Skeletal muscle	2.5 nTPM
Breast	2.3 nTPM
Skin	1.8 nTPM
Adipose tissue	1.8 nTPM
Esophagus	1.5 nTPM
Prostate	0.9 nTPM

Basal prostatic cells	4.3 nTPM
Prostate	4.3 nTPM

Basal respiratory cells	9.7 nTPM
Bronchus	9.7 nTPM

Basal squamous epithelial cells	4.6 nTPM
Esophagus	4.6 nTPM

Cone photoreceptor cells	2.1 nTPM
Eye	2.1 nTPM

T-cells	8.3 nTPM
Ovary	28.9 nTPM
Colon	17.1 nTPM
Esophagus	13.1 nTPM
Liver	12.6 nTPM
Skin	11.6 nTPM
Prostate	9.5 nTPM
Kidney	7.5 nTPM
Endometrium	6.5 nTPM
Lymph node	4.6 nTPM
Adipose tissue	4.3 nTPM
Breast	4.3 nTPM
PBMC	4.2 nTPM
Skeletal muscle	4.2 nTPM
Bone marrow	3.7 nTPM
Spleen	3.6 nTPM
Lung	3.0 nTPM
Stomach	1.8 nTPM

Undifferentiated cells	31.2 nTPM
Small intestine	46.5 nTPM
Rectum	25.9 nTPM
Colon	21.1 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