Single cell type - RIOK1 - 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.	RIOK1
Gene descriptionⁱ Full gene name according to HGNC.	RIO kinase 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes Metabolic proteins
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.	1

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	Spermatocytes - 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	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	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: 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

RIOK1 is part of cluster 66 Spermatocytes - Spermatogenesis with confidenceⁱ 0.99
507 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
C1orf52	Chromosome 1 open reading frame 52	0.5958	28
CTAGE9	CTAGE family member 9	0.5532	66
NIP7	Nucleolar pre-rRNA processing protein NIP7	0.5403	39
ZNF574	Zinc finger protein 574	0.5370	59
NXT1	Nuclear transport factor 2 like export factor 1	0.5288	28
CTAGE6	CTAGE family member 6	0.5057	66
LTV1	LTV1 ribosome biogenesis factor	0.5031	39
NLRP4	NLR family pyrin domain containing 4	0.4986	23
NOP16	NOP16 nucleolar protein	0.4981	39
PSMG1	Proteasome assembly chaperone 1	0.4968	66
LCE5A	Late cornified envelope 5A	0.4965	28
KRTAP20-4	Keratin associated protein 20-4	0.4961	20
SULT6B1	Sulfotransferase family 6B member 1	0.4954	66
ZNF200	Zinc finger protein 200	0.4952	20
NUDCD1	NudC domain containing 1	0.4906	23

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	22.2 nTPM
Breast	23.1 nTPM
Adipose tissue	21.2 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	26.4 nTPM
Lung	26.4 nTPM

Astrocytes	5.5 nTPM
Brain	5.5 nTPM

B-cells	27.5 nTPM
Adipose tissue	44.6 nTPM
Spleen	42.9 nTPM
Lymph node	39.1 nTPM
Stomach	36.3 nTPM
Breast	26.8 nTPM
Liver	25.2 nTPM
Bone marrow	20.4 nTPM
Colon	19.2 nTPM
PBMC	15.7 nTPM
Kidney	4.8 nTPM

Dendritic cells	25.3 nTPM
Adipose tissue	39.4 nTPM
Breast	32.4 nTPM
PBMC	4.0 nTPM

Endothelial cells	24.8 nTPM
Prostate	34.9 nTPM
Lung	34.3 nTPM
Heart muscle	29.5 nTPM
Pancreas	27.0 nTPM
Placenta	26.7 nTPM
Skin	25.6 nTPM
Endometrium	25.0 nTPM
Skeletal muscle	23.7 nTPM
Breast	23.1 nTPM
Esophagus	22.1 nTPM
Testis	21.0 nTPM
Eye	19.4 nTPM
Ovary	18.9 nTPM
Liver	16.5 nTPM

Fibroblasts	29.8 nTPM
Lung	74.8 nTPM
Heart muscle	34.0 nTPM
Prostate	32.7 nTPM
Skeletal muscle	29.0 nTPM
Stomach	28.2 nTPM
Ovary	23.6 nTPM
Breast	22.9 nTPM
Adipose tissue	22.0 nTPM
Skin	21.6 nTPM
Placenta	20.8 nTPM
Esophagus	18.1 nTPM

Intestinal goblet cells	17.4 nTPM
Colon	30.0 nTPM
Small intestine	11.4 nTPM
Rectum	10.8 nTPM

Macrophages	19.7 nTPM
Lung	39.7 nTPM
Esophagus	36.2 nTPM
Breast	34.2 nTPM
Endometrium	28.4 nTPM
Adipose tissue	23.5 nTPM
Ovary	19.8 nTPM
Skeletal muscle	18.3 nTPM
Pancreas	17.8 nTPM
Testis	16.9 nTPM
Kidney	15.2 nTPM
Stomach	14.7 nTPM
Spleen	13.5 nTPM
Bone marrow	10.0 nTPM
Prostate	8.1 nTPM
PBMC	0.0 nTPM

Paneth cells	8.2 nTPM
Rectum	14.3 nTPM
Colon	6.5 nTPM
Small intestine	3.7 nTPM

Plasma cells	27.0 nTPM
Adipose tissue	30.3 nTPM
Spleen	29.3 nTPM
Stomach	29.2 nTPM
Esophagus	24.6 nTPM
Bone marrow	21.4 nTPM

Respiratory ciliated cells	20.9 nTPM
Lung	27.7 nTPM
Bronchus	14.1 nTPM

Smooth muscle cells	23.9 nTPM
Prostate	31.0 nTPM
Heart muscle	28.9 nTPM
Skin	28.0 nTPM
Pancreas	27.6 nTPM
Skeletal muscle	25.5 nTPM
Ovary	23.8 nTPM
Breast	22.0 nTPM
Endometrium	21.7 nTPM
Esophagus	20.1 nTPM
Adipose tissue	19.7 nTPM
Bronchus	14.3 nTPM

T-cells	29.0 nTPM
Ovary	46.7 nTPM
Lung	44.0 nTPM
Adipose tissue	40.0 nTPM
Lymph node	34.7 nTPM
Stomach	34.5 nTPM
Endometrium	33.9 nTPM
Esophagus	32.8 nTPM
Spleen	31.7 nTPM
Breast	28.5 nTPM
Kidney	26.7 nTPM
Colon	26.1 nTPM
Bone marrow	25.2 nTPM
Skin	24.4 nTPM
Skeletal muscle	21.9 nTPM
Liver	19.8 nTPM
PBMC	17.6 nTPM
Prostate	4.7 nTPM

Basal keratinocytes	52.8 nTPM
Skin	52.8 nTPM

Basal prostatic cells	32.3 nTPM
Prostate	32.3 nTPM

Basal squamous epithelial cells	38.1 nTPM
Esophagus	38.1 nTPM

Cholangiocytes	4.3 nTPM
Liver	4.3 nTPM

Undifferentiated cells	16.9 nTPM
Colon	19.9 nTPM
Small intestine	16.1 nTPM
Rectum	14.6 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