Single cell type - PRR4 - 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.	PRR4
Gene descriptionⁱ Full gene name according to HGNC.	Proline rich 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Plasma 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	Secreted
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	Photoreceptor cells - Phototransduction (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 (Cone photoreceptor cells, Rod photoreceptor cells, Bipolar cells, Horizontal cells)
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	Not detected in immune cells
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	Not detected
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 enriched (OE19)
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 single
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data. Read more	Protein predicted to be secreted

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 (Cone photoreceptor cells, Rod photoreceptor cells, Bipolar cells, Horizontal cells)

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

PRR4 is part of cluster 9 Photoreceptor cells - Phototransduction with confidenceⁱ 1
227 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
PRPF8	Pre-mRNA processing factor 8	0.6168	9
ABHD18	Abhydrolase domain containing 18	0.5716	59
OPN1SW	Opsin 1, short wave sensitive	0.5632	9
GJD2	Gap junction protein delta 2	0.5628	9
RAB41	RAB41, member RAS oncogene family	0.5405	9
OPN1MW	Opsin 1, medium wave sensitive	0.5387	9
PLAG1	PLAG1 zinc finger	0.5317	52
KDM5D	Lysine demethylase 5D	0.5289	63
OPN1LW	Opsin 1, long wave sensitive	0.5248	9
NUTM2D	NUT family member 2D	0.5235	9
CATSPER2	Cation channel sperm associated 2	0.5169	9
POLR2J3	RNA polymerase II subunit J3	0.5151	52
ALX3	ALX homeobox 3	0.5106	9
GRK7	G protein-coupled receptor kinase 7	0.5096	9
AGGF1	Angiogenic factor with G-patch and FHA domains 1	0.5086	59

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	0.3 nTPM
Breast	0.4 nTPM
Adipose tissue	0.2 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	0.0 nTPM
Lung	0.0 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	22.0 nTPM
Bone marrow	44.9 nTPM
Lymph node	43.0 nTPM
PBMC	37.1 nTPM
Spleen	34.6 nTPM
Stomach	32.2 nTPM
Liver	15.7 nTPM
Colon	9.6 nTPM
Breast	2.6 nTPM
Kidney	0.0 nTPM
Adipose tissue	0.0 nTPM

Dendritic cells	20.1 nTPM
PBMC	59.8 nTPM
Breast	0.4 nTPM
Adipose tissue	0.2 nTPM

Endothelial cells	9.6 nTPM
Testis	27.2 nTPM
Skeletal muscle	21.0 nTPM
Liver	18.3 nTPM
Placenta	15.9 nTPM
Prostate	14.2 nTPM
Skin	11.6 nTPM
Esophagus	10.8 nTPM
Eye	9.7 nTPM
Heart muscle	4.0 nTPM
Breast	2.0 nTPM
Endometrium	0.2 nTPM
Lung	0.0 nTPM
Pancreas	0.0 nTPM
Ovary	0.0 nTPM

Fibroblasts	9.3 nTPM
Stomach	23.7 nTPM
Esophagus	19.7 nTPM
Skeletal muscle	19.6 nTPM
Placenta	14.0 nTPM
Skin	12.1 nTPM
Prostate	9.1 nTPM
Lung	2.2 nTPM
Heart muscle	0.9 nTPM
Breast	0.5 nTPM
Ovary	0.2 nTPM
Adipose tissue	0.1 nTPM

Intestinal goblet cells	6.4 nTPM
Small intestine	7.8 nTPM
Colon	6.5 nTPM
Rectum	5.0 nTPM

Macrophages	6.1 nTPM
Bone marrow	23.7 nTPM
Stomach	14.7 nTPM
Testis	14.0 nTPM
Skeletal muscle	13.4 nTPM
Esophagus	12.6 nTPM
Spleen	8.3 nTPM
Prostate	3.4 nTPM
Lung	0.4 nTPM
Breast	0.3 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Endometrium	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM

Paneth cells	14.4 nTPM
Small intestine	18.8 nTPM
Rectum	14.4 nTPM
Colon	9.9 nTPM

Plasma cells	17.1 nTPM
Bone marrow	29.7 nTPM
Stomach	24.8 nTPM
Spleen	18.2 nTPM
Esophagus	12.3 nTPM
Adipose tissue	0.6 nTPM

Respiratory ciliated cells	6.8 nTPM
Bronchus	13.6 nTPM
Lung	0.0 nTPM

Smooth muscle cells	7.1 nTPM
Skeletal muscle	25.0 nTPM
Esophagus	15.5 nTPM
Prostate	13.1 nTPM
Skin	11.5 nTPM
Heart muscle	6.1 nTPM
Bronchus	5.6 nTPM
Adipose tissue	0.6 nTPM
Breast	0.5 nTPM
Endometrium	0.4 nTPM
Pancreas	0.3 nTPM
Ovary	0.1 nTPM

T-cells	20.1 nTPM
PBMC	63.9 nTPM
Bone marrow	48.4 nTPM
Lymph node	48.3 nTPM
Spleen	36.4 nTPM
Skeletal muscle	34.3 nTPM
Stomach	27.0 nTPM
Esophagus	26.2 nTPM
Liver	24.8 nTPM
Colon	12.8 nTPM
Skin	9.7 nTPM
Prostate	9.5 nTPM
Breast	0.8 nTPM
Endometrium	0.2 nTPM
Kidney	0.0 nTPM
Lung	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM

Basal keratinocytes	3.1 nTPM
Skin	3.1 nTPM

Basal respiratory cells	19.9 nTPM
Bronchus	19.9 nTPM

Cholangiocytes	7.2 nTPM
Liver	7.2 nTPM

Collecting duct cells	1.8 nTPM
Kidney	1.8 nTPM

Undifferentiated cells	9.6 nTPM
Rectum	10.6 nTPM
Colon	9.8 nTPM
Small intestine	8.4 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