Single cell type - RUFY3 - 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.	RUFY3
Gene descriptionⁱ Full gene name according to HGNC.	RUN and FYVE domain containing 3
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.	7

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, Oligodendrocytes, Excitatory neurons, 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 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 (Cone photoreceptor cells, Rod photoreceptor cells, Oligodendrocytes, Excitatory neurons, 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

RUFY3 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
INTU	Inturned planar cell polarity protein	0.6094	9
MYO9A	Myosin IXA	0.6005	46
TRPV1	Transient receptor potential cation channel subfamily V member 1	0.5995	46
SNX29	Sorting nexin 29	0.5812	9
ARMC9	Armadillo repeat containing 9	0.5576	9
KCTD7	Potassium channel tetramerization domain containing 7	0.5554	46
AHI1	Abelson helper integration site 1	0.5521	9
PRTG	Protogenin	0.5492	9
CEP164	Centrosomal protein 164	0.5282	9
EML1	EMAP like 1	0.5223	9
CRB2	Crumbs cell polarity complex component 2	0.5194	9
CEP104	Centrosomal protein 104	0.5193	9
ANKS3	Ankyrin repeat and sterile alpha motif domain containing 3	0.5173	9
KIF1B	Kinesin family member 1B	0.5134	9
OSBP2	Oxysterol binding protein 2	0.5113	46

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	31.9 nTPM
Adipose tissue	38.9 nTPM
Breast	24.9 nTPM

Alveolar cells type 1	35.3 nTPM
Lung	35.3 nTPM

Alveolar cells type 2	82.1 nTPM
Lung	82.1 nTPM

B-cells	18.7 nTPM
Adipose tissue	38.6 nTPM
Bone marrow	25.3 nTPM
Colon	17.6 nTPM
PBMC	17.1 nTPM
Spleen	16.0 nTPM
Breast	16.0 nTPM
Lymph node	15.0 nTPM
Liver	14.5 nTPM
Kidney	14.3 nTPM
Stomach	12.7 nTPM

Basal keratinocytes	19.4 nTPM
Skin	19.4 nTPM

Dendritic cells	19.5 nTPM
PBMC	35.8 nTPM
Adipose tissue	12.1 nTPM
Breast	10.6 nTPM

Endothelial cells	32.6 nTPM
Lung	71.7 nTPM
Skeletal muscle	51.2 nTPM
Eye	47.7 nTPM
Prostate	38.0 nTPM
Endometrium	37.2 nTPM
Heart muscle	36.9 nTPM
Ovary	35.8 nTPM
Testis	35.6 nTPM
Placenta	24.5 nTPM
Breast	21.0 nTPM
Skin	19.9 nTPM
Liver	19.2 nTPM
Esophagus	17.5 nTPM
Pancreas	0.0 nTPM

Fibroblasts	43.7 nTPM
Skeletal muscle	80.7 nTPM
Adipose tissue	62.1 nTPM
Stomach	60.9 nTPM
Prostate	55.3 nTPM
Esophagus	46.0 nTPM
Breast	45.9 nTPM
Lung	31.3 nTPM
Ovary	31.3 nTPM
Heart muscle	29.6 nTPM
Skin	26.5 nTPM
Placenta	11.2 nTPM

Intestinal goblet cells	8.4 nTPM
Rectum	10.8 nTPM
Small intestine	8.7 nTPM
Colon	5.8 nTPM

Macrophages	31.0 nTPM
Adipose tissue	59.4 nTPM
Endometrium	53.7 nTPM
Spleen	41.4 nTPM
Ovary	39.2 nTPM
Testis	38.3 nTPM
Skeletal muscle	37.8 nTPM
Lung	35.2 nTPM
Breast	33.8 nTPM
Kidney	31.8 nTPM
Bone marrow	31.2 nTPM
Esophagus	26.8 nTPM
Prostate	21.8 nTPM
Stomach	8.8 nTPM
Pancreas	5.1 nTPM
PBMC	0.0 nTPM

Paneth cells	5.2 nTPM
Rectum	11.9 nTPM
Small intestine	3.7 nTPM
Colon	0.0 nTPM

Plasma cells	17.2 nTPM
Stomach	25.4 nTPM
Bone marrow	18.2 nTPM
Spleen	17.1 nTPM
Adipose tissue	13.0 nTPM
Esophagus	12.3 nTPM

Respiratory ciliated cells	28.3 nTPM
Lung	37.9 nTPM
Bronchus	18.7 nTPM

Smooth muscle cells	35.9 nTPM
Adipose tissue	63.7 nTPM
Prostate	60.7 nTPM
Skeletal muscle	52.9 nTPM
Endometrium	51.0 nTPM
Heart muscle	42.9 nTPM
Ovary	39.3 nTPM
Breast	27.1 nTPM
Skin	20.2 nTPM
Esophagus	18.6 nTPM
Pancreas	11.7 nTPM
Bronchus	6.5 nTPM

T-cells	11.5 nTPM
Lung	27.4 nTPM
Endometrium	19.5 nTPM
Skeletal muscle	18.7 nTPM
Skin	13.8 nTPM
Ovary	13.4 nTPM
Breast	13.4 nTPM
Esophagus	13.1 nTPM
Adipose tissue	12.6 nTPM
Liver	9.9 nTPM
Prostate	9.5 nTPM
Bone marrow	8.9 nTPM
PBMC	7.9 nTPM
Lymph node	6.4 nTPM
Colon	5.7 nTPM
Spleen	5.5 nTPM
Stomach	5.3 nTPM
Kidney	4.7 nTPM

Astrocytes	189.4 nTPM
Brain	189.4 nTPM

Cholangiocytes	12.8 nTPM
Liver	12.8 nTPM

Collecting duct cells	23.9 nTPM
Kidney	23.9 nTPM

Distal enterocytes	7.5 nTPM
Colon	8.2 nTPM
Rectum	6.8 nTPM

Undifferentiated cells	10.1 nTPM
Small intestine	10.8 nTPM
Rectum	10.0 nTPM
Colon	9.4 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