Single cell type - NPHP3 - 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.	NPHP3
Gene descriptionⁱ Full gene name according to HGNC.	Nephrocystin 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes
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.	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	Non-specific - Transcription (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	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	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 many
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

NPHP3 is part of cluster 52 Non-specific - Transcription with confidenceⁱ 1
611 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
ZNF284	Zinc finger protein 284	0.5780	43
STX16	Syntaxin 16	0.5684	52
GNRH1	Gonadotropin releasing hormone 1	0.5593	43
TAS2R30	Taste 2 receptor member 30	0.5524	43
NANOG	Nanog homeobox	0.5473	9
SYNE3	Spectrin repeat containing nuclear envelope family member 3	0.5363	46
PCSK7	Proprotein convertase subtilisin/kexin type 7	0.5295	63
ZNF500	Zinc finger protein 500	0.5240	52
IKBKB	Inhibitor of nuclear factor kappa B kinase subunit beta	0.5146	9
TAS2R31	Taste 2 receptor member 31	0.5102	43
GIGYF1	GRB10 interacting GYF protein 1	0.5081	52
ZNF7	Zinc finger protein 7	0.5074	52
POU5F2	POU domain class 5, transcription factor 2	0.5050	66
MLLT6	MLLT6, PHD finger containing	0.4976	56
ZNF783	Zinc finger family member 783	0.4908	52

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	25.5 nTPM
Adipose tissue	27.6 nTPM
Breast	23.4 nTPM

Alveolar cells type 1	28.9 nTPM
Lung	28.9 nTPM

Alveolar cells type 2	18.6 nTPM
Lung	18.6 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	12.4 nTPM
Kidney	28.5 nTPM
Breast	16.0 nTPM
PBMC	15.7 nTPM
Adipose tissue	14.6 nTPM
Liver	12.3 nTPM
Bone marrow	9.8 nTPM
Spleen	8.3 nTPM
Colon	6.4 nTPM
Lymph node	6.1 nTPM
Stomach	5.9 nTPM

Dendritic cells	13.5 nTPM
Breast	18.2 nTPM
PBMC	12.0 nTPM
Adipose tissue	10.4 nTPM

Endothelial cells	24.7 nTPM
Testis	46.2 nTPM
Liver	41.2 nTPM
Skeletal muscle	33.7 nTPM
Heart muscle	31.4 nTPM
Breast	27.3 nTPM
Skin	26.5 nTPM
Eye	22.7 nTPM
Lung	21.8 nTPM
Prostate	21.8 nTPM
Ovary	20.5 nTPM
Endometrium	18.5 nTPM
Placenta	12.5 nTPM
Pancreas	11.6 nTPM
Esophagus	10.9 nTPM

Fibroblasts	25.2 nTPM
Breast	39.5 nTPM
Adipose tissue	35.9 nTPM
Skin	35.4 nTPM
Skeletal muscle	32.6 nTPM
Prostate	29.9 nTPM
Ovary	25.3 nTPM
Heart muscle	21.9 nTPM
Placenta	18.0 nTPM
Lung	16.8 nTPM
Esophagus	12.7 nTPM
Stomach	8.9 nTPM

Intestinal goblet cells	11.6 nTPM
Small intestine	13.6 nTPM
Rectum	13.5 nTPM
Colon	7.8 nTPM

Macrophages	9.8 nTPM
Testis	22.1 nTPM
Breast	18.4 nTPM
Ovary	17.1 nTPM
Skeletal muscle	14.7 nTPM
Kidney	12.0 nTPM
Adipose tissue	10.7 nTPM
Spleen	8.3 nTPM
Pancreas	7.7 nTPM
Lung	7.1 nTPM
Prostate	6.9 nTPM
Stomach	5.9 nTPM
Endometrium	5.8 nTPM
Bone marrow	5.0 nTPM
Esophagus	4.8 nTPM
PBMC	0.0 nTPM

Paneth cells	5.4 nTPM
Rectum	12.8 nTPM
Colon	3.3 nTPM
Small intestine	0.0 nTPM

Plasma cells	5.6 nTPM
Adipose tissue	13.6 nTPM
Bone marrow	6.6 nTPM
Stomach	4.4 nTPM
Spleen	3.2 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	14.3 nTPM
Bronchus	15.5 nTPM
Lung	13.1 nTPM

Smooth muscle cells	20.6 nTPM
Skeletal muscle	33.3 nTPM
Breast	31.0 nTPM
Adipose tissue	30.9 nTPM
Heart muscle	26.9 nTPM
Skin	25.8 nTPM
Ovary	24.4 nTPM
Prostate	20.3 nTPM
Endometrium	17.5 nTPM
Pancreas	7.7 nTPM
Esophagus	4.6 nTPM
Bronchus	3.9 nTPM

T-cells	14.0 nTPM
PBMC	29.1 nTPM
Breast	27.4 nTPM
Liver	21.4 nTPM
Prostate	19.0 nTPM
Skeletal muscle	17.9 nTPM
Kidney	17.8 nTPM
Colon	17.6 nTPM
Adipose tissue	16.8 nTPM
Skin	15.2 nTPM
Endometrium	11.9 nTPM
Ovary	8.9 nTPM
Bone marrow	8.6 nTPM
Esophagus	6.6 nTPM
Lung	6.1 nTPM
Spleen	5.6 nTPM
Lymph node	5.2 nTPM
Stomach	3.5 nTPM

Basal keratinocytes	19.1 nTPM
Skin	19.1 nTPM

Basal prostatic cells	15.9 nTPM
Prostate	15.9 nTPM

Basal respiratory cells	10.5 nTPM
Bronchus	10.5 nTPM

Basal squamous epithelial cells	7.4 nTPM
Esophagus	7.4 nTPM

Undifferentiated cells	13.4 nTPM
Rectum	14.9 nTPM
Small intestine	13.1 nTPM
Colon	12.3 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