Single cell type - NPHP3-ACAD11 - 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-ACAD11
Gene descriptionⁱ Full gene name according to HGNC.	NPHP3-ACAD11 readthrough (NMD candidate)
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.	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.	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.	Cell type enhanced (Oligodendrocyte precursor cells, Microglial cells, Oligodendrocytes, Astrocytes, Basal squamous epithelial cells, Excitatory neurons, Inhibitory neurons, Squamous epithelial cells)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.88
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Not available
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.	Not detected in immune cells
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at transcript level

ASSAYSⁱ

Single cell type

Immune cells

Expression clustering

SINGLE CELL TYPESⁱ A summary of normalized 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 RNA single cell type specificity: Cell type enhanced (Oligodendrocyte precursor cells, Microglial cells, Oligodendrocytes, Astrocytes, Basal squamous epithelial cells, Excitatory neurons, Inhibitory neurons, Squamous epithelial cells)

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Not detected in immune cells
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

NPHP3-ACAD11 is part of cluster 49 Non-specific - Transcription with confidenceⁱ 1
378 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
CHTF8	Chromosome transmission fidelity factor 8	0.7271	49
ENSG00000249209	Novel protein similar to ATP synthase delta (OSCP) subunit domain	0.7244	49
RNF31	Ring finger protein 31	0.7174	49
ENSG00000263620	Novel protein	0.7105	49
ENSG00000275740	Novel readthrough transcript	0.7044	49
EEF1G	Eukaryotic translation elongation factor 1 gamma	0.7011	49
ENSG00000285827	Novel protein	0.6986	49
GTF2H4	General transcription factor IIH subunit 4	0.6913	49
ENSG00000268870	Novel zinc finger protein	0.6909	49
DIABLO	Diablo IAP-binding mitochondrial protein	0.6899	49
TMEM35B	Transmembrane protein 35B	0.6874	49
C11orf98	Chromosome 11 open reading frame 98	0.6864	49
MRPL38	Mitochondrial ribosomal protein L38	0.6858	49
HTD2	Hydroxyacyl-thioester dehydratase type 2	0.6847	49
ENSG00000280571	Novel protein	0.6845	49

IMMUNE CELLS

NPHP3-ACAD11 is part of cluster 45 Eosinophils - Unknown function with confidenceⁱ 1
257 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
CEBPB	CCAAT enhancer binding protein beta	1.0000	45
SMARCC2	SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2	1.0000	45
LPCAT2	Lysophosphatidylcholine acyltransferase 2	1.0000	45
MMP24OS	MMP24 opposite strand	1.0000	45
STK11	Serine/threonine kinase 11	0.9762	45
SUOX	Sulfite oxidase	0.9762	45
CMPK2	Cytidine/uridine monophosphate kinase 2	0.9762	19
CAMK1	Calcium/calmodulin dependent protein kinase I	0.9762	45
MKRN1	Makorin ring finger protein 1	0.9762	45
ARPP19	CAMP regulated phosphoprotein 19	0.9762	45
MAP2K2	Mitogen-activated protein kinase kinase 2	0.9762	45
ZNF263	Zinc finger protein 263	0.9762	45
HES1	Hes family bHLH transcription factor 1	0.9762	45
SLC7A6OS	Solute carrier family 7 member 6 opposite strand	0.9762	45
SLC25A1	Solute carrier family 25 member 1	0.9762	45