Single cell type - NHLRC3 - 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.	NHLRC3
Gene descriptionⁱ Full gene name according to HGNC.	NHL repeat 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,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	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	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
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: 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

NHLRC3 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
ELMOD3	ELMO domain containing 3	0.7508	52
ATF6B	Activating transcription factor 6 beta	0.7406	40
ZFP14	ZFP14 zinc finger protein	0.6835	52
TTC14	Tetratricopeptide repeat domain 14	0.6782	52
LRIG2	Leucine rich repeats and immunoglobulin like domains 2	0.6626	52
ZNF224	Zinc finger protein 224	0.6483	52
TRMT13	TRNA methyltransferase 13 homolog	0.6466	52
DDX17	DEAD-box helicase 17	0.6451	52
SHPRH	SNF2 histone linker PHD RING helicase	0.6301	52
ZNF500	Zinc finger protein 500	0.6283	52
POLR2J2	RNA polymerase II subunit J2	0.6088	52
CARF	Calcium responsive transcription factor	0.6013	52
ZNF445	Zinc finger protein 445	0.5944	52
ZNF397	Zinc finger protein 397	0.5939	52
ZNF169	Zinc finger protein 169	0.5884	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	20.6 nTPM
Adipose tissue	27.0 nTPM
Breast	14.2 nTPM

Alveolar cells type 1	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	20.2 nTPM
Lung	20.2 nTPM

Astrocytes	22.9 nTPM
Brain	22.9 nTPM

B-cells	36.7 nTPM
PBMC	77.1 nTPM
Colon	44.8 nTPM
Adipose tissue	42.6 nTPM
Bone marrow	36.8 nTPM
Liver	35.5 nTPM
Stomach	29.0 nTPM
Kidney	28.5 nTPM
Breast	28.1 nTPM
Spleen	25.3 nTPM
Lymph node	19.7 nTPM

Dendritic cells	52.5 nTPM
PBMC	95.6 nTPM
Adipose tissue	43.8 nTPM
Breast	18.2 nTPM

Endothelial cells	22.4 nTPM
Liver	47.7 nTPM
Testis	38.8 nTPM
Heart muscle	35.3 nTPM
Placenta	28.4 nTPM
Lung	24.9 nTPM
Skeletal muscle	21.1 nTPM
Eye	21.0 nTPM
Skin	18.8 nTPM
Breast	17.4 nTPM
Ovary	17.1 nTPM
Esophagus	14.4 nTPM
Endometrium	12.5 nTPM
Prostate	8.7 nTPM
Pancreas	7.7 nTPM

Fibroblasts	21.8 nTPM
Ovary	42.0 nTPM
Adipose tissue	35.8 nTPM
Placenta	33.2 nTPM
Skeletal muscle	22.3 nTPM
Breast	21.8 nTPM
Skin	18.0 nTPM
Stomach	16.3 nTPM
Esophagus	15.8 nTPM
Lung	14.5 nTPM
Heart muscle	10.8 nTPM
Prostate	8.9 nTPM

Intestinal goblet cells	28.6 nTPM
Small intestine	41.7 nTPM
Rectum	29.1 nTPM
Colon	15.0 nTPM

Macrophages	35.2 nTPM
Ovary	64.5 nTPM
Kidney	49.1 nTPM
Lung	48.7 nTPM
Testis	44.1 nTPM
Prostate	42.3 nTPM
Spleen	37.4 nTPM
Bone marrow	36.3 nTPM
Stomach	32.2 nTPM
Esophagus	29.9 nTPM
Breast	29.9 nTPM
Adipose tissue	29.0 nTPM
Pancreas	25.5 nTPM
Skeletal muscle	24.5 nTPM
Endometrium	21.2 nTPM
PBMC	13.6 nTPM

Paneth cells	25.0 nTPM
Small intestine	37.6 nTPM
Rectum	37.5 nTPM
Colon	0.0 nTPM

Plasma cells	30.7 nTPM
Esophagus	49.4 nTPM
Adipose tissue	46.4 nTPM
Stomach	25.8 nTPM
Bone marrow	16.5 nTPM
Spleen	15.2 nTPM

Respiratory ciliated cells	32.1 nTPM
Bronchus	36.5 nTPM
Lung	27.7 nTPM

Smooth muscle cells	18.7 nTPM
Endometrium	32.6 nTPM
Ovary	30.1 nTPM
Adipose tissue	27.8 nTPM
Breast	20.2 nTPM
Skeletal muscle	19.6 nTPM
Skin	17.1 nTPM
Esophagus	15.5 nTPM
Bronchus	13.2 nTPM
Heart muscle	12.3 nTPM
Pancreas	11.4 nTPM
Prostate	6.0 nTPM

T-cells	30.5 nTPM
PBMC	89.5 nTPM
Liver	58.8 nTPM
Ovary	51.2 nTPM
Kidney	43.1 nTPM
Colon	36.1 nTPM
Bone marrow	30.7 nTPM
Lung	25.8 nTPM
Adipose tissue	24.1 nTPM
Skeletal muscle	22.9 nTPM
Spleen	20.4 nTPM
Skin	20.2 nTPM
Endometrium	19.2 nTPM
Stomach	19.1 nTPM
Breast	18.8 nTPM
Lymph node	17.5 nTPM
Prostate	14.2 nTPM
Esophagus	6.6 nTPM

Basal keratinocytes	8.4 nTPM
Skin	8.4 nTPM

Basal prostatic cells	16.9 nTPM
Prostate	16.9 nTPM

Basal respiratory cells	40.8 nTPM
Bronchus	40.8 nTPM

Basal squamous epithelial cells	15.9 nTPM
Esophagus	15.9 nTPM

Undifferentiated cells	28.4 nTPM
Rectum	35.9 nTPM
Small intestine	33.5 nTPM
Colon	15.8 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