Single cell type - CTR9 - 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.	CTR9
Gene descriptionⁱ Full gene name according to HGNC.	CTR9 homolog, Paf1/RNA polymerase II complex component
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.	2

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	Granulocytes - Receptor signaling (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 all
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 enhanced (HEL)
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: 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

CTR9 is part of cluster 60 Granulocytes - Receptor signaling with confidenceⁱ 1
79 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
LSG1	Large 60S subunit nuclear export GTPase 1	0.5705	60
NPIPA8	Nuclear pore complex interacting protein family member A8	0.5644	60
LEO1	LEO1 homolog, Paf1/RNA polymerase II complex component	0.5500	60
ACIN1	Apoptotic chromatin condensation inducer 1	0.5202	60
AL139011.2	Novel protein	0.5195	60
AC018630.2	PRH1-PRR4 readthrough	0.5065	60
NOL8	Nucleolar protein 8	0.4985	52
OR14J1	Olfactory receptor family 14 subfamily J member 1	0.4919	60
SLC18A2	Solute carrier family 18 member A2	0.4917	60
TTC4	Tetratricopeptide repeat domain 4	0.4889	59
AL136295.1	Novel protein	0.4869	60
ZNF770	Zinc finger protein 770	0.4822	13
TPR	Translocated promoter region, nuclear basket protein	0.4792	13
MAS1L	MAS1 proto-oncogene like, G protein-coupled receptor	0.4791	60
HDC	Histidine decarboxylase	0.4773	60

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	51.5 nTPM
Adipose tissue	54.8 nTPM
Breast	48.2 nTPM

Alveolar cells type 1	57.7 nTPM
Lung	57.7 nTPM

Alveolar cells type 2	48.8 nTPM
Lung	48.8 nTPM

Astrocytes	14.7 nTPM
Brain	14.7 nTPM

B-cells	49.0 nTPM
Stomach	75.4 nTPM
Lymph node	71.0 nTPM
Spleen	69.9 nTPM
Bone marrow	60.5 nTPM
Adipose tissue	60.2 nTPM
Liver	33.6 nTPM
Breast	33.4 nTPM
PBMC	31.5 nTPM
Colon	30.3 nTPM
Kidney	23.8 nTPM

Dendritic cells	42.7 nTPM
Adipose tissue	60.0 nTPM
Breast	44.1 nTPM
PBMC	23.9 nTPM

Endothelial cells	37.7 nTPM
Heart muscle	85.1 nTPM
Lung	59.3 nTPM
Esophagus	46.2 nTPM
Skeletal muscle	45.4 nTPM
Eye	43.7 nTPM
Endometrium	39.3 nTPM
Breast	35.8 nTPM
Prostate	35.0 nTPM
Ovary	30.4 nTPM
Placenta	24.5 nTPM
Skin	24.5 nTPM
Testis	20.1 nTPM
Pancreas	19.3 nTPM
Liver	19.2 nTPM

Fibroblasts	36.4 nTPM
Heart muscle	53.3 nTPM
Ovary	48.2 nTPM
Esophagus	44.8 nTPM
Lung	41.3 nTPM
Skeletal muscle	41.2 nTPM
Stomach	32.7 nTPM
Prostate	30.6 nTPM
Adipose tissue	30.6 nTPM
Breast	30.2 nTPM
Placenta	24.5 nTPM
Skin	23.5 nTPM

Intestinal goblet cells	45.1 nTPM
Colon	64.4 nTPM
Small intestine	35.8 nTPM
Rectum	34.9 nTPM

Macrophages	36.1 nTPM
Esophagus	58.3 nTPM
Bone marrow	57.5 nTPM
Lung	57.0 nTPM
Breast	43.5 nTPM
PBMC	40.9 nTPM
Endometrium	39.0 nTPM
Ovary	38.0 nTPM
Spleen	33.2 nTPM
Skeletal muscle	28.0 nTPM
Adipose tissue	27.8 nTPM
Kidney	27.2 nTPM
Stomach	26.4 nTPM
Prostate	26.3 nTPM
Testis	23.2 nTPM
Pancreas	15.3 nTPM

Paneth cells	17.5 nTPM
Colon	26.4 nTPM
Rectum	22.4 nTPM
Small intestine	3.7 nTPM

Plasma cells	37.2 nTPM
Esophagus	43.0 nTPM
Spleen	40.3 nTPM
Adipose tissue	39.4 nTPM
Stomach	37.1 nTPM
Bone marrow	26.4 nTPM

Respiratory ciliated cells	33.7 nTPM
Lung	39.4 nTPM
Bronchus	28.1 nTPM

Smooth muscle cells	33.1 nTPM
Bronchus	53.8 nTPM
Esophagus	46.5 nTPM
Breast	40.2 nTPM
Ovary	36.5 nTPM
Skeletal muscle	35.3 nTPM
Endometrium	29.3 nTPM
Heart muscle	26.3 nTPM
Skin	25.8 nTPM
Prostate	25.0 nTPM
Adipose tissue	24.7 nTPM
Pancreas	20.5 nTPM

T-cells	48.0 nTPM
Endometrium	81.8 nTPM
Adipose tissue	68.6 nTPM
Lymph node	58.4 nTPM
Bone marrow	56.4 nTPM
Breast	53.5 nTPM
Spleen	52.7 nTPM
Esophagus	52.4 nTPM
Stomach	52.3 nTPM
Prostate	47.3 nTPM
Lung	44.0 nTPM
Colon	42.7 nTPM
Skeletal muscle	41.3 nTPM
Kidney	35.6 nTPM
Ovary	33.3 nTPM
Skin	32.6 nTPM
Liver	32.3 nTPM
PBMC	30.6 nTPM

Basal keratinocytes	87.2 nTPM
Skin	87.2 nTPM

Basal respiratory cells	29.7 nTPM
Bronchus	29.7 nTPM

Basal squamous epithelial cells	64.3 nTPM
Esophagus	64.3 nTPM

Cone photoreceptor cells	56.3 nTPM
Eye	56.3 nTPM

Undifferentiated cells	25.3 nTPM
Colon	29.2 nTPM
Rectum	24.9 nTPM
Small intestine	21.7 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