Single cell type - YTHDF3 - 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.	YTHDF3
Gene descriptionⁱ Full gene name according to HGNC.	YTH N6-methyladenosine RNA binding protein 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.	12

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	Endometrium - 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 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	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: 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

YTHDF3 is part of cluster 44 Endometrium - Transcription with confidenceⁱ 1
491 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
EP300	E1A binding protein p300	0.6478	44
MED13	Mediator complex subunit 13	0.6161	44
TAOK1	TAO kinase 1	0.6050	10
TSC22D2	TSC22 domain family member 2	0.5989	44
ZBTB11	Zinc finger and BTB domain containing 11	0.5961	44
ATP13A3	ATPase 13A3	0.5833	41
USP9X	Ubiquitin specific peptidase 9 X-linked	0.5699	44
NUP153	Nucleoporin 153	0.5684	44
NFIL3	Nuclear factor, interleukin 3 regulated	0.5677	41
CREBBP	CREB binding protein	0.5628	44
PPP1R15B	Protein phosphatase 1 regulatory subunit 15B	0.5537	41
EMILIN2	Elastin microfibril interfacer 2	0.5529	41
KMT2C	Lysine methyltransferase 2C	0.5519	44
MED13L	Mediator complex subunit 13L	0.5471	44
IRS2	Insulin receptor substrate 2	0.5439	41

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	33.0 nTPM
Adipose tissue	43.2 nTPM
Breast	23.0 nTPM

Alveolar cells type 1	32.1 nTPM
Lung	32.1 nTPM

Alveolar cells type 2	51.1 nTPM
Lung	51.1 nTPM

Astrocytes	41.8 nTPM
Brain	41.8 nTPM

B-cells	28.2 nTPM
Adipose tissue	52.1 nTPM
Stomach	40.4 nTPM
Spleen	39.4 nTPM
Lymph node	37.4 nTPM
Colon	27.1 nTPM
Bone marrow	24.5 nTPM
Breast	24.1 nTPM
PBMC	20.0 nTPM
Liver	16.5 nTPM
Kidney	0.0 nTPM

Dendritic cells	34.1 nTPM
Adipose tissue	58.5 nTPM
Breast	23.6 nTPM
PBMC	20.0 nTPM

Endothelial cells	28.2 nTPM
Endometrium	60.1 nTPM
Prostate	39.3 nTPM
Skin	38.8 nTPM
Esophagus	31.5 nTPM
Breast	31.3 nTPM
Lung	28.1 nTPM
Placenta	27.3 nTPM
Ovary	25.6 nTPM
Skeletal muscle	24.4 nTPM
Liver	23.8 nTPM
Heart muscle	21.9 nTPM
Eye	18.6 nTPM
Testis	16.0 nTPM
Pancreas	7.7 nTPM

Fibroblasts	33.5 nTPM
Prostate	44.7 nTPM
Heart muscle	41.0 nTPM
Skin	38.9 nTPM
Stomach	37.1 nTPM
Lung	34.7 nTPM
Esophagus	34.4 nTPM
Adipose tissue	34.1 nTPM
Skeletal muscle	28.1 nTPM
Placenta	26.4 nTPM
Ovary	25.1 nTPM
Breast	24.4 nTPM

Intestinal goblet cells	31.8 nTPM
Rectum	38.9 nTPM
Colon	32.2 nTPM
Small intestine	24.2 nTPM

Macrophages	54.4 nTPM
Adipose tissue	131.0 nTPM
Spleen	107.8 nTPM
Endometrium	70.4 nTPM
Skeletal muscle	66.0 nTPM
Ovary	65.7 nTPM
Bone marrow	57.5 nTPM
Esophagus	56.6 nTPM
Prostate	53.9 nTPM
Stomach	52.7 nTPM
Lung	46.9 nTPM
Kidney	40.1 nTPM
Breast	33.5 nTPM
Pancreas	17.8 nTPM
Testis	16.3 nTPM
PBMC	0.0 nTPM

Paneth cells	30.6 nTPM
Rectum	32.1 nTPM
Small intestine	30.0 nTPM
Colon	29.6 nTPM

Plasma cells	22.9 nTPM
Adipose tissue	40.7 nTPM
Stomach	31.5 nTPM
Spleen	26.4 nTPM
Bone marrow	9.9 nTPM
Esophagus	6.1 nTPM

Respiratory ciliated cells	31.2 nTPM
Bronchus	31.8 nTPM
Lung	30.6 nTPM

Smooth muscle cells	31.5 nTPM
Endometrium	54.8 nTPM
Prostate	39.0 nTPM
Bronchus	39.0 nTPM
Esophagus	35.7 nTPM
Skin	35.2 nTPM
Adipose tissue	35.1 nTPM
Skeletal muscle	24.6 nTPM
Ovary	23.5 nTPM
Heart muscle	22.2 nTPM
Pancreas	20.7 nTPM
Breast	16.2 nTPM

T-cells	28.8 nTPM
Endometrium	58.6 nTPM
Adipose tissue	52.2 nTPM
Spleen	38.1 nTPM
Skin	36.4 nTPM
Stomach	34.6 nTPM
Lung	33.4 nTPM
Lymph node	32.9 nTPM
Breast	29.5 nTPM
Bone marrow	28.7 nTPM
Colon	28.0 nTPM
Esophagus	26.2 nTPM
Skeletal muscle	22.6 nTPM
Liver	18.4 nTPM
Prostate	14.2 nTPM
Ovary	13.4 nTPM
PBMC	12.5 nTPM
Kidney	10.2 nTPM

Basal keratinocytes	38.7 nTPM
Skin	38.7 nTPM

Basal respiratory cells	19.1 nTPM
Bronchus	19.1 nTPM

Cholangiocytes	28.6 nTPM
Liver	28.6 nTPM

Collecting duct cells	20.2 nTPM
Kidney	20.2 nTPM

Undifferentiated cells	28.5 nTPM
Rectum	32.2 nTPM
Colon	30.2 nTPM
Small intestine	23.2 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