Single cell type - DDX3Y - 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.	DDX3Y
Gene descriptionⁱ Full gene name according to HGNC.	DEAD-box helicase 3 Y-linked
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Plasma proteins Potential drug targets
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.	4

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	Spermatids - Spermatogenesis (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	Cell type enhanced (Late spermatids, Early spermatids)
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 (Daudi, HEL, U-266/84, U-698)
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: Cell type enhanced (Late spermatids, Early spermatids)

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

DDX3Y is part of cluster 25 Spermatids - Spermatogenesis with confidenceⁱ 1
458 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
ZFY	Zinc finger protein Y-linked	0.7321	59
MFSD14A	Major facilitator superfamily domain containing 14A	0.6221	25
EGLN2	Egl-9 family hypoxia inducible factor 2	0.6006	25
PSMA6	Proteasome 20S subunit alpha 6	0.5924	25
IL13	Interleukin 13	0.5820	25
GPR137	G protein-coupled receptor 137	0.5765	25
MIS12	MIS12 kinetochore complex component	0.5619	25
TSSK6	Testis specific serine kinase 6	0.5528	25
CERS1	Ceramide synthase 1	0.5509	25
PHKG2	Phosphorylase kinase catalytic subunit gamma 2	0.5495	25
LYPD4	LY6/PLAUR domain containing 4	0.5452	25
ELOF1	Elongation factor 1 homolog	0.5423	25
ODF1	Outer dense fiber of sperm tails 1	0.5407	25
C1QL4	Complement C1q like 4	0.5403	25
KRT85	Keratin 85	0.5392	25

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	0.1 nTPM
Adipose tissue	0.2 nTPM
Breast	0.0 nTPM

Alveolar cells type 1	48.1 nTPM
Lung	48.1 nTPM

Alveolar cells type 2	75.8 nTPM
Lung	75.8 nTPM

Astrocytes	10.1 nTPM
Brain	10.1 nTPM

B-cells	58.0 nTPM
Stomach	149.4 nTPM
Lymph node	128.6 nTPM
Spleen	98.3 nTPM
Colon	52.7 nTPM
Bone marrow	49.8 nTPM
Liver	47.8 nTPM
PBMC	34.3 nTPM
Kidney	19.0 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

Dendritic cells	13.3 nTPM
PBMC	39.8 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

Endothelial cells	56.5 nTPM
Prostate	184.1 nTPM
Eye	104.4 nTPM
Skin	94.4 nTPM
Lung	90.5 nTPM
Esophagus	73.3 nTPM
Skeletal muscle	65.9 nTPM
Testis	61.1 nTPM
Heart muscle	49.2 nTPM
Liver	41.2 nTPM
Pancreas	11.6 nTPM
Placenta	10.2 nTPM
Ovary	5.5 nTPM
Endometrium	0.0 nTPM
Breast	0.0 nTPM

Fibroblasts	63.4 nTPM
Prostate	214.1 nTPM
Lung	137.4 nTPM
Stomach	106.9 nTPM
Skin	78.5 nTPM
Esophagus	59.4 nTPM
Skeletal muscle	51.1 nTPM
Heart muscle	28.6 nTPM
Placenta	21.4 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

Intestinal goblet cells	9.3 nTPM
Small intestine	17.8 nTPM
Colon	10.0 nTPM
Rectum	0.0 nTPM

Macrophages	58.2 nTPM
Spleen	150.3 nTPM
Prostate	149.0 nTPM
Esophagus	122.8 nTPM
Stomach	117.2 nTPM
Testis	102.2 nTPM
Lung	81.5 nTPM
Skeletal muscle	61.1 nTPM
Kidney	46.2 nTPM
Bone marrow	28.7 nTPM
PBMC	13.6 nTPM
Pancreas	0.0 nTPM
Endometrium	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

Paneth cells	8.8 nTPM
Colon	26.4 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Plasma cells	54.7 nTPM
Stomach	125.2 nTPM
Esophagus	61.7 nTPM
Spleen	45.6 nTPM
Bone marrow	41.2 nTPM
Adipose tissue	0.0 nTPM

Respiratory ciliated cells	101.2 nTPM
Lung	128.2 nTPM
Bronchus	74.1 nTPM

Smooth muscle cells	39.2 nTPM
Prostate	154.8 nTPM
Skin	91.8 nTPM
Skeletal muscle	77.3 nTPM
Esophagus	54.3 nTPM
Heart muscle	34.0 nTPM
Bronchus	12.2 nTPM
Pancreas	6.8 nTPM
Ovary	0.1 nTPM
Endometrium	0.0 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

T-cells	66.2 nTPM
Prostate	127.8 nTPM
Stomach	121.3 nTPM
Lung	120.0 nTPM
Lymph node	119.4 nTPM
Spleen	119.2 nTPM
Skin	111.4 nTPM
Esophagus	85.2 nTPM
Colon	72.7 nTPM
Liver	67.9 nTPM
Skeletal muscle	61.5 nTPM
Bone marrow	53.3 nTPM
PBMC	39.6 nTPM
Kidney	26.7 nTPM
Endometrium	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

Basal keratinocytes	94.1 nTPM
Skin	94.1 nTPM

Basal prostatic cells	92.7 nTPM
Prostate	92.7 nTPM

Basal respiratory cells	37.5 nTPM
Bronchus	37.5 nTPM

Basal squamous epithelial cells	89.4 nTPM
Esophagus	89.4 nTPM

Undifferentiated cells	8.1 nTPM
Small intestine	15.8 nTPM
Colon	8.5 nTPM
Rectum	0.0 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