Single cell type - SCML4 - 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.	SCML4
Gene descriptionⁱ Full gene name according to HGNC.	Scm polycomb group protein like 4
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.	5

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	T-cells - T-cell receptor (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, T-cells, Early spermatids, NK-cells, dendritic cells)
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	Group enriched (memory CD4 T-cell, naive CD4 T-cell, memory CD8 T-cell, naive CD8 T-cell, NK-cell, gdT-cell, MAIT T-cell)
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	Cell line enriched (HDLM-2)
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 some
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, T-cells, Early spermatids, NK-cells, dendritic cells)

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

SCML4 is part of cluster 58 T-cells - T-cell receptor with confidenceⁱ 1
180 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
TRBV5-6	T cell receptor beta variable 5-6	0.8560	58
TRGV10	T cell receptor gamma variable 10 (non-functional)	0.8483	58
TRBV7-3	T cell receptor beta variable 7-3	0.8426	58
CD3E	CD3e molecule	0.8347	58
TRAV22	T cell receptor alpha variable 22	0.8242	58
TRGV11	T cell receptor gamma variable 11 (non-functional)	0.8199	58
TRBV9	T cell receptor beta variable 9	0.8172	58
TRAV12-2	T cell receptor alpha variable 12-2	0.8152	58
TRAV34	T cell receptor alpha variable 34	0.8128	58
TRAV25	T cell receptor alpha variable 25	0.8126	58
TRAV14DV4	T cell receptor alpha variable 14/delta variable 4	0.8121	58
TRAV16	T cell receptor alpha variable 16	0.8117	58
CD8A	CD8a molecule	0.8115	58
TRAV1-2	T cell receptor alpha variable 1-2	0.8098	58
TRAV21	T cell receptor alpha variable 21	0.8057	58

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	0.5 nTPM
Breast	0.8 nTPM
Adipose tissue	0.3 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	0.0 nTPM
Lung	0.0 nTPM

Astrocytes	0.7 nTPM
Brain	0.7 nTPM

B-cells	18.0 nTPM
Stomach	47.7 nTPM
Bone marrow	24.5 nTPM
Spleen	23.9 nTPM
Lymph node	23.0 nTPM
Adipose tissue	17.6 nTPM
Breast	17.3 nTPM
PBMC	15.7 nTPM
Colon	8.0 nTPM
Liver	2.1 nTPM
Kidney	0.0 nTPM

Dendritic cells	31.7 nTPM
Adipose tissue	56.4 nTPM
Breast	34.6 nTPM
PBMC	4.0 nTPM

Endothelial cells	0.7 nTPM
Liver	3.7 nTPM
Skin	1.8 nTPM
Esophagus	1.0 nTPM
Heart muscle	0.9 nTPM
Eye	0.8 nTPM
Breast	0.6 nTPM
Testis	0.3 nTPM
Skeletal muscle	0.3 nTPM
Endometrium	0.1 nTPM
Lung	0.0 nTPM
Placenta	0.0 nTPM
Prostate	0.0 nTPM
Pancreas	0.0 nTPM
Ovary	0.0 nTPM

Fibroblasts	1.0 nTPM
Stomach	7.4 nTPM
Skin	1.7 nTPM
Esophagus	1.1 nTPM
Breast	0.8 nTPM
Placenta	0.2 nTPM
Skeletal muscle	0.2 nTPM
Heart muscle	0.1 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM

Intestinal goblet cells	1.4 nTPM
Small intestine	2.8 nTPM
Rectum	1.3 nTPM
Colon	0.0 nTPM

Macrophages	1.2 nTPM
Breast	8.7 nTPM
Adipose tissue	3.0 nTPM
Lung	1.7 nTPM
Prostate	1.2 nTPM
Endometrium	1.0 nTPM
Spleen	1.0 nTPM
Testis	0.6 nTPM
Skeletal muscle	0.4 nTPM
Ovary	0.1 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	2.6 nTPM
Small intestine	7.5 nTPM
Rectum	0.4 nTPM
Colon	0.0 nTPM

Plasma cells	11.6 nTPM
Adipose tissue	47.7 nTPM
Stomach	5.0 nTPM
Bone marrow	3.3 nTPM
Spleen	2.2 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	0.7 nTPM
Lung	1.5 nTPM
Bronchus	0.0 nTPM

Smooth muscle cells	0.6 nTPM
Breast	2.1 nTPM
Esophagus	1.5 nTPM
Skin	1.4 nTPM
Heart muscle	1.2 nTPM
Ovary	0.3 nTPM
Pancreas	0.1 nTPM
Prostate	0.0 nTPM
Bronchus	0.0 nTPM
Endometrium	0.0 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM

T-cells	73.3 nTPM
Stomach	219.0 nTPM
Lymph node	119.8 nTPM
Esophagus	104.8 nTPM
Spleen	101.9 nTPM
Bone marrow	96.0 nTPM
PBMC	68.6 nTPM
Skeletal muscle	67.9 nTPM
Adipose tissue	64.7 nTPM
Liver	59.5 nTPM
Colon	56.1 nTPM
Breast	53.1 nTPM
Skin	51.6 nTPM
Ovary	48.9 nTPM
Kidney	43.8 nTPM
Lung	38.0 nTPM
Endometrium	29.5 nTPM
Prostate	23.6 nTPM

Excitatory neurons	2.7 nTPM
Brain	2.7 nTPM

Undifferentiated cells	4.7 nTPM
Small intestine	11.0 nTPM
Rectum	2.0 nTPM
Colon	1.2 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