Single cell type - SCRN1 - 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.	SCRN1
Gene descriptionⁱ Full gene name according to HGNC.	Secernin 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes
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.	9

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	Muller glia cells - Visual perception (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 (Muller glia 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	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	Cell line enhanced (WM-115)
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 (Muller glia 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

SCRN1 is part of cluster 5 Muller glia cells - Visual perception with confidenceⁱ 1
155 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
BEX1	Brain expressed X-linked 1	0.5201	5
TCEAL5	Transcription elongation factor A like 5	0.5078	5
TCEAL2	Transcription elongation factor A like 2	0.4629	56
CADM4	Cell adhesion molecule 4	0.4482	67
DLGAP4	DLG associated protein 4	0.4480	10
DKK3	Dickkopf WNT signaling pathway inhibitor 3	0.4461	5
ABHD12B	Abhydrolase domain containing 12B	0.4425	5
FAM131C	Family with sequence similarity 131 member C	0.4394	5
GAS8	Growth arrest specific 8	0.4381	34
TGFB2	Transforming growth factor beta 2	0.4301	64
GPR162	G protein-coupled receptor 162	0.4282	56
SCRG1	Stimulator of chondrogenesis 1	0.4266	5
SYNGR1	Synaptogyrin 1	0.4228	33
MAPK8IP1	Mitogen-activated protein kinase 8 interacting protein 1	0.4223	62
HOOK1	Hook microtubule tethering protein 1	0.4198	34

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	5.9 nTPM
Adipose tissue	6.7 nTPM
Breast	5.1 nTPM

Alveolar cells type 1	28.9 nTPM
Lung	28.9 nTPM

Alveolar cells type 2	14.1 nTPM
Lung	14.1 nTPM

Astrocytes	42.7 nTPM
Brain	42.7 nTPM

B-cells	15.4 nTPM
Adipose tissue	24.6 nTPM
Bone marrow	19.6 nTPM
Stomach	17.7 nTPM
PBMC	17.1 nTPM
Lymph node	16.6 nTPM
Breast	16.0 nTPM
Spleen	15.6 nTPM
Liver	9.9 nTPM
Kidney	9.5 nTPM
Colon	8.0 nTPM

Dendritic cells	16.2 nTPM
PBMC	39.8 nTPM
Adipose tissue	5.7 nTPM
Breast	3.3 nTPM

Endothelial cells	10.9 nTPM
Ovary	51.0 nTPM
Eye	28.3 nTPM
Lung	28.1 nTPM
Testis	10.9 nTPM
Heart muscle	10.1 nTPM
Placenta	6.2 nTPM
Breast	4.8 nTPM
Prostate	3.2 nTPM
Esophagus	3.0 nTPM
Skin	2.5 nTPM
Skeletal muscle	2.5 nTPM
Endometrium	2.3 nTPM
Liver	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	17.2 nTPM
Heart muscle	46.7 nTPM
Skeletal muscle	29.7 nTPM
Adipose tissue	26.8 nTPM
Placenta	23.3 nTPM
Esophagus	14.5 nTPM
Ovary	10.9 nTPM
Prostate	9.8 nTPM
Breast	9.5 nTPM
Stomach	7.4 nTPM
Skin	5.6 nTPM
Lung	4.5 nTPM

Intestinal goblet cells	0.7 nTPM
Rectum	1.4 nTPM
Small intestine	0.8 nTPM
Colon	0.0 nTPM

Macrophages	11.1 nTPM
Esophagus	23.6 nTPM
Testis	15.7 nTPM
Bone marrow	15.0 nTPM
Skeletal muscle	14.6 nTPM
Adipose tissue	14.1 nTPM
Kidney	13.7 nTPM
Breast	13.0 nTPM
Spleen	10.4 nTPM
Prostate	10.3 nTPM
Endometrium	10.3 nTPM
Ovary	8.3 nTPM
Lung	6.7 nTPM
Stomach	5.9 nTPM
Pancreas	5.1 nTPM
PBMC	0.0 nTPM

Paneth cells	17.3 nTPM
Small intestine	26.3 nTPM
Colon	19.7 nTPM
Rectum	5.8 nTPM

Plasma cells	12.5 nTPM
Stomach	19.9 nTPM
Spleen	13.6 nTPM
Esophagus	12.3 nTPM
Bone marrow	11.5 nTPM
Adipose tissue	5.2 nTPM

Respiratory ciliated cells	29.2 nTPM
Bronchus	35.0 nTPM
Lung	23.3 nTPM

Smooth muscle cells	11.9 nTPM
Esophagus	20.1 nTPM
Prostate	17.8 nTPM
Ovary	14.6 nTPM
Breast	13.3 nTPM
Bronchus	12.2 nTPM
Pancreas	11.1 nTPM
Endometrium	10.1 nTPM
Adipose tissue	9.9 nTPM
Heart muscle	9.0 nTPM
Skin	6.6 nTPM
Skeletal muscle	6.5 nTPM

T-cells	2.8 nTPM
Liver	7.9 nTPM
Endometrium	6.4 nTPM
Lung	4.5 nTPM
Ovary	4.5 nTPM
PBMC	3.5 nTPM
Colon	2.9 nTPM
Skeletal muscle	2.5 nTPM
Lymph node	2.2 nTPM
Adipose tissue	2.1 nTPM
Kidney	2.0 nTPM
Breast	2.0 nTPM
Bone marrow	1.9 nTPM
Spleen	1.8 nTPM
Skin	1.4 nTPM
Stomach	1.3 nTPM
Prostate	0.0 nTPM
Esophagus	0.0 nTPM

Basal keratinocytes	3.1 nTPM
Skin	3.1 nTPM

Basal prostatic cells	12.6 nTPM
Prostate	12.6 nTPM

Basal respiratory cells	14.0 nTPM
Bronchus	14.0 nTPM

Basal squamous epithelial cells	14.2 nTPM
Esophagus	14.2 nTPM

Undifferentiated cells	1.2 nTPM
Rectum	1.8 nTPM
Colon	1.0 nTPM
Small intestine	0.9 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