Single cell type - STN1 - The Human Protein Atlas

STN1

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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.	STN1
Gene descriptionⁱ Full gene name according to HGNC.	STN1 subunit of CST complex
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes
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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	16

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.	Late spermatids - Unknown function (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.	Cell type enhanced (Late spermatids)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.40
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Cell type enhanced (Leukocyte)
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.	Low immune cell specificity
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized 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 RNA single cell type specificity: Cell type enhanced (Late spermatids)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Cell type enhanced (Leukocyte)

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Low immune cell specificity
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

STN1 is part of cluster 11 Late spermatids - Unknown function with confidenceⁱ 1
430 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
GDPD3	Glycerophosphodiester phosphodiesterase domain containing 3	0.5847	63
IL36B	Interleukin 36 beta	0.5254	11
MAL2	Mal, T cell differentiation protein 2	0.5176	59
KLK13	Kallikrein related peptidase 13	0.4917	59
NIBAN2	Niban apoptosis regulator 2	0.4904	59
EEF2KMT	Eukaryotic elongation factor 2 lysine methyltransferase	0.4862	11
SCEL	Sciellin	0.4778	59
EIF5A2	Eukaryotic translation initiation factor 5A2	0.4758	11
ARPC5L	Actin related protein 2/3 complex subunit 5 like	0.4731	11
HOPX	HOP homeobox	0.4529	59
SCLY	Selenocysteine lyase	0.4518	11
KLK11	Kallikrein related peptidase 11	0.4481	59
LCE3D	Late cornified envelope 3D	0.4447	59
ORMDL2	ORMDL sphingolipid biosynthesis regulator 2	0.4430	45
GIPC1	GIPC PDZ domain containing family member 1	0.4414	5

IMMUNE CELLS

STN1 is part of cluster 3 Non-specific - Nuclear processes with confidenceⁱ 0.93
471 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
TKTL1	Transketolase like 1	0.9762	3
ITGA6	Integrin subunit alpha 6	0.9762	3
ZDHHC6	Zinc finger DHHC-type palmitoyltransferase 6	0.9524	36
ACP6	Acid phosphatase 6, lysophosphatidic	0.9524	3
PEX14	Peroxisomal biogenesis factor 14	0.9524	3
TRMO	TRNA methyltransferase O	0.9524	3
ANTKMT	Adenine nucleotide translocase lysine methyltransferase	0.9286	45
HMOX2	Heme oxygenase 2	0.9286	36
NCBP2AS2	NCBP2 antisense 2 (head to head)	0.9048	3
ANKZF1	Ankyrin repeat and zinc finger peptidyl tRNA hydrolase 1	0.9048	36
PITPNC1	Phosphatidylinositol transfer protein cytoplasmic 1	0.9048	3
BBS7	Bardet-Biedl syndrome 7	0.9048	3
C9orf78	Chromosome 9 open reading frame 78	0.9048	36
DGCR6L	DiGeorge syndrome critical region gene 6 like	0.9048	3
CDC37L1	Cell division cycle 37 like 1, HSP90 cochaperone	0.9048	3

Adipocytes	17.3 nTPM
Breast	20.9 nTPM
Adipose tissue	13.6 nTPM

Alveolar cells type 1	64.5 nTPM
Lung	64.5 nTPM

Alveolar cells type 2	44.1 nTPM
Lung	44.1 nTPM

Astrocytes	10.8 nTPM
Brain	10.8 nTPM

B-cells	12.3 nTPM
Lung	24.1 nTPM
PBMC	20.0 nTPM
Kidney	15.6 nTPM
Thymus	14.0 nTPM
Salivary gland	13.7 nTPM
Skin	13.6 nTPM
Spleen	13.4 nTPM
Bone marrow	11.1 nTPM
Lymph node	10.2 nTPM
Stomach	8.4 nTPM
Esophagus	5.9 nTPM
Adipose tissue	5.3 nTPM
Liver	4.8 nTPM

Ciliated cells	20.5 nTPM
Bronchus	32.2 nTPM
Lung	24.2 nTPM
Fallopian tube	13.8 nTPM
Endometrium	11.8 nTPM

Club cells	41.1 nTPM
Bronchus	51.4 nTPM
Prostate	43.2 nTPM
Lung	28.5 nTPM

Endothelial cells	20.1 nTPM
Tongue	33.6 nTPM
Lung	31.1 nTPM
Heart muscle	28.2 nTPM
Testis	26.6 nTPM
Placenta	24.4 nTPM
Skin	24.1 nTPM
Salivary gland	21.0 nTPM
Pancreas	20.7 nTPM
Vascular	20.7 nTPM
Breast	20.2 nTPM
Thymus	17.2 nTPM
Esophagus	15.1 nTPM
Skeletal muscle	14.9 nTPM
Ovary	14.8 nTPM
Prostate	14.4 nTPM
Fallopian tube	13.4 nTPM
Endometrium	12.2 nTPM
Liver	8.8 nTPM

Enteroendocrine cells	17.4 nTPM
Colon	31.9 nTPM
Small intestine	10.3 nTPM
Rectum	10.1 nTPM

Fibroblasts	12.3 nTPM
Placenta	23.2 nTPM
Lung	20.4 nTPM
Pancreas	19.1 nTPM
Esophagus	18.6 nTPM
Breast	13.4 nTPM
Heart muscle	12.8 nTPM
Skin	11.9 nTPM
Prostate	11.9 nTPM
Salivary gland	11.5 nTPM
Vascular	10.4 nTPM
Fallopian tube	9.7 nTPM
Adipose tissue	9.6 nTPM
Thymus	9.6 nTPM
Skeletal muscle	9.2 nTPM
Liver	4.7 nTPM
Stomach	1.4 nTPM

Granulocytes	26.4 nTPM
Tongue	38.8 nTPM
Lung	28.2 nTPM
Fallopian tube	12.3 nTPM

Intestinal goblet cells	24.1 nTPM
Colon	25.1 nTPM
Small intestine	24.4 nTPM
Rectum	22.7 nTPM

Lymphatic endothelial cells	12.8 nTPM
Fallopian tube	20.2 nTPM
Ovary	5.5 nTPM

Macrophages	14.0 nTPM
Testis	29.8 nTPM
Kidney	23.0 nTPM
Tongue	22.9 nTPM
Pancreas	18.5 nTPM
Prostate	17.8 nTPM
Skeletal muscle	14.8 nTPM
Breast	14.0 nTPM
Stomach	12.9 nTPM
Salivary gland	12.8 nTPM
Thymus	12.2 nTPM
Adipose tissue	11.7 nTPM
Lung	11.1 nTPM
Bone marrow	10.1 nTPM
Fallopian tube	10.1 nTPM
Skin	10.0 nTPM
Spleen	10.0 nTPM
Vascular	9.3 nTPM
Endometrium	8.0 nTPM
Esophagus	6.4 nTPM

Paneth cells	28.3 nTPM
Colon	57.9 nTPM
Rectum	23.6 nTPM
Small intestine	3.5 nTPM

Basal prostatic cells	13.9 nTPM
Prostate	13.9 nTPM

Bipolar cells	4.2 nTPM
Eye	4.2 nTPM

Cholangiocytes	24.8 nTPM
Liver	24.8 nTPM

Collecting duct cells	19.4 nTPM
Kidney	19.4 nTPM

Plasma cells	14.9 nTPM
Liver	19.5 nTPM
Salivary gland	17.9 nTPM
Fallopian tube	15.4 nTPM
Thymus	15.1 nTPM
Stomach	14.7 nTPM
Spleen	14.2 nTPM
Bone marrow	12.1 nTPM
Esophagus	10.4 nTPM

Schwann cells	7.7 nTPM
Adipose tissue	14.8 nTPM
Vascular	8.4 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	15.8 nTPM
Tongue	17.7 nTPM
Salivary gland	14.0 nTPM

Smooth muscle cells	12.5 nTPM
Liver	24.6 nTPM
Placenta	20.2 nTPM
Skin	15.4 nTPM
Vascular	15.3 nTPM
Breast	15.0 nTPM
Ovary	13.0 nTPM
Tongue	12.6 nTPM
Prostate	12.2 nTPM
Skeletal muscle	11.4 nTPM
Lung	10.6 nTPM
Fallopian tube	10.3 nTPM
Salivary gland	9.1 nTPM
Thymus	8.7 nTPM
Endometrium	8.6 nTPM
Adipose tissue	8.5 nTPM
Esophagus	4.8 nTPM

Suprabasal keratinocytes	72.2 nTPM
Tongue	134.4 nTPM
Skin	10.0 nTPM

T-cells	42.2 nTPM
Lung	68.7 nTPM
Liver	61.7 nTPM
Prostate	59.6 nTPM
Stomach	55.6 nTPM
Colon	54.6 nTPM
Breast	53.9 nTPM
Skin	49.4 nTPM
Kidney	47.0 nTPM
PBMC	43.5 nTPM
Esophagus	41.4 nTPM
Skeletal muscle	40.1 nTPM
Fallopian tube	38.6 nTPM
Spleen	38.0 nTPM
Vascular	37.4 nTPM
Bone marrow	35.8 nTPM
Tongue	31.9 nTPM
Thymus	31.1 nTPM
Endometrium	28.0 nTPM
Salivary gland	27.4 nTPM
Adipose tissue	21.7 nTPM
Lymph node	21.6 nTPM

Undifferentiated cells	15.6 nTPM
Colon	23.8 nTPM
Rectum	13.9 nTPM
Small intestine	9.2 nTPM

Amygdala excitatory	8.0 nTPM
Hypothalamus	9.9 nTPM
Basal ganglia	9.2 nTPM
Cerebral cortex	8.2 nTPM
Amygdala	7.8 nTPM
Hippocampus	7.6 nTPM
Thalamus	5.4 nTPM

Astrocyte	17.2 nTPM
Amygdala	19.6 nTPM
Hippocampus	18.6 nTPM
Cerebral cortex	18.5 nTPM
Hypothalamus	18.0 nTPM
Cerebellum	17.9 nTPM
Spinal cord	17.9 nTPM
Midbrain	16.9 nTPM
Thalamus	16.1 nTPM
Pons	16.0 nTPM
Basal ganglia	15.5 nTPM
Medulla oblongata	14.0 nTPM

Bergmann glia	19.9 nTPM
Medulla oblongata	29.8 nTPM
Cerebellum	16.9 nTPM
Pons	12.9 nTPM

Central nervous system macrophage	22.9 nTPM
Amygdala	27.8 nTPM
Hippocampus	25.9 nTPM
Basal ganglia	25.0 nTPM
Medulla oblongata	25.0 nTPM
Midbrain	24.1 nTPM
Hypothalamus	23.6 nTPM
Cerebellum	22.0 nTPM
Thalamus	21.9 nTPM
Cerebral cortex	19.7 nTPM
Pons	19.1 nTPM
Spinal cord	18.5 nTPM

Cerebellar inhibitory	8.2 nTPM
Midbrain	10.6 nTPM
Medulla oblongata	10.3 nTPM
Pons	7.4 nTPM
Cerebellum	7.0 nTPM
Spinal cord	5.5 nTPM

Cge interneuron	5.9 nTPM
Hippocampus	7.3 nTPM
Amygdala	6.6 nTPM
Cerebral cortex	6.0 nTPM
Hypothalamus	6.0 nTPM
Basal ganglia	5.7 nTPM
Thalamus	5.1 nTPM
Midbrain	4.9 nTPM

Choroid plexus epithelial cell	25.3 nTPM
Basal ganglia	38.6 nTPM
Hippocampus	27.7 nTPM
Medulla oblongata	24.0 nTPM
Thalamus	11.0 nTPM

Committed oligodendrocyte precursor	14.7 nTPM
Amygdala	20.9 nTPM
Cerebellum	19.0 nTPM
Hypothalamus	17.8 nTPM
Thalamus	17.8 nTPM
Medulla oblongata	16.8 nTPM
Spinal cord	14.7 nTPM
Basal ganglia	14.2 nTPM
Hippocampus	13.5 nTPM
Pons	10.6 nTPM
Midbrain	9.2 nTPM
Cerebral cortex	7.6 nTPM

Deep-layer corticothalamic and 6b	7.4 nTPM
Hypothalamus	9.1 nTPM
Basal ganglia	8.0 nTPM
Cerebral cortex	7.7 nTPM
Amygdala	7.5 nTPM
Hippocampus	7.4 nTPM
Midbrain	4.4 nTPM

Deep-layer intratelencephalic	9.1 nTPM
Hypothalamus	10.1 nTPM
Amygdala	10.0 nTPM
Basal ganglia	8.9 nTPM
Cerebral cortex	8.5 nTPM
Hippocampus	7.9 nTPM

Deep-layer near-projecting	9.3 nTPM
Hypothalamus	11.6 nTPM
Basal ganglia	9.9 nTPM
Cerebral cortex	9.7 nTPM
Amygdala	8.0 nTPM
Hippocampus	7.5 nTPM

Eccentric medium spiny neuron	12.6 nTPM
Hypothalamus	16.0 nTPM
Basal ganglia	14.7 nTPM
Thalamus	12.9 nTPM
Cerebral cortex	12.6 nTPM
Amygdala	10.1 nTPM
Hippocampus	9.1 nTPM

Endothelial cell	47.4 nTPM
Cerebellum	62.7 nTPM
Hippocampus	57.7 nTPM
Cerebral cortex	53.7 nTPM
Spinal cord	53.5 nTPM
Amygdala	50.3 nTPM
Midbrain	47.3 nTPM
Medulla oblongata	41.0 nTPM
Thalamus	40.1 nTPM
Hypothalamus	39.7 nTPM
Pons	38.7 nTPM
Basal ganglia	36.4 nTPM