Single cell type - SERTAD3 - The Human Protein Atlas

SERTAD3

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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.	SERTAD3
Gene descriptionⁱ Full gene name according to HGNC.	SERTA domain containing 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.	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.	Non-specific - 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.	Cell type enhanced (Syncytiotrophoblasts)
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 (Vascular associated smooth muscle cell)
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 (Syncytiotrophoblasts)

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 (Vascular associated smooth muscle cell)

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

SERTAD3 is part of cluster 80 Non-specific - Transcription with confidenceⁱ 1
184 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.
RGL2	Ral guanine nucleotide dissociation stimulator like 2	0.5743	17
CRABP2	Cellular retinoic acid binding protein 2	0.5693	50
SDF2	Stromal cell derived factor 2	0.5163	27
ID3	Inhibitor of DNA binding 3	0.5094	41
DVL2	Dishevelled segment polarity protein 2	0.4920	6
FBXL12	F-box and leucine rich repeat protein 12	0.4880	50
NAB2	NGFI-A binding protein 2	0.4830	80
MYLIP	Myosin regulatory light chain interacting protein	0.4759	80
PPIC	Peptidylprolyl isomerase C	0.4757	50
SERTAD1	SERTA domain containing 1	0.4604	80
PGBD2	PiggyBac transposable element derived 2	0.4597	27
HILPDA	Hypoxia inducible lipid droplet associated	0.4596	35
EIF4A2	Eukaryotic translation initiation factor 4A2	0.4585	6
NXF1	Nuclear RNA export factor 1	0.4566	80
TMEM59	Transmembrane protein 59	0.4472	35

IMMUNE CELLS

SERTAD3 is part of cluster 38 Monocytes & Neutrophils - Degranulation with confidenceⁱ 0.97
501 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.
GRN	Granulin precursor	1.0000	38
CNPY3	Canopy FGF signaling regulator 3	1.0000	38
CORO1C	Coronin 1C	0.9762	38
ENSG00000279073	Novel protein	0.9762	38
GPR162	G protein-coupled receptor 162	0.9762	38
ANKRD50	Ankyrin repeat domain containing 50	0.9762	38
SPOPL	Speckle type BTB/POZ protein like	0.9762	38
AKIRIN2	Akirin 2	0.9762	38
RNF130	Ring finger protein 130	0.9762	38
TRPM4	Transient receptor potential cation channel subfamily M member 4	0.9524	38
FURIN	Furin, paired basic amino acid cleaving enzyme	0.9524	38
UBR4	Ubiquitin protein ligase E3 component n-recognin 4	0.9524	38
OSBPL11	Oxysterol binding protein like 11	0.9524	38
TRIM6	Tripartite motif containing 6	0.9524	38
RNASEK-C17orf49	RNASEK-C17orf49 readthrough	0.9524	38

Adipocytes	78.7 nTPM
Adipose tissue	87.6 nTPM
Breast	69.8 nTPM

Alveolar cells type 1	15.0 nTPM
Lung	15.0 nTPM

Alveolar cells type 2	16.8 nTPM
Lung	16.8 nTPM

Astrocytes	2.8 nTPM
Brain	2.8 nTPM

B-cells	43.3 nTPM
Lymph node	133.0 nTPM
Esophagus	106.2 nTPM
Skin	66.1 nTPM
Kidney	41.6 nTPM
Adipose tissue	41.2 nTPM
Spleen	39.2 nTPM
Lung	37.6 nTPM
Stomach	26.6 nTPM
Liver	19.3 nTPM
Thymus	14.9 nTPM
Bone marrow	14.8 nTPM
Salivary gland	11.1 nTPM
PBMC	10.8 nTPM

Ciliated cells	29.9 nTPM
Bronchus	41.7 nTPM
Endometrium	28.3 nTPM
Lung	26.2 nTPM
Fallopian tube	23.5 nTPM

Club cells	50.4 nTPM
Bronchus	73.1 nTPM
Prostate	43.6 nTPM
Lung	34.4 nTPM

Dendritic cells	24.2 nTPM
Adipose tissue	26.8 nTPM
PBMC	21.6 nTPM

Endothelial cells	40.0 nTPM
Esophagus	89.6 nTPM
Skin	76.2 nTPM
Skeletal muscle	62.4 nTPM
Prostate	47.7 nTPM
Tongue	45.2 nTPM
Ovary	40.7 nTPM
Placenta	40.3 nTPM
Endometrium	40.0 nTPM
Breast	36.0 nTPM
Fallopian tube	35.3 nTPM
Salivary gland	34.9 nTPM
Pancreas	31.0 nTPM
Thymus	30.7 nTPM
Lung	29.7 nTPM
Liver	27.7 nTPM
Testis	22.0 nTPM
Vascular	15.2 nTPM
Heart muscle	14.7 nTPM

Enteroendocrine cells	41.5 nTPM
Colon	58.5 nTPM
Rectum	38.6 nTPM
Small intestine	27.5 nTPM

Fibroblasts	35.6 nTPM
Skin	67.1 nTPM
Placenta	64.5 nTPM
Fallopian tube	53.2 nTPM
Breast	49.1 nTPM
Esophagus	46.1 nTPM
Lung	42.6 nTPM
Liver	35.6 nTPM
Prostate	34.3 nTPM
Adipose tissue	30.8 nTPM
Skeletal muscle	29.6 nTPM
Pancreas	29.4 nTPM
Thymus	27.2 nTPM
Stomach	18.7 nTPM
Salivary gland	17.5 nTPM
Heart muscle	13.5 nTPM
Vascular	9.7 nTPM

Granulocytes	26.3 nTPM
Fallopian tube	33.6 nTPM
Tongue	24.3 nTPM
Lung	21.2 nTPM

Intestinal goblet cells	60.7 nTPM
Colon	90.1 nTPM
Rectum	47.0 nTPM
Small intestine	44.9 nTPM

Lymphatic endothelial cells	28.0 nTPM
Fallopian tube	39.5 nTPM
Ovary	16.4 nTPM

Macrophages	31.6 nTPM
Skin	61.3 nTPM
Lung	58.6 nTPM
Breast	57.2 nTPM
Adipose tissue	52.9 nTPM
Esophagus	51.4 nTPM
Kidney	46.0 nTPM
Pancreas	41.1 nTPM
Skeletal muscle	31.7 nTPM
Bone marrow	29.4 nTPM
Prostate	23.8 nTPM
Tongue	21.5 nTPM
Spleen	21.1 nTPM
Endometrium	20.9 nTPM
Fallopian tube	19.6 nTPM
Stomach	18.0 nTPM
Testis	16.1 nTPM
Thymus	12.2 nTPM
Salivary gland	9.9 nTPM
Vascular	7.3 nTPM

Basal prostatic cells	50.7 nTPM
Prostate	50.7 nTPM

Basal respiratory cells	133.6 nTPM
Bronchus	133.6 nTPM

Basal squamous epithelial cells	68.5 nTPM
Esophagus	68.5 nTPM

Bipolar cells	5.1 nTPM
Eye	5.1 nTPM

Paneth cells	58.4 nTPM
Small intestine	82.9 nTPM
Rectum	52.5 nTPM
Colon	39.8 nTPM

Plasma cells	11.8 nTPM
Fallopian tube	21.2 nTPM
Esophagus	20.8 nTPM
Liver	13.0 nTPM
Bone marrow	10.6 nTPM
Spleen	9.4 nTPM
Stomach	8.4 nTPM
Salivary gland	6.3 nTPM
Thymus	4.4 nTPM

Schwann cells	52.7 nTPM
Adipose tissue	137.8 nTPM
Esophagus	12.0 nTPM
Vascular	8.4 nTPM

Serous glandular cells	20.6 nTPM
Tongue	30.9 nTPM
Salivary gland	10.3 nTPM

Smooth muscle cells	56.1 nTPM
Lung	92.9 nTPM
Esophagus	85.3 nTPM
Breast	82.3 nTPM
Fallopian tube	82.1 nTPM
Placenta	76.5 nTPM
Adipose tissue	74.4 nTPM
Skin	70.5 nTPM
Skeletal muscle	67.9 nTPM
Ovary	59.5 nTPM
Thymus	36.9 nTPM
Prostate	36.5 nTPM
Endometrium	34.8 nTPM
Liver	31.0 nTPM
Tongue	30.5 nTPM
Salivary gland	24.9 nTPM
Vascular	11.9 nTPM

Suprabasal keratinocytes	32.3 nTPM
Skin	38.0 nTPM
Tongue	26.5 nTPM

T-cells	27.7 nTPM
Esophagus	80.3 nTPM
Skin	64.5 nTPM
Adipose tissue	59.5 nTPM
Lymph node	59.3 nTPM
Breast	45.8 nTPM
Skeletal muscle	31.8 nTPM
Endometrium	29.2 nTPM
Lung	24.2 nTPM
Prostate	23.8 nTPM
Colon	22.4 nTPM
Liver	21.3 nTPM
Tongue	20.3 nTPM
Kidney	18.6 nTPM
Spleen	17.5 nTPM
Fallopian tube	11.2 nTPM
Stomach	10.7 nTPM
Bone marrow	9.6 nTPM
Salivary gland	8.9 nTPM
Vascular	8.0 nTPM
PBMC	7.4 nTPM
Thymus	7.0 nTPM

Undifferentiated cells	30.0 nTPM
Colon	34.6 nTPM
Small intestine	28.6 nTPM
Rectum	26.8 nTPM

Amygdala excitatory	0.6 nTPM
Thalamus	0.9 nTPM
Cerebral cortex	0.6 nTPM
Amygdala	0.5 nTPM
Hippocampus	0.5 nTPM
Hypothalamus	0.5 nTPM
Basal ganglia	0.4 nTPM

Astrocyte	3.1 nTPM
Spinal cord	5.4 nTPM
Hippocampus	3.8 nTPM
Cerebral cortex	3.5 nTPM
Pons	3.2 nTPM
Basal ganglia	3.0 nTPM
Medulla oblongata	3.0 nTPM
Cerebellum	2.9 nTPM
Midbrain	2.7 nTPM
Thalamus	2.4 nTPM
Amygdala	2.2 nTPM
Hypothalamus	2.1 nTPM

Bergmann glia	5.5 nTPM
Medulla oblongata	6.4 nTPM
Pons	5.8 nTPM
Cerebellum	4.5 nTPM

Central nervous system macrophage	9.4 nTPM
Medulla oblongata	12.0 nTPM
Cerebral cortex	11.8 nTPM
Basal ganglia	11.6 nTPM
Hippocampus	10.8 nTPM
Spinal cord	9.7 nTPM
Pons	9.4 nTPM
Cerebellum	9.3 nTPM
Thalamus	9.0 nTPM
Midbrain	8.7 nTPM
Hypothalamus	6.4 nTPM
Amygdala	4.9 nTPM

Cerebellar inhibitory	0.8 nTPM
Midbrain	1.9 nTPM
Pons	1.1 nTPM
Cerebellum	0.7 nTPM
Medulla oblongata	0.2 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.8 nTPM
Midbrain	1.0 nTPM
Thalamus	1.0 nTPM
Basal ganglia	0.9 nTPM
Hippocampus	0.8 nTPM
Cerebral cortex	0.7 nTPM
Amygdala	0.6 nTPM
Hypothalamus	0.5 nTPM

Choroid plexus epithelial cell	2.8 nTPM
Thalamus	5.5 nTPM
Medulla oblongata	3.7 nTPM
Basal ganglia	2.2 nTPM
Hippocampus	0.0 nTPM

Committed oligodendrocyte precursor	4.2 nTPM
Spinal cord	11.0 nTPM
Cerebellum	7.9 nTPM
Cerebral cortex	5.1 nTPM
Hippocampus	4.7 nTPM
Pons	3.5 nTPM
Midbrain	3.4 nTPM
Thalamus	2.7 nTPM
Medulla oblongata	2.6 nTPM
Basal ganglia	2.2 nTPM
Hypothalamus	2.0 nTPM
Amygdala	1.1 nTPM

Deep-layer corticothalamic and 6b	0.5 nTPM
Amygdala	0.7 nTPM
Basal ganglia	0.6 nTPM
Cerebral cortex	0.6 nTPM
Hippocampus	0.6 nTPM
Hypothalamus	0.4 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.6 nTPM
Basal ganglia	0.8 nTPM
Hippocampus	0.7 nTPM
Amygdala	0.5 nTPM
Cerebral cortex	0.5 nTPM
Hypothalamus	0.5 nTPM

Deep-layer near-projecting	0.8 nTPM
Hippocampus	1.6 nTPM
Basal ganglia	0.8 nTPM
Cerebral cortex	0.6 nTPM
Amygdala	0.5 nTPM
Hypothalamus	0.2 nTPM

Eccentric medium spiny neuron	0.9 nTPM
Hippocampus	2.1 nTPM
Basal ganglia	0.8 nTPM
Thalamus	0.8 nTPM
Cerebral cortex	0.7 nTPM
Amygdala	0.6 nTPM
Hypothalamus	0.5 nTPM