Single cell type - SMG1 - The Human Protein Atlas

SMG1

Search result

Field

Term

Cluster

Pathway

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.	SMG1
Gene descriptionⁱ Full gene name according to HGNC.	SMG1 nonsense mediated mRNA decay associated PI3K related kinase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	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.	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.	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 (Skeletal myocytes)
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.	0.34
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.	Low cell type specificity
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.	Immune cell enhanced (basophil)
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 (Skeletal myocytes)

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: Low cell type specificity

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: Immune cell enhanced (basophil)
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

SMG1 is part of cluster 55 Non-specific - Transcription with confidenceⁱ 0.98
709 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.
NUP153	Nucleoporin 153	0.6066	37
SERTAD2	SERTA domain containing 2	0.5742	12
IRF2BP2	Interferon regulatory factor 2 binding protein 2	0.5727	28
FHIP1A	FHF complex subunit HOOK interacting protein 1A	0.5709	28
MED13	Mediator complex subunit 13	0.5593	55
UBXN7	UBX domain protein 7	0.5557	55
RCOR1	REST corepressor 1	0.5523	29
ZBTB11	Zinc finger and BTB domain containing 11	0.5451	37
FEM1A	Fem-1 homolog A	0.5423	2
SLC38A2	Solute carrier family 38 member 2	0.5376	12
SPEN	Spen family transcriptional repressor	0.5362	37
SIK1	Salt inducible kinase 1	0.5311	12
TENT4A	Terminal nucleotidyltransferase 4A	0.5191	28
PPTC7	Protein phosphatase targeting COQ7	0.5142	29
TP63	Tumor protein p63	0.5118	12

IMMUNE CELLS

SMG1 is part of cluster 22 Eosinophils - Transcription with confidenceⁱ 1
357 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.
CBFA2T2	CBFA2/RUNX1 partner transcriptional co-repressor 2	0.9762	22
ABHD18	Abhydrolase domain containing 18	0.9762	22
MT-ND2	Mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 2	0.9524	22
RNPC3	RNA binding region (RNP1, RRM) containing 3	0.9524	21
CHD7	Chromodomain helicase DNA binding protein 7	0.9524	22
ZNF439	Zinc finger protein 439	0.9524	22
HIRA	Histone cell cycle regulator	0.9524	22
CNTRL	Centriolin	0.9286	22
SECISBP2	SECIS binding protein 2	0.9286	21
CNTN1	Contactin 1	0.9286	22
PNISR	PNN interacting serine and arginine rich protein	0.9048	20
PCBD2	Pterin-4 alpha-carbinolamine dehydratase 2	0.9048	22
TUT4	Terminal uridylyl transferase 4	0.9048	22
DEPDC5	DEP domain containing 5, GATOR1 subcomplex subunit	0.9048	22
ZNF154	Zinc finger protein 154	0.9048	21

Adipocytes	55.3 nTPM
Adipose tissue	64.1 nTPM
Breast	46.5 nTPM

Alveolar cells type 1	48.0 nTPM
Lung	48.0 nTPM

Alveolar cells type 2	51.1 nTPM
Lung	51.1 nTPM

Astrocytes	55.4 nTPM
Brain	55.4 nTPM

B-cells	81.4 nTPM
Adipose tissue	157.6 nTPM
Spleen	102.4 nTPM
Salivary gland	97.6 nTPM
Stomach	96.2 nTPM
Lymph node	92.0 nTPM
Thymus	88.2 nTPM
Bone marrow	83.5 nTPM
Skin	76.2 nTPM
Liver	72.5 nTPM
Esophagus	59.0 nTPM
Lung	52.3 nTPM
Kidney	41.6 nTPM
PBMC	38.5 nTPM

Basal squamous epithelial cells	100.4 nTPM
Esophagus	100.4 nTPM

Ciliated cells	41.0 nTPM
Endometrium	62.6 nTPM
Bronchus	39.6 nTPM
Lung	36.1 nTPM
Fallopian tube	25.7 nTPM

Club cells	44.8 nTPM
Prostate	56.5 nTPM
Lung	43.6 nTPM
Bronchus	34.2 nTPM

Dendritic cells	131.3 nTPM
Adipose tissue	223.1 nTPM
PBMC	39.6 nTPM

Endothelial cells	48.7 nTPM
Salivary gland	77.3 nTPM
Endometrium	75.2 nTPM
Skin	67.8 nTPM
Heart muscle	66.8 nTPM
Skeletal muscle	64.8 nTPM
Vascular	61.9 nTPM
Esophagus	53.8 nTPM
Tongue	53.5 nTPM
Prostate	51.3 nTPM
Thymus	51.0 nTPM
Lung	41.1 nTPM
Testis	36.6 nTPM
Breast	35.2 nTPM
Fallopian tube	34.1 nTPM
Liver	32.8 nTPM
Ovary	31.7 nTPM
Pancreas	25.9 nTPM
Placenta	15.9 nTPM

Enteroendocrine cells	30.7 nTPM
Colon	37.7 nTPM
Small intestine	30.9 nTPM
Rectum	23.5 nTPM

Fibroblasts	39.3 nTPM
Skin	74.4 nTPM
Skeletal muscle	66.2 nTPM
Salivary gland	52.0 nTPM
Heart muscle	44.8 nTPM
Vascular	43.3 nTPM
Thymus	39.1 nTPM
Prostate	38.3 nTPM
Liver	36.8 nTPM
Adipose tissue	36.8 nTPM
Stomach	36.0 nTPM
Esophagus	35.5 nTPM
Fallopian tube	32.2 nTPM
Breast	31.3 nTPM
Lung	26.3 nTPM
Placenta	19.1 nTPM
Pancreas	16.5 nTPM

Granulocytes	41.2 nTPM
Tongue	67.9 nTPM
Fallopian tube	29.0 nTPM
Lung	26.7 nTPM

Intestinal goblet cells	41.0 nTPM
Small intestine	50.8 nTPM
Rectum	43.2 nTPM
Colon	29.0 nTPM

Lymphatic endothelial cells	27.2 nTPM
Ovary	27.3 nTPM
Fallopian tube	27.1 nTPM

Cholangiocytes	22.9 nTPM
Liver	22.9 nTPM

Cone photoreceptor cells	45.9 nTPM
Eye	45.9 nTPM

Cytotrophoblasts	19.0 nTPM
Placenta	19.0 nTPM

Distal tubular cells	3.1 nTPM
Kidney	3.1 nTPM

Macrophages	70.6 nTPM
Adipose tissue	157.2 nTPM
Skeletal muscle	110.4 nTPM
Tongue	99.4 nTPM
Endometrium	94.1 nTPM
Salivary gland	93.8 nTPM
Spleen	85.2 nTPM
Fallopian tube	74.0 nTPM
Skin	72.4 nTPM
Vascular	62.6 nTPM
Bone marrow	61.8 nTPM
Prostate	60.1 nTPM
Thymus	60.1 nTPM
Stomach	56.6 nTPM
Breast	53.0 nTPM
Esophagus	52.7 nTPM
Lung	52.0 nTPM
Kidney	42.5 nTPM
Testis	33.5 nTPM
Pancreas	20.6 nTPM

Paneth cells	64.0 nTPM
Small intestine	89.8 nTPM
Rectum	51.5 nTPM
Colon	50.7 nTPM

Plasma cells	41.3 nTPM
Salivary gland	58.2 nTPM
Bone marrow	49.8 nTPM
Stomach	49.8 nTPM
Thymus	46.3 nTPM
Spleen	37.3 nTPM
Fallopian tube	36.0 nTPM
Liver	27.0 nTPM
Esophagus	26.0 nTPM

Schwann cells	69.1 nTPM
Adipose tissue	109.3 nTPM
Vascular	50.1 nTPM
Esophagus	47.9 nTPM

Serous glandular cells	51.4 nTPM
Tongue	57.4 nTPM
Salivary gland	45.4 nTPM

Smooth muscle cells	43.4 nTPM
Skin	67.9 nTPM
Skeletal muscle	67.6 nTPM
Endometrium	62.9 nTPM
Salivary gland	58.1 nTPM
Adipose tissue	57.2 nTPM
Tongue	55.7 nTPM
Vascular	48.2 nTPM
Thymus	44.9 nTPM
Prostate	38.3 nTPM
Esophagus	37.2 nTPM
Breast	36.7 nTPM
Lung	32.9 nTPM
Liver	25.5 nTPM
Ovary	24.2 nTPM
Fallopian tube	22.4 nTPM
Placenta	15.5 nTPM

Suprabasal keratinocytes	129.1 nTPM
Skin	207.7 nTPM
Tongue	50.4 nTPM

T-cells	73.3 nTPM
Skeletal muscle	118.0 nTPM
Tongue	108.2 nTPM
Adipose tissue	105.4 nTPM
Endometrium	101.5 nTPM
Vascular	90.5 nTPM
Salivary gland	88.4 nTPM
Bone marrow	82.8 nTPM
Lymph node	81.2 nTPM
Spleen	76.2 nTPM
Thymus	71.9 nTPM
Breast	68.7 nTPM
Esophagus	68.1 nTPM
Stomach	66.5 nTPM
Skin	64.8 nTPM
Prostate	61.5 nTPM
PBMC	58.9 nTPM
Lung	56.5 nTPM
Colon	48.7 nTPM
Fallopian tube	48.1 nTPM
Liver	47.1 nTPM
Kidney	26.6 nTPM

Undifferentiated cells	30.8 nTPM
Rectum	34.2 nTPM
Small intestine	33.8 nTPM
Colon	24.4 nTPM

Amygdala excitatory	128.1 nTPM
Hypothalamus	138.3 nTPM
Amygdala	133.1 nTPM
Hippocampus	132.7 nTPM
Cerebral cortex	131.3 nTPM
Basal ganglia	124.2 nTPM
Thalamus	108.9 nTPM

Astrocyte	147.0 nTPM
Midbrain	170.5 nTPM
Amygdala	168.2 nTPM
Pons	166.2 nTPM
Thalamus	161.2 nTPM
Cerebellum	149.8 nTPM
Basal ganglia	145.8 nTPM
Cerebral cortex	137.2 nTPM
Hypothalamus	132.8 nTPM
Hippocampus	132.6 nTPM
Spinal cord	128.1 nTPM
Medulla oblongata	124.3 nTPM

Bergmann glia	97.0 nTPM
Cerebellum	114.3 nTPM
Medulla oblongata	91.6 nTPM
Pons	84.9 nTPM

Central nervous system macrophage	182.1 nTPM
Amygdala	238.0 nTPM
Hypothalamus	195.2 nTPM
Midbrain	183.8 nTPM
Basal ganglia	183.1 nTPM
Thalamus	180.3 nTPM
Cerebral cortex	176.7 nTPM
Hippocampus	175.8 nTPM
Cerebellum	174.3 nTPM
Pons	172.6 nTPM
Medulla oblongata	166.0 nTPM
Spinal cord	157.8 nTPM

Cerebellar inhibitory	89.0 nTPM
Spinal cord	107.2 nTPM
Pons	92.5 nTPM
Cerebellum	85.3 nTPM
Midbrain	84.3 nTPM
Medulla oblongata	75.5 nTPM

Cge interneuron	95.8 nTPM
Hypothalamus	110.5 nTPM
Amygdala	106.8 nTPM
Hippocampus	96.2 nTPM
Cerebral cortex	94.8 nTPM
Basal ganglia	94.0 nTPM
Thalamus	87.7 nTPM
Midbrain	80.9 nTPM

Choroid plexus epithelial cell	125.5 nTPM
Basal ganglia	163.3 nTPM
Medulla oblongata	137.8 nTPM
Thalamus	120.6 nTPM
Hippocampus	80.4 nTPM

Committed oligodendrocyte precursor	91.1 nTPM
Hypothalamus	105.8 nTPM
Thalamus	105.8 nTPM
Amygdala	102.6 nTPM
Basal ganglia	95.3 nTPM
Cerebral cortex	95.0 nTPM
Cerebellum	93.5 nTPM
Medulla oblongata	93.0 nTPM
Hippocampus	85.6 nTPM
Pons	81.5 nTPM
Midbrain	73.9 nTPM
Spinal cord	69.9 nTPM

Deep-layer corticothalamic and 6b	122.9 nTPM
Amygdala	138.8 nTPM
Hypothalamus	124.3 nTPM
Cerebral cortex	120.6 nTPM
Basal ganglia	119.9 nTPM
Hippocampus	118.1 nTPM
Midbrain	115.4 nTPM

Deep-layer intratelencephalic	127.1 nTPM
Amygdala	141.7 nTPM
Hypothalamus	129.9 nTPM
Hippocampus	127.0 nTPM
Basal ganglia	119.3 nTPM
Cerebral cortex	117.4 nTPM

Deep-layer near-projecting	92.7 nTPM
Amygdala	108.0 nTPM
Hypothalamus	94.8 nTPM
Cerebral cortex	94.6 nTPM
Basal ganglia	91.2 nTPM
Hippocampus	74.8 nTPM