Single cell type - SMC2 - The Human Protein Atlas

SMC2

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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.	SMC2
Gene descriptionⁱ Full gene name according to HGNC.	Structural maintenance of chromosomes 2
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 - Cell proliferation (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 (Extravillous trophoblasts)
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.	0.35
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.	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 (Extravillous trophoblasts)

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: 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

SMC2 is part of cluster 52 Non-specific - Cell proliferation with confidenceⁱ 1
248 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.
TPX2	TPX2 microtubule nucleation factor	0.8076	52
ARHGAP11A	Rho GTPase activating protein 11A	0.7879	52
MKI67	Marker of proliferation Ki-67	0.7814	52
ASPM	Assembly factor for spindle microtubules	0.7795	52
CENPA	Centromere protein A	0.7770	52
SKA3	Spindle and kinetochore associated complex subunit 3	0.7758	52
KIF11	Kinesin family member 11	0.7746	52
KIF4A	Kinesin family member 4A	0.7734	52
MCM10	Minichromosome maintenance 10 replication initiation factor	0.7697	52
CENPE	Centromere protein E	0.7631	52
PRR11	Proline rich 11	0.7623	52
ERCC6L	ERCC excision repair 6 like, spindle assembly checkpoint helicase	0.7616	52
KIF18B	Kinesin family member 18B	0.7605	52
KIFC1	Kinesin family member C1	0.7501	52
MELK	Maternal embryonic leucine zipper kinase	0.7497	52

IMMUNE CELLS

SMC2 is part of cluster 33 Non-specific - ATP binding with confidenceⁱ 0.99
757 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.
HSPH1	Heat shock protein family H (Hsp110) member 1	1.0000	33
AP4E1	Adaptor related protein complex 4 subunit epsilon 1	0.9762	33
DDHD1	DDHD domain containing 1	0.9762	14
DGKQ	Diacylglycerol kinase theta	0.9762	33
ZNF280C	Zinc finger protein 280C	0.9524	33
ENSG00000285253	Novel protein	0.9524	33
TCAF1	TRPM8 channel associated factor 1	0.9524	33
ZNF71	Zinc finger protein 71	0.9524	33
RGPD8	RANBP2 like and GRIP domain containing 8	0.9524	33
WDCP	WD repeat and coiled coil containing	0.9524	33
OXSM	3-oxoacyl-ACP synthase, mitochondrial	0.9524	33
NME7	NME/NM23 family member 7	0.9524	33
SMYD5	SMYD family member 5	0.9524	14
TESK1	Testis associated actin remodelling kinase 1	0.9524	14
LZTR1	Leucine zipper like transcription regulator 1	0.9524	33

Adipocytes	19.7 nTPM
Breast	19.8 nTPM
Adipose tissue	19.6 nTPM

Alveolar cells type 1	14.9 nTPM
Lung	14.9 nTPM

Alveolar cells type 2	33.0 nTPM
Lung	33.0 nTPM

Astrocytes	6.2 nTPM
Brain	6.2 nTPM

B-cells	17.3 nTPM
Lung	33.5 nTPM
Salivary gland	32.8 nTPM
Skin	32.2 nTPM
Thymus	18.9 nTPM
Esophagus	17.7 nTPM
Kidney	15.6 nTPM
PBMC	13.9 nTPM
Adipose tissue	13.2 nTPM
Spleen	11.8 nTPM
Lymph node	11.4 nTPM
Liver	9.7 nTPM
Bone marrow	7.2 nTPM
Stomach	7.2 nTPM

Ciliated cells	50.0 nTPM
Endometrium	123.4 nTPM
Fallopian tube	52.1 nTPM
Lung	13.6 nTPM
Bronchus	11.1 nTPM

Club cells	23.1 nTPM
Lung	33.0 nTPM
Bronchus	19.0 nTPM
Prostate	17.3 nTPM

Endothelial cells	20.9 nTPM
Endometrium	33.2 nTPM
Placenta	32.4 nTPM
Vascular	28.2 nTPM
Breast	28.1 nTPM
Salivary gland	25.8 nTPM
Testis	23.2 nTPM
Skeletal muscle	23.0 nTPM
Tongue	22.3 nTPM
Prostate	20.0 nTPM
Thymus	19.8 nTPM
Heart muscle	18.7 nTPM
Ovary	17.3 nTPM
Fallopian tube	17.0 nTPM
Liver	16.4 nTPM
Skin	15.4 nTPM
Lung	15.4 nTPM
Esophagus	13.0 nTPM
Pancreas	7.8 nTPM

Enteroendocrine cells	14.2 nTPM
Colon	18.8 nTPM
Rectum	13.4 nTPM
Small intestine	10.3 nTPM

Fibroblasts	21.0 nTPM
Pancreas	63.7 nTPM
Heart muscle	38.6 nTPM
Placenta	29.5 nTPM
Vascular	26.4 nTPM
Skeletal muscle	23.4 nTPM
Breast	20.4 nTPM
Salivary gland	19.4 nTPM
Prostate	17.8 nTPM
Adipose tissue	16.8 nTPM
Lung	14.9 nTPM
Thymus	14.7 nTPM
Skin	14.5 nTPM
Liver	11.9 nTPM
Fallopian tube	10.9 nTPM
Esophagus	9.4 nTPM
Stomach	4.3 nTPM

Granulocytes	22.9 nTPM
Lung	32.3 nTPM
Tongue	19.4 nTPM
Fallopian tube	16.9 nTPM

Intestinal goblet cells	15.3 nTPM
Colon	22.9 nTPM
Small intestine	15.3 nTPM
Rectum	7.6 nTPM

Lymphatic endothelial cells	29.9 nTPM
Ovary	32.7 nTPM
Fallopian tube	27.1 nTPM

Macrophages	22.8 nTPM
Tongue	46.6 nTPM
Testis	35.3 nTPM
Endometrium	30.7 nTPM
Pancreas	28.8 nTPM
Vascular	27.6 nTPM
Prostate	26.8 nTPM
Salivary gland	25.0 nTPM
Lung	24.1 nTPM
Bone marrow	22.3 nTPM
Skeletal muscle	22.2 nTPM
Breast	22.2 nTPM
Esophagus	20.6 nTPM
Adipose tissue	18.8 nTPM
Thymus	18.3 nTPM
Fallopian tube	17.4 nTPM
Spleen	15.0 nTPM
Kidney	13.3 nTPM
Stomach	10.3 nTPM
Skin	7.8 nTPM

Paneth cells	6.9 nTPM
Rectum	10.2 nTPM
Small intestine	6.9 nTPM
Colon	3.6 nTPM

Basal keratinocytes	36.3 nTPM
Tongue	47.4 nTPM
Skin	25.2 nTPM

Basal respiratory cells	26.3 nTPM
Bronchus	26.3 nTPM

Bipolar cells	31.9 nTPM
Eye	31.9 nTPM

Cytotrophoblasts	59.3 nTPM
Placenta	59.3 nTPM

Plasma cells	53.1 nTPM
Thymus	110.0 nTPM
Spleen	102.0 nTPM
Liver	80.6 nTPM
Bone marrow	72.5 nTPM
Salivary gland	27.3 nTPM
Stomach	11.3 nTPM
Fallopian tube	10.9 nTPM
Esophagus	10.4 nTPM

Schwann cells	19.9 nTPM
Vascular	30.8 nTPM
Adipose tissue	16.8 nTPM
Esophagus	12.0 nTPM

Serous glandular cells	12.8 nTPM
Tongue	13.3 nTPM
Salivary gland	12.3 nTPM

Smooth muscle cells	19.3 nTPM
Endometrium	41.5 nTPM
Placenta	29.5 nTPM
Skeletal muscle	26.2 nTPM
Vascular	21.3 nTPM
Adipose tissue	20.5 nTPM
Breast	20.4 nTPM
Ovary	19.6 nTPM
Liver	17.0 nTPM
Fallopian tube	16.8 nTPM
Lung	16.5 nTPM
Skin	15.4 nTPM
Tongue	15.3 nTPM
Esophagus	14.4 nTPM
Salivary gland	14.2 nTPM
Thymus	13.2 nTPM
Prostate	7.3 nTPM

Suprabasal keratinocytes	25.1 nTPM
Skin	26.6 nTPM
Tongue	23.7 nTPM

T-cells	19.8 nTPM
Liver	31.6 nTPM
Tongue	29.4 nTPM
Skeletal muscle	27.6 nTPM
Kidney	25.7 nTPM
Lung	25.2 nTPM
Endometrium	24.9 nTPM
Prostate	24.3 nTPM
Salivary gland	23.8 nTPM
Vascular	22.5 nTPM
Thymus	21.7 nTPM
Colon	18.5 nTPM
Bone marrow	17.6 nTPM
Breast	17.6 nTPM
PBMC	16.6 nTPM
Fallopian tube	15.3 nTPM
Skin	15.1 nTPM
Spleen	14.6 nTPM
Adipose tissue	12.2 nTPM
Lymph node	11.9 nTPM
Esophagus	9.7 nTPM
Stomach	9.1 nTPM

Undifferentiated cells	62.4 nTPM
Colon	90.3 nTPM
Small intestine	50.0 nTPM
Rectum	46.8 nTPM

Amygdala excitatory	8.4 nTPM
Thalamus	10.4 nTPM
Amygdala	8.6 nTPM
Basal ganglia	8.0 nTPM
Cerebral cortex	7.9 nTPM
Hippocampus	7.9 nTPM
Hypothalamus	7.8 nTPM

Astrocyte	9.5 nTPM
Thalamus	12.6 nTPM
Midbrain	10.3 nTPM
Amygdala	9.5 nTPM
Cerebral cortex	9.5 nTPM
Hypothalamus	9.4 nTPM
Medulla oblongata	9.4 nTPM
Pons	9.4 nTPM
Basal ganglia	9.1 nTPM
Spinal cord	9.0 nTPM
Cerebellum	8.4 nTPM
Hippocampus	8.3 nTPM

Bergmann glia	10.2 nTPM
Cerebellum	13.4 nTPM
Pons	8.6 nTPM
Medulla oblongata	8.5 nTPM

Central nervous system macrophage	27.0 nTPM
Amygdala	32.6 nTPM
Cerebral cortex	28.9 nTPM
Cerebellum	28.4 nTPM
Midbrain	27.9 nTPM
Hypothalamus	27.3 nTPM
Thalamus	26.5 nTPM
Hippocampus	26.2 nTPM
Basal ganglia	25.1 nTPM
Pons	25.0 nTPM
Spinal cord	25.0 nTPM
Medulla oblongata	24.1 nTPM

Cerebellar inhibitory	17.9 nTPM
Cerebellum	24.1 nTPM
Midbrain	21.8 nTPM
Pons	19.8 nTPM
Medulla oblongata	15.7 nTPM
Spinal cord	8.2 nTPM

Cge interneuron	13.0 nTPM
Thalamus	21.7 nTPM
Midbrain	14.8 nTPM
Cerebral cortex	14.2 nTPM
Hippocampus	12.4 nTPM
Basal ganglia	11.2 nTPM
Amygdala	9.6 nTPM
Hypothalamus	7.2 nTPM

Choroid plexus epithelial cell	7.9 nTPM
Hippocampus	16.6 nTPM
Medulla oblongata	6.7 nTPM
Basal ganglia	5.7 nTPM
Thalamus	2.7 nTPM

Committed oligodendrocyte precursor	15.7 nTPM
Spinal cord	33.1 nTPM
Hypothalamus	17.8 nTPM
Pons	16.8 nTPM
Cerebellum	15.9 nTPM
Amygdala	15.8 nTPM
Medulla oblongata	14.2 nTPM
Thalamus	13.7 nTPM
Cerebral cortex	12.7 nTPM
Hippocampus	12.7 nTPM
Basal ganglia	12.0 nTPM
Midbrain	8.4 nTPM

Deep-layer corticothalamic and 6b	10.2 nTPM
Basal ganglia	12.5 nTPM
Midbrain	11.1 nTPM
Cerebral cortex	10.8 nTPM
Hippocampus	10.1 nTPM
Amygdala	9.2 nTPM
Hypothalamus	7.4 nTPM

Deep-layer intratelencephalic	9.5 nTPM
Cerebral cortex	11.8 nTPM
Basal ganglia	10.4 nTPM
Amygdala	10.1 nTPM
Hippocampus	8.4 nTPM
Hypothalamus	6.9 nTPM

Deep-layer near-projecting	9.7 nTPM
Basal ganglia	10.8 nTPM
Hippocampus	10.7 nTPM
Cerebral cortex	10.5 nTPM
Amygdala	9.1 nTPM
Hypothalamus	7.5 nTPM

Eccentric medium spiny neuron	10.7 nTPM
Hypothalamus	15.4 nTPM
Basal ganglia	11.9 nTPM
Cerebral cortex	11.3 nTPM
Thalamus	10.5 nTPM
Amygdala	10.3 nTPM
Hippocampus	4.6 nTPM

Endothelial cell	13.2 nTPM
Spinal cord	20.7 nTPM
Pons	20.6 nTPM
Hypothalamus	17.4 nTPM
Hippocampus	15.7 nTPM
Cerebral cortex	12.8 nTPM
Amygdala	12.3 nTPM
Basal ganglia	11.2 nTPM
Thalamus	10.7 nTPM
Medulla oblongata	10.3 nTPM
Cerebellum	7.7 nTPM
Midbrain	5.7 nTPM