Single cell type - SMIM12 - The Human Protein Atlas

SMIM12

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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.	SMIM12
Gene descriptionⁱ Full gene name according to HGNC.	Small integral membrane protein 12
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.	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	5

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 - Basic cellular processes (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.	Low cell type specificity
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.	0.25
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: Low cell type specificity

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

SMIM12 is part of cluster 39 Non-specific - Basic cellular processes with confidenceⁱ 1
835 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.
CCL2	C-C motif chemokine ligand 2	0.5366	48
BRMS1	BRMS1 transcriptional repressor and anoikis regulator	0.5107	5
FDX2	Ferredoxin 2	0.5009	38
GADD45GIP1	GADD45G interacting protein 1	0.5009	39
IMP4	IMP U3 small nucleolar ribonucleoprotein 4	0.5000	39
CYB5R3	Cytochrome b5 reductase 3	0.4912	32
SCAND1	SCAN domain containing 1	0.4679	39
ACTR1A	Actin related protein 1A	0.4648	45
RUSC2	RUN and SH3 domain containing 2	0.4627	32
CCM2	CCM2 scaffold protein	0.4606	14
MRPS12	Mitochondrial ribosomal protein S12	0.4599	39
EIF2S1	Eukaryotic translation initiation factor 2 subunit alpha	0.4580	39
ABCF2	ATP binding cassette subfamily F member 2	0.4480	39
DOHH	Deoxyhypusine hydroxylase	0.4459	39
IL32	Interleukin 32	0.4430	45

IMMUNE CELLS

SMIM12 is part of cluster 36 Eosinophils - Protein ubiquitination with confidenceⁱ 0.68
179 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.
HP	Haptoglobin	1.0000	36
AURKAIP1	Aurora kinase A interacting protein 1	1.0000	36
ECH1	Enoyl-CoA hydratase 1	0.9762	36
GPATCH3	G-patch domain containing 3	0.9762	36
TRAPPC1	Trafficking protein particle complex subunit 1	0.9762	36
UQCR11	Ubiquinol-cytochrome c reductase, complex III subunit XI	0.9762	36
CTSA	Cathepsin A	0.9762	36
GRPEL1	GrpE like 1, mitochondrial	0.9524	36
ATP6V1F	ATPase H+ transporting V1 subunit F	0.9524	29
NEDD8	NEDD8 ubiquitin like modifier	0.9524	29
RRP8	Ribosomal RNA processing 8	0.9524	36
SAP18	Sin3A associated protein 18	0.9524	36
UBE2J2	Ubiquitin conjugating enzyme E2 J2	0.9524	36
GPX4	Glutathione peroxidase 4	0.9524	29
RNASE3	Ribonuclease A family member 3	0.9524	29

Adipocytes	50.1 nTPM
Breast	56.4 nTPM
Adipose tissue	43.9 nTPM

Alveolar cells type 1	51.3 nTPM
Lung	51.3 nTPM

Alveolar cells type 2	34.4 nTPM
Lung	34.4 nTPM

Astrocytes	4.6 nTPM
Brain	4.6 nTPM

B-cells	33.5 nTPM
Liver	53.1 nTPM
Kidney	46.8 nTPM
Skin	45.7 nTPM
Thymus	41.8 nTPM
Stomach	39.7 nTPM
Spleen	38.9 nTPM
Lung	33.5 nTPM
Esophagus	29.5 nTPM
Salivary gland	29.2 nTPM
PBMC	21.6 nTPM
Adipose tissue	21.4 nTPM
Bone marrow	21.3 nTPM
Lymph node	13.6 nTPM

Ciliated cells	23.1 nTPM
Fallopian tube	30.3 nTPM
Bronchus	22.9 nTPM
Lung	21.6 nTPM
Endometrium	17.7 nTPM

Club cells	27.2 nTPM
Bronchus	34.9 nTPM
Prostate	26.2 nTPM
Lung	20.5 nTPM

Dendritic cells	32.8 nTPM
Adipose tissue	33.3 nTPM
PBMC	32.4 nTPM

Endothelial cells	50.8 nTPM
Pancreas	142.2 nTPM
Skin	69.6 nTPM
Lung	66.8 nTPM
Fallopian tube	65.1 nTPM
Placenta	64.2 nTPM
Thymus	54.7 nTPM
Breast	54.5 nTPM
Testis	51.0 nTPM
Skeletal muscle	48.5 nTPM
Vascular	42.7 nTPM
Tongue	40.4 nTPM
Salivary gland	36.8 nTPM
Heart muscle	35.6 nTPM
Esophagus	34.6 nTPM
Ovary	33.4 nTPM
Liver	29.0 nTPM
Endometrium	24.9 nTPM
Prostate	21.4 nTPM

Enteroendocrine cells	39.3 nTPM
Colon	56.8 nTPM
Rectum	33.5 nTPM
Small intestine	27.5 nTPM

Fibroblasts	29.7 nTPM
Pancreas	74.5 nTPM
Heart muscle	41.3 nTPM
Lung	37.4 nTPM
Thymus	36.2 nTPM
Liver	33.2 nTPM
Placenta	31.5 nTPM
Skin	28.2 nTPM
Adipose tissue	26.9 nTPM
Skeletal muscle	25.6 nTPM
Vascular	24.8 nTPM
Stomach	23.1 nTPM
Prostate	21.8 nTPM
Salivary gland	20.5 nTPM
Fallopian tube	19.9 nTPM
Breast	18.7 nTPM
Esophagus	12.1 nTPM

Granulocytes	39.2 nTPM
Fallopian tube	45.9 nTPM
Lung	37.8 nTPM
Tongue	34.0 nTPM

Intestinal goblet cells	22.7 nTPM
Colon	29.0 nTPM
Small intestine	19.5 nTPM
Rectum	19.5 nTPM

Lymphatic endothelial cells	36.3 nTPM
Fallopian tube	50.9 nTPM
Ovary	21.8 nTPM

Macrophages	40.9 nTPM
Pancreas	69.9 nTPM
Lung	53.6 nTPM
Testis	52.7 nTPM
Kidney	52.2 nTPM
Skin	47.9 nTPM
Thymus	45.9 nTPM
Stomach	43.7 nTPM
Prostate	40.3 nTPM
Esophagus	38.5 nTPM
Bone marrow	38.5 nTPM
Adipose tissue	36.9 nTPM
Fallopian tube	36.2 nTPM
Tongue	35.8 nTPM
Skeletal muscle	33.6 nTPM
Salivary gland	32.3 nTPM
Breast	30.7 nTPM
Vascular	30.6 nTPM
Endometrium	29.5 nTPM
Spleen	29.1 nTPM

Basal keratinocytes	54.3 nTPM
Skin	63.2 nTPM
Tongue	45.5 nTPM

Basal prostatic cells	32.0 nTPM
Prostate	32.0 nTPM

Basal squamous epithelial cells	21.9 nTPM
Esophagus	21.9 nTPM

Bipolar cells	15.1 nTPM
Eye	15.1 nTPM

Paneth cells	29.9 nTPM
Rectum	36.7 nTPM
Small intestine	27.6 nTPM
Colon	25.3 nTPM

Plasma cells	34.0 nTPM
Liver	50.1 nTPM
Thymus	45.4 nTPM
Bone marrow	40.8 nTPM
Spleen	39.5 nTPM
Fallopian tube	37.6 nTPM
Stomach	30.2 nTPM
Salivary gland	28.7 nTPM
Esophagus	0.0 nTPM

Schwann cells	28.8 nTPM
Adipose tissue	40.6 nTPM
Vascular	34.0 nTPM
Esophagus	12.0 nTPM

Serous glandular cells	26.0 nTPM
Tongue	26.5 nTPM
Salivary gland	25.5 nTPM

Smooth muscle cells	53.1 nTPM
Thymus	91.1 nTPM
Lung	78.8 nTPM
Skin	73.0 nTPM
Fallopian tube	70.7 nTPM
Breast	65.7 nTPM
Vascular	57.8 nTPM
Skeletal muscle	51.3 nTPM
Prostate	50.5 nTPM
Liver	48.8 nTPM
Esophagus	46.8 nTPM
Ovary	44.0 nTPM
Adipose tissue	40.8 nTPM
Placenta	39.7 nTPM
Salivary gland	32.3 nTPM
Endometrium	30.1 nTPM
Tongue	27.5 nTPM

Suprabasal keratinocytes	64.8 nTPM
Skin	67.8 nTPM
Tongue	61.8 nTPM

T-cells	39.2 nTPM
Skin	59.2 nTPM
Liver	55.1 nTPM
Fallopian tube	51.4 nTPM
Kidney	49.7 nTPM
Adipose tissue	48.3 nTPM
Colon	47.8 nTPM
Tongue	43.7 nTPM
Lung	42.7 nTPM
PBMC	41.9 nTPM
Thymus	40.9 nTPM
Stomach	39.8 nTPM
Spleen	38.8 nTPM
Prostate	38.0 nTPM
Breast	36.8 nTPM
Skeletal muscle	31.4 nTPM
Bone marrow	30.6 nTPM
Salivary gland	30.3 nTPM
Vascular	27.3 nTPM
Endometrium	27.2 nTPM
Esophagus	26.8 nTPM
Lymph node	15.7 nTPM

Undifferentiated cells	40.5 nTPM
Colon	47.2 nTPM
Small intestine	38.2 nTPM
Rectum	36.0 nTPM

Amygdala excitatory	52.6 nTPM
Amygdala	61.9 nTPM
Hypothalamus	60.5 nTPM
Hippocampus	60.0 nTPM
Cerebral cortex	55.2 nTPM
Thalamus	39.0 nTPM
Basal ganglia	38.8 nTPM

Astrocyte	33.5 nTPM
Amygdala	44.3 nTPM
Hippocampus	36.6 nTPM
Hypothalamus	36.4 nTPM
Pons	34.3 nTPM
Cerebral cortex	33.8 nTPM
Thalamus	32.5 nTPM
Midbrain	32.4 nTPM
Basal ganglia	32.3 nTPM
Cerebellum	29.6 nTPM
Spinal cord	29.5 nTPM
Medulla oblongata	26.9 nTPM

Bergmann glia	24.6 nTPM
Cerebellum	28.1 nTPM
Pons	24.5 nTPM
Medulla oblongata	21.3 nTPM

Central nervous system macrophage	28.6 nTPM
Amygdala	32.0 nTPM
Pons	31.5 nTPM
Hypothalamus	30.9 nTPM
Basal ganglia	30.7 nTPM
Thalamus	29.6 nTPM
Cerebral cortex	28.3 nTPM
Midbrain	27.5 nTPM
Cerebellum	27.3 nTPM
Hippocampus	26.7 nTPM
Medulla oblongata	25.2 nTPM
Spinal cord	25.0 nTPM

Cerebellar inhibitory	87.1 nTPM
Medulla oblongata	104.6 nTPM
Spinal cord	101.7 nTPM
Cerebellum	85.5 nTPM
Midbrain	82.7 nTPM
Pons	60.7 nTPM

Cge interneuron	37.5 nTPM
Amygdala	40.5 nTPM
Basal ganglia	39.8 nTPM
Hypothalamus	38.6 nTPM
Cerebral cortex	37.6 nTPM
Hippocampus	37.3 nTPM
Thalamus	35.5 nTPM
Midbrain	33.2 nTPM

Choroid plexus epithelial cell	20.3 nTPM
Basal ganglia	23.3 nTPM
Hippocampus	19.4 nTPM
Medulla oblongata	19.2 nTPM
Thalamus	19.2 nTPM

Committed oligodendrocyte precursor	23.3 nTPM
Spinal cord	36.8 nTPM
Thalamus	27.5 nTPM
Amygdala	27.1 nTPM
Medulla oblongata	23.2 nTPM
Cerebellum	22.2 nTPM
Cerebral cortex	22.2 nTPM
Pons	22.1 nTPM
Basal ganglia	20.8 nTPM
Hypothalamus	19.8 nTPM
Midbrain	18.5 nTPM
Hippocampus	16.3 nTPM

Deep-layer corticothalamic and 6b	43.2 nTPM
Hypothalamus	47.6 nTPM
Cerebral cortex	44.8 nTPM
Hippocampus	44.0 nTPM
Amygdala	43.9 nTPM
Basal ganglia	39.8 nTPM
Midbrain	38.8 nTPM

Deep-layer intratelencephalic	46.7 nTPM
Hypothalamus	52.7 nTPM
Amygdala	52.4 nTPM
Cerebral cortex	45.8 nTPM
Hippocampus	42.2 nTPM
Basal ganglia	40.6 nTPM

Deep-layer near-projecting	49.5 nTPM
Hippocampus	55.6 nTPM
Hypothalamus	51.4 nTPM
Cerebral cortex	48.3 nTPM
Amygdala	47.6 nTPM
Basal ganglia	44.4 nTPM

Eccentric medium spiny neuron	53.2 nTPM
Basal ganglia	59.5 nTPM
Thalamus	57.5 nTPM
Hypothalamus	55.5 nTPM
Cerebral cortex	53.2 nTPM
Amygdala	51.7 nTPM
Hippocampus	41.9 nTPM