Single cell type - SPIN3 - The Human Protein Atlas

SPIN3

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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.	SPIN3
Gene descriptionⁱ Full gene name according to HGNC.	Spindlin family member 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.	Membrane, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	10

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.	Neurons - Synaptic 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 (Oligodendrocyte precursor cells, Excitatory neurons, Inhibitory neurons)
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.	0.56
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 (Oligodendrocyte precursor cells, Excitatory neurons, Inhibitory neurons)

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

SPIN3 is part of cluster 65 Neurons - Synaptic function with confidenceⁱ 0.99
250 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.
RPS6KA6	Ribosomal protein S6 kinase A6	0.4681	65
EML5	EMAP like 5	0.4504	69
SLITRK4	SLIT and NTRK like family member 4	0.4469	69
CACNA1D	Calcium voltage-gated channel subunit alpha1 D	0.4391	69
SHISA9	Shisa family member 9	0.4389	65
PRICKLE2	Prickle planar cell polarity protein 2	0.4379	65
PTPRG	Protein tyrosine phosphatase receptor type G	0.4375	76
PAK3	P21 (RAC1) activated kinase 3	0.4336	69
NPR2	Natriuretic peptide receptor 2	0.4333	65
SLC2A13	Solute carrier family 2 member 13	0.4332	65
RPRD2	Regulation of nuclear pre-mRNA domain containing 2	0.4318	65
ZNF343	Zinc finger protein 343	0.4310	69
LHFPL4	LHFPL tetraspan subfamily member 4	0.4293	69
CACNG2	Calcium voltage-gated channel auxiliary subunit gamma 2	0.4285	8
ASTN1	Astrotactin 1	0.4270	65

IMMUNE CELLS

SPIN3 is part of cluster 32 Basophils - Transcription with confidenceⁱ 0.99
291 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.
GABRG2	Gamma-aminobutyric acid type A receptor subunit gamma2	1.0000	32
ZNF559-ZNF177	ZNF559-ZNF177 readthrough	1.0000	32
TAPBP	TAP binding protein	1.0000	32
KRBOX5	KRAB box domain containing 5	1.0000	32
HCRT	Hypocretin neuropeptide precursor	1.0000	32
KIT	KIT proto-oncogene, receptor tyrosine kinase	1.0000	32
SETD9	SET domain containing 9	1.0000	32
SPATA4	Spermatogenesis associated 4	1.0000	32
FBXO11	F-box protein 11	1.0000	32
POLR3G	RNA polymerase III subunit G	1.0000	32
NOD1	Nucleotide binding oligomerization domain containing 1	1.0000	32
SUCO	SUN domain containing ossification factor	1.0000	32
HOXA9	Homeobox A9	1.0000	32
PTPN23	Protein tyrosine phosphatase non-receptor type 23	1.0000	32
BTBD7	BTB domain containing 7	0.9762	32

Adipocytes	3.0 nTPM
Breast	3.4 nTPM
Adipose tissue	2.6 nTPM

Alveolar cells type 1	3.3 nTPM
Lung	3.3 nTPM

Alveolar cells type 2	3.7 nTPM
Lung	3.7 nTPM

Astrocytes	11.1 nTPM
Brain	11.1 nTPM

B-cells	4.9 nTPM
Kidney	10.4 nTPM
Bone marrow	7.2 nTPM
Thymus	6.6 nTPM
Esophagus	5.9 nTPM
Lung	5.4 nTPM
Salivary gland	5.0 nTPM
Liver	4.8 nTPM
PBMC	4.6 nTPM
Adipose tissue	4.1 nTPM
Lymph node	3.2 nTPM
Stomach	2.5 nTPM
Spleen	1.9 nTPM
Skin	1.7 nTPM

Ciliated cells	2.6 nTPM
Bronchus	3.3 nTPM
Endometrium	3.2 nTPM
Fallopian tube	2.3 nTPM
Lung	1.5 nTPM

Club cells	4.5 nTPM
Prostate	5.6 nTPM
Bronchus	4.8 nTPM
Lung	3.1 nTPM

Endothelial cells	2.8 nTPM
Breast	5.3 nTPM
Testis	5.2 nTPM
Placenta	4.0 nTPM
Ovary	3.8 nTPM
Prostate	3.6 nTPM
Vascular	3.5 nTPM
Esophagus	3.4 nTPM
Skin	3.1 nTPM
Pancreas	2.6 nTPM
Endometrium	2.4 nTPM
Salivary gland	2.4 nTPM
Thymus	2.3 nTPM
Heart muscle	1.7 nTPM
Skeletal muscle	1.6 nTPM
Lung	1.6 nTPM
Tongue	1.6 nTPM
Fallopian tube	1.6 nTPM
Liver	0.0 nTPM

Enteroendocrine cells	3.2 nTPM
Small intestine	3.4 nTPM
Rectum	3.4 nTPM
Colon	2.9 nTPM

Fibroblasts	5.2 nTPM
Heart muscle	14.2 nTPM
Esophagus	7.6 nTPM
Breast	6.8 nTPM
Salivary gland	6.7 nTPM
Placenta	5.9 nTPM
Adipose tissue	5.5 nTPM
Vascular	5.4 nTPM
Liver	4.7 nTPM
Prostate	4.6 nTPM
Thymus	4.6 nTPM
Skeletal muscle	4.5 nTPM
Skin	3.8 nTPM
Fallopian tube	3.8 nTPM
Pancreas	2.6 nTPM
Lung	2.3 nTPM
Stomach	0.0 nTPM

Granulocytes	2.0 nTPM
Lung	4.5 nTPM
Fallopian tube	1.5 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	3.0 nTPM
Rectum	4.0 nTPM
Small intestine	2.7 nTPM
Colon	2.2 nTPM

Lymphatic endothelial cells	1.2 nTPM
Fallopian tube	2.4 nTPM
Ovary	0.0 nTPM

Macrophages	1.4 nTPM
Breast	3.4 nTPM
Prostate	2.4 nTPM
Salivary gland	2.4 nTPM
Adipose tissue	2.3 nTPM
Spleen	2.0 nTPM
Testis	1.9 nTPM
Vascular	1.9 nTPM
Kidney	1.8 nTPM
Tongue	1.7 nTPM
Fallopian tube	1.7 nTPM
Skeletal muscle	1.5 nTPM
Thymus	1.2 nTPM
Skin	1.1 nTPM
Lung	1.1 nTPM
Bone marrow	1.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	2.1 nTPM
Colon	3.6 nTPM
Rectum	2.7 nTPM
Small intestine	0.0 nTPM

Bipolar cells	9.2 nTPM
Eye	9.2 nTPM

Collecting duct cells	5.8 nTPM
Kidney	5.8 nTPM

Cytotrophoblasts	4.3 nTPM
Placenta	4.3 nTPM

Early spermatids	0.1 nTPM
Testis	0.1 nTPM

Plasma cells	2.9 nTPM
Esophagus	5.2 nTPM
Fallopian tube	3.5 nTPM
Thymus	3.4 nTPM
Bone marrow	3.0 nTPM
Stomach	2.9 nTPM
Spleen	1.9 nTPM
Salivary gland	1.8 nTPM
Liver	1.5 nTPM

Schwann cells	2.1 nTPM
Vascular	4.7 nTPM
Adipose tissue	1.6 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	8.3 nTPM
Tongue	13.3 nTPM
Salivary gland	3.4 nTPM

Smooth muscle cells	3.5 nTPM
Prostate	6.1 nTPM
Tongue	5.7 nTPM
Ovary	4.7 nTPM
Breast	4.6 nTPM
Vascular	4.4 nTPM
Salivary gland	4.3 nTPM
Placenta	4.1 nTPM
Skeletal muscle	3.3 nTPM
Liver	3.0 nTPM
Endometrium	2.8 nTPM
Skin	2.8 nTPM
Thymus	2.8 nTPM
Fallopian tube	2.7 nTPM
Esophagus	2.4 nTPM
Adipose tissue	2.2 nTPM
Lung	0.0 nTPM

T-cells	2.1 nTPM
Salivary gland	6.1 nTPM
PBMC	5.5 nTPM
Lymph node	5.2 nTPM
Thymus	3.1 nTPM
Bone marrow	3.0 nTPM
Vascular	2.8 nTPM
Prostate	2.6 nTPM
Esophagus	2.4 nTPM
Endometrium	1.9 nTPM
Liver	1.5 nTPM
Skeletal muscle	1.5 nTPM
Skin	1.4 nTPM
Adipose tissue	1.2 nTPM
Breast	1.2 nTPM
Lung	1.1 nTPM
Fallopian tube	0.9 nTPM
Spleen	0.8 nTPM
Tongue	0.7 nTPM
Stomach	0.4 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM

Undifferentiated cells	2.6 nTPM
Small intestine	3.0 nTPM
Rectum	3.0 nTPM
Colon	1.9 nTPM

Amygdala excitatory	61.1 nTPM
Hippocampus	69.0 nTPM
Hypothalamus	62.9 nTPM
Thalamus	62.2 nTPM
Cerebral cortex	61.5 nTPM
Amygdala	56.6 nTPM
Basal ganglia	54.3 nTPM

Astrocyte	25.9 nTPM
Amygdala	35.8 nTPM
Hippocampus	28.7 nTPM
Basal ganglia	27.7 nTPM
Cerebral cortex	26.5 nTPM
Hypothalamus	25.3 nTPM
Spinal cord	24.8 nTPM
Cerebellum	24.6 nTPM
Thalamus	24.4 nTPM
Midbrain	23.6 nTPM
Pons	22.1 nTPM
Medulla oblongata	21.5 nTPM

Bergmann glia	23.4 nTPM
Pons	28.8 nTPM
Cerebellum	22.1 nTPM
Medulla oblongata	19.2 nTPM

Central nervous system macrophage	22.4 nTPM
Amygdala	25.7 nTPM
Thalamus	25.2 nTPM
Medulla oblongata	24.7 nTPM
Hypothalamus	24.6 nTPM
Hippocampus	23.5 nTPM
Basal ganglia	23.3 nTPM
Midbrain	22.9 nTPM
Cerebral cortex	20.5 nTPM
Pons	19.8 nTPM
Cerebellum	19.7 nTPM
Spinal cord	16.8 nTPM

Cerebellar inhibitory	44.4 nTPM
Medulla oblongata	50.8 nTPM
Midbrain	49.8 nTPM
Cerebellum	47.9 nTPM
Pons	46.0 nTPM
Spinal cord	27.5 nTPM

Cge interneuron	56.3 nTPM
Amygdala	60.0 nTPM
Thalamus	59.7 nTPM
Hypothalamus	58.8 nTPM
Midbrain	58.1 nTPM
Basal ganglia	54.8 nTPM
Cerebral cortex	51.8 nTPM
Hippocampus	51.2 nTPM

Choroid plexus epithelial cell	27.0 nTPM
Basal ganglia	35.3 nTPM
Medulla oblongata	28.8 nTPM
Thalamus	27.4 nTPM
Hippocampus	16.6 nTPM

Committed oligodendrocyte precursor	25.8 nTPM
Medulla oblongata	42.6 nTPM
Hypothalamus	33.5 nTPM
Hippocampus	28.2 nTPM
Basal ganglia	27.9 nTPM
Thalamus	24.5 nTPM
Pons	23.9 nTPM
Amygdala	23.1 nTPM
Cerebral cortex	22.8 nTPM
Midbrain	19.3 nTPM
Cerebellum	19.0 nTPM
Spinal cord	18.4 nTPM

Deep-layer corticothalamic and 6b	62.7 nTPM
Amygdala	69.1 nTPM
Hypothalamus	64.8 nTPM
Hippocampus	64.5 nTPM
Midbrain	63.2 nTPM
Cerebral cortex	60.5 nTPM
Basal ganglia	54.1 nTPM

Deep-layer intratelencephalic	52.6 nTPM
Hypothalamus	56.9 nTPM
Amygdala	55.6 nTPM
Hippocampus	55.2 nTPM
Cerebral cortex	50.8 nTPM
Basal ganglia	44.6 nTPM

Deep-layer near-projecting	57.2 nTPM
Amygdala	64.8 nTPM
Cerebral cortex	58.0 nTPM
Basal ganglia	55.0 nTPM
Hippocampus	55.0 nTPM
Hypothalamus	53.3 nTPM

Eccentric medium spiny neuron	59.2 nTPM
Amygdala	66.1 nTPM
Thalamus	60.1 nTPM
Hypothalamus	58.8 nTPM
Basal ganglia	58.0 nTPM
Cerebral cortex	57.3 nTPM
Hippocampus	55.1 nTPM

Endothelial cell	17.0 nTPM
Cerebral cortex	22.4 nTPM
Hippocampus	21.2 nTPM
Midbrain	20.8 nTPM
Thalamus	19.8 nTPM
Cerebellum	17.8 nTPM
Amygdala	15.6 nTPM
Spinal cord	15.5 nTPM
Basal ganglia	14.9 nTPM
Hypothalamus	14.9 nTPM
Pons	13.1 nTPM
Medulla oblongata	11.3 nTPM

Ependymal cell	16.8 nTPM
Thalamus	19.8 nTPM
Pons	19.6 nTPM
Spinal cord	19.2 nTPM
Basal ganglia	18.7 nTPM
Amygdala	17.6 nTPM
Hippocampus	15.6 nTPM
Medulla oblongata	13.6 nTPM
Hypothalamus	13.4 nTPM
Midbrain	13.3 nTPM