Single cell type - LMTK3 - The Human Protein Atlas

LMTK3

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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.	LMTK3
Gene descriptionⁱ Full gene name according to HGNC.	Lemur tyrosine kinase 3
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.	Membrane, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	6

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 - Mixed 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 (Inhibitory neurons, Excitatory neurons, Club cells, Ionocytes)
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.	0.61
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.	Not detected in immune cells
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 (Inhibitory neurons, Excitatory neurons, Club cells, Ionocytes)

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: Not detected in immune cells
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

LMTK3 is part of cluster 45 Non-specific - Mixed function with confidenceⁱ 1
349 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.
PRSS22	Serine protease 22	0.7983	45
LCN2	Lipocalin 2	0.7962	45
ERO1A	Endoplasmic reticulum oxidoreductase 1 alpha	0.7261	35
GJB4	Gap junction protein beta 4	0.6976	45
PORCN	Porcupine O-acyltransferase	0.6804	35
SLC6A14	Solute carrier family 6 member 14	0.6765	35
SERPINB7	Serpin family B member 7	0.6722	45
CXCL17	C-X-C motif chemokine ligand 17	0.6632	35
DEFB4A	Defensin beta 4A	0.6631	45
PI3	Peptidase inhibitor 3	0.6609	35
BIK	BCL2 interacting killer	0.6583	35
LAMB3	Laminin subunit beta 3	0.6552	45
RHBDL2	Rhomboid like 2	0.6430	35
CDKN2A	Cyclin dependent kinase inhibitor 2A	0.6310	45
DYNLT1	Dynein light chain Tctex-type 1	0.6271	35

Adipocytes	0.6 nTPM
Breast	1.1 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	4.6 nTPM
Lung	4.6 nTPM

Alveolar cells type 2	4.1 nTPM
Lung	4.1 nTPM

Astrocytes	11.1 nTPM
Brain	11.1 nTPM

B-cells	1.4 nTPM
Skin	6.8 nTPM
Adipose tissue	3.7 nTPM
Bone marrow	2.8 nTPM
Stomach	1.7 nTPM
Lymph node	1.2 nTPM
Thymus	1.0 nTPM
Spleen	0.7 nTPM
Salivary gland	0.6 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM

Ciliated cells	14.1 nTPM
Bronchus	40.5 nTPM
Endometrium	8.3 nTPM
Lung	5.3 nTPM
Fallopian tube	2.5 nTPM

Club cells	30.1 nTPM
Bronchus	67.3 nTPM
Lung	15.9 nTPM
Prostate	7.3 nTPM

Endothelial cells	0.4 nTPM
Tongue	2.0 nTPM
Prostate	1.2 nTPM
Breast	0.9 nTPM
Fallopian tube	0.9 nTPM
Salivary gland	0.6 nTPM
Ovary	0.6 nTPM
Heart muscle	0.4 nTPM
Thymus	0.3 nTPM
Skin	0.2 nTPM
Endometrium	0.1 nTPM
Vascular	0.1 nTPM
Testis	0.0 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM

Enteroendocrine cells	3.0 nTPM
Small intestine	6.9 nTPM
Rectum	1.7 nTPM
Colon	0.4 nTPM

Fibroblasts	1.5 nTPM
Placenta	7.4 nTPM
Liver	2.4 nTPM
Pancreas	2.1 nTPM
Prostate	2.0 nTPM
Fallopian tube	1.7 nTPM
Stomach	1.4 nTPM
Adipose tissue	1.2 nTPM
Thymus	1.2 nTPM
Lung	0.9 nTPM
Skin	0.8 nTPM
Esophagus	0.8 nTPM
Salivary gland	0.7 nTPM
Vascular	0.6 nTPM
Breast	0.5 nTPM
Skeletal muscle	0.2 nTPM
Heart muscle	0.0 nTPM

Granulocytes	0.4 nTPM
Fallopian tube	1.3 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	1.1 nTPM
Small intestine	2.9 nTPM
Colon	0.2 nTPM
Rectum	0.2 nTPM

Lymphatic endothelial cells	0.3 nTPM
Fallopian tube	0.6 nTPM
Ovary	0.0 nTPM

Macrophages	0.7 nTPM
Breast	2.9 nTPM
Endometrium	1.8 nTPM
Prostate	1.5 nTPM
Esophagus	1.3 nTPM
Salivary gland	1.3 nTPM
Skin	1.1 nTPM
Tongue	1.0 nTPM
Kidney	0.9 nTPM
Vascular	0.5 nTPM
Adipose tissue	0.4 nTPM
Thymus	0.4 nTPM
Fallopian tube	0.4 nTPM
Lung	0.3 nTPM
Skeletal muscle	0.2 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	1.2 nTPM
Small intestine	3.5 nTPM
Rectum	0.2 nTPM
Colon	0.0 nTPM

Basal prostatic cells	5.7 nTPM
Prostate	5.7 nTPM

Basal respiratory cells	16.9 nTPM
Bronchus	16.9 nTPM

Basal squamous epithelial cells	6.4 nTPM
Esophagus	6.4 nTPM

Bipolar cells	19.5 nTPM
Eye	19.5 nTPM

Plasma cells	15.1 nTPM
Fallopian tube	33.1 nTPM
Stomach	26.8 nTPM
Esophagus	26.0 nTPM
Bone marrow	9.1 nTPM
Liver	9.0 nTPM
Salivary gland	8.1 nTPM
Spleen	4.6 nTPM
Thymus	4.0 nTPM

Schwann cells	0.4 nTPM
Adipose tissue	1.2 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Serous glandular cells	2.7 nTPM
Tongue	4.4 nTPM
Salivary gland	0.9 nTPM

Smooth muscle cells	0.7 nTPM
Tongue	1.8 nTPM
Fallopian tube	1.7 nTPM
Lung	1.2 nTPM
Adipose tissue	1.1 nTPM
Endometrium	0.9 nTPM
Salivary gland	0.8 nTPM
Breast	0.8 nTPM
Skeletal muscle	0.7 nTPM
Ovary	0.7 nTPM
Placenta	0.6 nTPM
Thymus	0.5 nTPM
Vascular	0.4 nTPM
Skin	0.3 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Prostate	0.0 nTPM

T-cells	2.6 nTPM
Esophagus	7.3 nTPM
Thymus	5.9 nTPM
Lymph node	5.2 nTPM
Spleen	3.2 nTPM
Salivary gland	3.1 nTPM
Breast	3.0 nTPM
Prostate	2.9 nTPM
Vascular	2.8 nTPM
Bone marrow	2.6 nTPM
PBMC	2.5 nTPM
Stomach	2.4 nTPM
Tongue	2.3 nTPM
Fallopian tube	2.3 nTPM
Skeletal muscle	1.9 nTPM
Adipose tissue	1.8 nTPM
Lung	1.6 nTPM
Endometrium	1.4 nTPM
Liver	1.1 nTPM
Colon	1.0 nTPM
Kidney	0.9 nTPM
Skin	0.0 nTPM

Undifferentiated cells	5.5 nTPM
Colon	14.2 nTPM
Small intestine	1.9 nTPM
Rectum	0.3 nTPM

Amygdala excitatory	83.8 nTPM
Hypothalamus	127.9 nTPM
Amygdala	85.3 nTPM
Hippocampus	78.7 nTPM
Basal ganglia	75.2 nTPM
Cerebral cortex	72.2 nTPM
Thalamus	63.5 nTPM

Astrocyte	25.3 nTPM
Pons	27.9 nTPM
Thalamus	27.8 nTPM
Hippocampus	26.7 nTPM
Medulla oblongata	26.7 nTPM
Midbrain	26.4 nTPM
Cerebral cortex	25.3 nTPM
Cerebellum	25.2 nTPM
Spinal cord	25.0 nTPM
Hypothalamus	23.7 nTPM
Basal ganglia	21.9 nTPM
Amygdala	21.3 nTPM

Bergmann glia	18.8 nTPM
Cerebellum	20.0 nTPM
Medulla oblongata	19.2 nTPM
Pons	17.3 nTPM

Central nervous system macrophage	9.1 nTPM
Cerebral cortex	11.8 nTPM
Medulla oblongata	11.7 nTPM
Hypothalamus	10.5 nTPM
Basal ganglia	9.5 nTPM
Thalamus	9.3 nTPM
Hippocampus	9.2 nTPM
Cerebellum	9.0 nTPM
Pons	8.7 nTPM
Amygdala	8.5 nTPM
Midbrain	6.5 nTPM
Spinal cord	5.0 nTPM

Cerebellar inhibitory	74.7 nTPM
Cerebellum	84.0 nTPM
Midbrain	79.6 nTPM
Pons	74.1 nTPM
Medulla oblongata	70.0 nTPM
Spinal cord	66.0 nTPM

Cge interneuron	79.0 nTPM
Hypothalamus	111.8 nTPM
Amygdala	80.9 nTPM
Cerebral cortex	77.2 nTPM
Hippocampus	76.3 nTPM
Basal ganglia	74.2 nTPM
Midbrain	68.2 nTPM
Thalamus	64.5 nTPM

Choroid plexus epithelial cell	3.3 nTPM
Hippocampus	8.3 nTPM
Thalamus	2.7 nTPM
Basal ganglia	1.1 nTPM
Medulla oblongata	1.0 nTPM

Committed oligodendrocyte precursor	36.3 nTPM
Cerebellum	50.7 nTPM
Cerebral cortex	41.8 nTPM
Spinal cord	40.5 nTPM
Hippocampus	40.1 nTPM
Thalamus	36.5 nTPM
Amygdala	36.1 nTPM
Midbrain	36.1 nTPM
Pons	34.5 nTPM
Hypothalamus	32.8 nTPM
Basal ganglia	28.5 nTPM
Medulla oblongata	21.9 nTPM

Deep-layer corticothalamic and 6b	77.8 nTPM
Hypothalamus	117.6 nTPM
Amygdala	76.0 nTPM
Hippocampus	75.0 nTPM
Cerebral cortex	73.8 nTPM
Basal ganglia	65.3 nTPM
Midbrain	58.8 nTPM

Deep-layer intratelencephalic	78.6 nTPM
Hypothalamus	121.7 nTPM
Amygdala	76.0 nTPM
Hippocampus	69.0 nTPM
Cerebral cortex	66.2 nTPM
Basal ganglia	60.0 nTPM

Deep-layer near-projecting	83.8 nTPM
Hypothalamus	128.2 nTPM
Amygdala	80.7 nTPM
Cerebral cortex	76.2 nTPM
Basal ganglia	68.7 nTPM
Hippocampus	65.0 nTPM

Eccentric medium spiny neuron	98.9 nTPM
Thalamus	102.3 nTPM
Hippocampus	100.3 nTPM
Amygdala	100.1 nTPM
Hypothalamus	100.1 nTPM
Cerebral cortex	95.4 nTPM
Basal ganglia	95.3 nTPM

Endothelial cell	2.7 nTPM
Hypothalamus	5.0 nTPM
Hippocampus	4.2 nTPM
Pons	3.7 nTPM
Thalamus	3.4 nTPM
Cerebral cortex	3.2 nTPM
Midbrain	2.8 nTPM
Medulla oblongata	2.1 nTPM
Basal ganglia	1.9 nTPM
Spinal cord	1.7 nTPM
Amygdala	1.1 nTPM
Cerebellum	0.8 nTPM

Ependymal cell	11.0 nTPM
Pons	14.5 nTPM
Midbrain	14.0 nTPM
Amygdala	13.1 nTPM
Medulla oblongata	12.1 nTPM
Thalamus	12.1 nTPM
Hippocampus	12.0 nTPM
Hypothalamus	10.7 nTPM
Basal ganglia	7.1 nTPM
Spinal cord	3.8 nTPM