Single cell type - LRRC3B - The Human Protein Atlas

LRRC3B

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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.	LRRC3B
Gene descriptionⁱ Full gene name according to HGNC.	Leucine rich repeat containing 3B
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.	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.	Astrocytes - Unknown 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.	Group enriched (Astrocytes, Early spermatids)
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.	0.91
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.	Cell type enhanced (Astrocyte, Upper rhombic lip)
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: Group enriched (Astrocytes, Early spermatids)

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: Cell type enhanced (Astrocyte, Upper rhombic lip)

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

LRRC3B is part of cluster 47 Astrocytes - Unknown function with confidenceⁱ 1
196 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.
GOLGA8H	Golgin A8 family member H	0.7263	18
EYA1	EYA transcriptional coactivator and phosphatase 1	0.7039	47
OR9A4	Olfactory receptor family 9 subfamily A member 4	0.6759	47
GABRG1	Gamma-aminobutyric acid type A receptor subunit gamma1	0.6723	47
SPACA5	Sperm acrosome associated 5	0.6642	18
BCKDHB	Branched chain keto acid dehydrogenase E1 subunit beta	0.6512	47
OR51S1	Olfactory receptor family 51 subfamily S member 1	0.6313	18
LGI1	Leucine rich glioma inactivated 1	0.6288	47
PARD3B	Par-3 family cell polarity regulator beta	0.6281	47
HEATR4	HEAT repeat containing 4	0.6178	18
GRIFIN	Galectin-related inter-fiber protein	0.6130	47
CCDC154	Coiled-coil domain containing 154	0.6096	18
CC2D2B	Coiled-coil and C2 domain containing 2B	0.6090	18
MMD2	Monocyte to macrophage differentiation associated 2	0.6036	47
SLCO1C1	Solute carrier organic anion transporter family member 1C1	0.6031	47

Adipocytes	1.1 nTPM
Adipose tissue	1.2 nTPM
Breast	0.9 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	0.0 nTPM
Lung	0.0 nTPM

B-cells	0.0 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM

Basal keratinocytes	0.1 nTPM
Skin	0.2 nTPM
Tongue	0.1 nTPM

Ciliated cells	0.1 nTPM
Endometrium	0.5 nTPM
Fallopian tube	0.1 nTPM
Bronchus	0.0 nTPM
Lung	0.0 nTPM

Club cells	0.0 nTPM
Bronchus	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM

Endothelial cells	0.9 nTPM
Prostate	4.1 nTPM
Skeletal muscle	3.4 nTPM
Ovary	2.2 nTPM
Breast	1.8 nTPM
Thymus	1.7 nTPM
Lung	0.8 nTPM
Salivary gland	0.8 nTPM
Vascular	0.8 nTPM
Endometrium	0.6 nTPM
Testis	0.3 nTPM
Tongue	0.2 nTPM
Fallopian tube	0.2 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM

Enteroendocrine cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	0.4 nTPM
Placenta	4.5 nTPM
Prostate	1.3 nTPM
Skeletal muscle	0.3 nTPM
Skin	0.1 nTPM
Salivary gland	0.1 nTPM
Thymus	0.1 nTPM
Breast	0.1 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Pancreas	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Vascular	0.0 nTPM
Fallopian tube	0.0 nTPM

Granulocytes	0.0 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM
Fallopian tube	0.0 nTPM

Intestinal goblet cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

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

Macrophages	0.1 nTPM
Endometrium	0.6 nTPM
Skeletal muscle	0.3 nTPM
Salivary gland	0.1 nTPM
Breast	0.1 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Thymus	0.0 nTPM
Tongue	0.0 nTPM
Vascular	0.0 nTPM
Fallopian tube	0.0 nTPM

Paneth cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Bipolar cells	1.6 nTPM
Eye	1.6 nTPM

Endometrial stromal cells	4.0 nTPM
Endometrium	4.0 nTPM

Excitatory neurons	12.6 nTPM
Brain	12.6 nTPM

Plasma cells	0.0 nTPM
Thymus	0.1 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM
Fallopian tube	0.0 nTPM

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

Serous glandular cells	0.0 nTPM
Salivary gland	0.0 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	0.8 nTPM
Liver	4.2 nTPM
Lung	3.5 nTPM
Tongue	1.2 nTPM
Skeletal muscle	1.0 nTPM
Endometrium	0.9 nTPM
Salivary gland	0.8 nTPM
Ovary	0.2 nTPM
Placenta	0.1 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Prostate	0.0 nTPM
Thymus	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM

T-cells	0.1 nTPM
Skeletal muscle	0.8 nTPM
Endometrium	0.4 nTPM
Breast	0.1 nTPM
Fallopian tube	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Tongue	0.0 nTPM
Vascular	0.0 nTPM

Undifferentiated cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Amygdala excitatory	78.3 nTPM
Thalamus	129.3 nTPM
Basal ganglia	83.1 nTPM
Hippocampus	72.7 nTPM
Cerebral cortex	64.5 nTPM
Amygdala	62.9 nTPM
Hypothalamus	57.0 nTPM

Astrocyte	382.8 nTPM
Amygdala	808.8 nTPM
Hippocampus	765.9 nTPM
Cerebral cortex	667.5 nTPM
Basal ganglia	343.7 nTPM
Pons	323.8 nTPM
Hypothalamus	273.4 nTPM
Medulla oblongata	253.2 nTPM
Midbrain	240.1 nTPM
Cerebellum	226.9 nTPM
Spinal cord	183.8 nTPM
Thalamus	123.3 nTPM

Bergmann glia	104.6 nTPM
Pons	118.0 nTPM
Medulla oblongata	108.7 nTPM
Cerebellum	87.1 nTPM

Central nervous system macrophage	2.9 nTPM
Thalamus	5.9 nTPM
Hippocampus	4.4 nTPM
Cerebral cortex	4.1 nTPM
Amygdala	3.1 nTPM
Medulla oblongata	3.0 nTPM
Hypothalamus	2.5 nTPM
Cerebellum	1.8 nTPM
Spinal cord	1.8 nTPM
Midbrain	1.7 nTPM
Pons	1.7 nTPM
Basal ganglia	1.6 nTPM

Cerebellar inhibitory	33.8 nTPM
Pons	115.7 nTPM
Medulla oblongata	19.9 nTPM
Midbrain	18.4 nTPM
Spinal cord	8.2 nTPM
Cerebellum	6.9 nTPM

Cge interneuron	127.2 nTPM
Amygdala	143.5 nTPM
Cerebral cortex	143.5 nTPM
Thalamus	137.3 nTPM
Midbrain	132.2 nTPM
Hypothalamus	125.4 nTPM
Basal ganglia	114.9 nTPM
Hippocampus	94.1 nTPM

Choroid plexus epithelial cell	3.1 nTPM
Thalamus	8.2 nTPM
Medulla oblongata	3.0 nTPM
Basal ganglia	1.0 nTPM
Hippocampus	0.0 nTPM

Committed oligodendrocyte precursor	21.2 nTPM
Cerebral cortex	32.9 nTPM
Thalamus	29.9 nTPM
Pons	22.1 nTPM
Amygdala	21.4 nTPM
Hypothalamus	21.2 nTPM
Basal ganglia	20.8 nTPM
Medulla oblongata	19.4 nTPM
Hippocampus	18.9 nTPM
Midbrain	17.6 nTPM
Cerebellum	17.4 nTPM
Spinal cord	11.0 nTPM

Deep-layer corticothalamic and 6b	127.4 nTPM
Amygdala	197.2 nTPM
Hippocampus	137.4 nTPM
Hypothalamus	128.4 nTPM
Cerebral cortex	108.6 nTPM
Midbrain	96.5 nTPM
Basal ganglia	96.0 nTPM

Deep-layer intratelencephalic	54.7 nTPM
Hypothalamus	75.5 nTPM
Hippocampus	63.4 nTPM
Amygdala	58.3 nTPM
Basal ganglia	45.0 nTPM
Cerebral cortex	31.1 nTPM

Deep-layer near-projecting	149.0 nTPM
Amygdala	197.4 nTPM
Hypothalamus	171.9 nTPM
Cerebral cortex	143.4 nTPM
Hippocampus	134.3 nTPM
Basal ganglia	98.2 nTPM

Eccentric medium spiny neuron	66.5 nTPM
Amygdala	77.2 nTPM
Hippocampus	75.9 nTPM
Thalamus	68.7 nTPM
Hypothalamus	68.1 nTPM
Cerebral cortex	63.2 nTPM
Basal ganglia	45.8 nTPM

Endothelial cell	2.3 nTPM
Cerebral cortex	6.4 nTPM
Hypothalamus	6.2 nTPM
Hippocampus	4.5 nTPM
Cerebellum	2.3 nTPM
Basal ganglia	1.9 nTPM
Pons	1.9 nTPM
Thalamus	1.7 nTPM
Midbrain	0.9 nTPM
Amygdala	0.0 nTPM
Medulla oblongata	0.0 nTPM
Spinal cord	0.0 nTPM

Ependymal cell	196.7 nTPM
Amygdala	296.4 nTPM
Pons	265.2 nTPM
Midbrain	251.4 nTPM
Hippocampus	222.5 nTPM
Medulla oblongata	187.5 nTPM
Thalamus	166.0 nTPM
Hypothalamus	148.1 nTPM
Basal ganglia	147.2 nTPM
Spinal cord	86.2 nTPM