Single cell type - SEC31B - The Human Protein Atlas

SEC31B

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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.	SEC31B
Gene descriptionⁱ Full gene name according to HGNC.	SEC31 homolog B, COPII coat complex component
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.	1

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.	Horizontal & Bipolar cells - Neuronal signaling (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, Horizontal cells, Oligodendrocyte precursor cells, Bipolar cells, Astrocytes)
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.	0.62
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, Horizontal cells, Oligodendrocyte precursor cells, Bipolar cells, Astrocytes)

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

SEC31B is part of cluster 71 Horizontal & Bipolar cells - Neuronal signaling with confidenceⁱ 1
205 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.
CEND1	Cell cycle exit and neuronal differentiation 1	0.6924	71
TMEM179	Transmembrane protein 179	0.6304	71
CASKIN1	CASK interacting protein 1	0.6285	71
PLEKHD1	Pleckstrin homology and coiled-coil domain containing D1	0.6246	71
SHANK1	SH3 and multiple ankyrin repeat domains 1	0.6164	71
SV2A	Synaptic vesicle glycoprotein 2A	0.6107	71
SLC23A2	Solute carrier family 23 member 2	0.5950	25
ATCAY	ATCAY kinesin light chain interacting caytaxin	0.5877	71
ADGRB1	Adhesion G protein-coupled receptor B1	0.5782	76
GPR61	G protein-coupled receptor 61	0.5761	71
LRFN1	Leucine rich repeat and fibronectin type III domain containing 1	0.5682	25
KCNG4	Potassium voltage-gated channel modifier subfamily G member 4	0.5662	71
RNF157	Ring finger protein 157	0.5582	71
CABP2	Calcium binding protein 2	0.5528	25
CACNA1G	Calcium voltage-gated channel subunit alpha1 G	0.5473	71

Adipocytes	2.2 nTPM
Adipose tissue	3.0 nTPM
Breast	1.5 nTPM

Alveolar cells type 1	1.8 nTPM
Lung	1.8 nTPM

Alveolar cells type 2	1.9 nTPM
Lung	1.9 nTPM

B-cells	3.2 nTPM
Lung	6.7 nTPM
Adipose tissue	6.6 nTPM
PBMC	6.2 nTPM
Salivary gland	5.5 nTPM
Kidney	5.2 nTPM
Thymus	4.1 nTPM
Spleen	1.9 nTPM
Skin	1.7 nTPM
Stomach	1.7 nTPM
Lymph node	1.1 nTPM
Bone marrow	1.0 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM

Basal keratinocytes	1.8 nTPM
Tongue	2.2 nTPM
Skin	1.4 nTPM

Ciliated cells	1.8 nTPM
Bronchus	2.7 nTPM
Fallopian tube	2.1 nTPM
Lung	1.6 nTPM
Endometrium	0.9 nTPM

Club cells	2.4 nTPM
Lung	3.4 nTPM
Bronchus	2.0 nTPM
Prostate	1.7 nTPM

Endothelial cells	2.1 nTPM
Heart muscle	5.1 nTPM
Liver	5.0 nTPM
Ovary	3.6 nTPM
Vascular	3.1 nTPM
Testis	2.7 nTPM
Endometrium	2.4 nTPM
Salivary gland	2.4 nTPM
Skeletal muscle	1.8 nTPM
Placenta	1.7 nTPM
Prostate	1.7 nTPM
Thymus	1.5 nTPM
Lung	1.4 nTPM
Tongue	1.4 nTPM
Skin	1.2 nTPM
Breast	0.9 nTPM
Esophagus	0.8 nTPM
Fallopian tube	0.6 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	4.3 nTPM
Rectum	8.4 nTPM
Small intestine	3.4 nTPM
Colon	1.2 nTPM

Fibroblasts	2.4 nTPM
Liver	4.7 nTPM
Vascular	4.3 nTPM
Heart muscle	4.2 nTPM
Salivary gland	3.9 nTPM
Adipose tissue	3.1 nTPM
Breast	2.8 nTPM
Skeletal muscle	2.4 nTPM
Placenta	1.9 nTPM
Thymus	1.8 nTPM
Fallopian tube	1.6 nTPM
Skin	1.4 nTPM
Stomach	1.4 nTPM
Esophagus	1.3 nTPM
Prostate	1.3 nTPM
Lung	1.2 nTPM
Pancreas	0.7 nTPM

Granulocytes	3.4 nTPM
Tongue	4.9 nTPM
Lung	3.5 nTPM
Fallopian tube	1.9 nTPM

Intestinal goblet cells	3.1 nTPM
Rectum	4.5 nTPM
Small intestine	2.9 nTPM
Colon	1.7 nTPM

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

Macrophages	3.5 nTPM
Bone marrow	6.1 nTPM
Salivary gland	5.6 nTPM
Kidney	5.3 nTPM
Adipose tissue	5.1 nTPM
Esophagus	5.1 nTPM
Prostate	4.3 nTPM
Skeletal muscle	4.2 nTPM
Tongue	4.2 nTPM
Endometrium	3.7 nTPM
Vascular	3.7 nTPM
Breast	3.2 nTPM
Fallopian tube	3.1 nTPM
Spleen	3.0 nTPM
Thymus	2.9 nTPM
Lung	2.3 nTPM
Skin	2.2 nTPM
Testis	1.9 nTPM
Pancreas	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	1.7 nTPM
Rectum	5.1 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Astrocytes	27.2 nTPM
Brain	27.2 nTPM

Collecting duct cells	9.7 nTPM
Kidney	9.7 nTPM

Cone photoreceptor cells	6.8 nTPM
Eye	6.8 nTPM

Plasma cells	1.6 nTPM
Liver	5.0 nTPM
Salivary gland	3.6 nTPM
Thymus	2.0 nTPM
Spleen	1.2 nTPM
Stomach	0.4 nTPM
Fallopian tube	0.3 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Schwann cells	4.3 nTPM
Vascular	8.9 nTPM
Adipose tissue	3.9 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	4.3 nTPM
Tongue	4.4 nTPM
Salivary gland	4.1 nTPM

Smooth muscle cells	2.5 nTPM
Esophagus	4.8 nTPM
Lung	4.7 nTPM
Liver	3.4 nTPM
Adipose tissue	3.3 nTPM
Tongue	3.3 nTPM
Prostate	3.0 nTPM
Salivary gland	2.6 nTPM
Vascular	2.6 nTPM
Placenta	2.2 nTPM
Endometrium	2.2 nTPM
Thymus	1.8 nTPM
Breast	1.8 nTPM
Ovary	1.4 nTPM
Skin	1.3 nTPM
Fallopian tube	1.3 nTPM
Skeletal muscle	1.1 nTPM

T-cells	4.6 nTPM
Vascular	11.7 nTPM
PBMC	8.3 nTPM
Tongue	8.0 nTPM
Adipose tissue	7.9 nTPM
Liver	6.7 nTPM
Salivary gland	6.7 nTPM
Skeletal muscle	6.0 nTPM
Thymus	5.2 nTPM
Lung	5.0 nTPM
Fallopian tube	4.6 nTPM
Prostate	4.2 nTPM
Endometrium	4.1 nTPM
Breast	3.3 nTPM
Colon	2.9 nTPM
Bone marrow	2.8 nTPM
Kidney	2.7 nTPM
Skin	2.5 nTPM
Lymph node	1.7 nTPM
Stomach	1.6 nTPM
Spleen	1.5 nTPM
Esophagus	0.0 nTPM

Undifferentiated cells	2.9 nTPM
Rectum	4.2 nTPM
Small intestine	3.4 nTPM
Colon	1.0 nTPM

Amygdala excitatory	27.8 nTPM
Hippocampus	29.2 nTPM
Hypothalamus	28.5 nTPM
Cerebral cortex	28.4 nTPM
Thalamus	27.2 nTPM
Amygdala	26.9 nTPM
Basal ganglia	26.7 nTPM

Astrocyte	37.9 nTPM
Cerebellum	48.0 nTPM
Midbrain	44.2 nTPM
Thalamus	41.2 nTPM
Cerebral cortex	39.0 nTPM
Pons	39.0 nTPM
Medulla oblongata	37.7 nTPM
Basal ganglia	36.8 nTPM
Hippocampus	35.5 nTPM
Amygdala	34.1 nTPM
Spinal cord	33.7 nTPM
Hypothalamus	27.8 nTPM

Bergmann glia	21.4 nTPM
Cerebellum	26.9 nTPM
Pons	20.1 nTPM
Medulla oblongata	17.0 nTPM

Central nervous system macrophage	19.5 nTPM
Cerebellum	23.7 nTPM
Midbrain	21.4 nTPM
Hypothalamus	20.9 nTPM
Spinal cord	20.6 nTPM
Hippocampus	20.2 nTPM
Amygdala	19.8 nTPM
Basal ganglia	18.9 nTPM
Cerebral cortex	18.4 nTPM
Pons	18.2 nTPM
Thalamus	17.8 nTPM
Medulla oblongata	14.7 nTPM

Cerebellar inhibitory	35.4 nTPM
Spinal cord	49.5 nTPM
Midbrain	34.5 nTPM
Medulla oblongata	32.6 nTPM
Cerebellum	31.2 nTPM
Pons	29.3 nTPM

Cge interneuron	21.6 nTPM
Hypothalamus	25.9 nTPM
Cerebral cortex	22.7 nTPM
Amygdala	22.3 nTPM
Hippocampus	21.5 nTPM
Basal ganglia	20.5 nTPM
Midbrain	19.2 nTPM
Thalamus	18.9 nTPM

Choroid plexus epithelial cell	24.3 nTPM
Hippocampus	27.7 nTPM
Thalamus	27.4 nTPM
Medulla oblongata	21.3 nTPM
Basal ganglia	20.9 nTPM

Committed oligodendrocyte precursor	22.8 nTPM
Midbrain	31.9 nTPM
Hippocampus	30.5 nTPM
Cerebral cortex	29.8 nTPM
Hypothalamus	25.3 nTPM
Pons	23.0 nTPM
Cerebellum	22.2 nTPM
Thalamus	22.1 nTPM
Amygdala	21.4 nTPM
Basal ganglia	18.6 nTPM
Spinal cord	18.4 nTPM
Medulla oblongata	7.7 nTPM

Deep-layer corticothalamic and 6b	23.2 nTPM
Hypothalamus	25.8 nTPM
Cerebral cortex	24.2 nTPM
Amygdala	23.6 nTPM
Hippocampus	22.9 nTPM
Midbrain	22.2 nTPM
Basal ganglia	20.5 nTPM

Deep-layer intratelencephalic	23.8 nTPM
Hypothalamus	26.3 nTPM
Amygdala	25.6 nTPM
Cerebral cortex	24.8 nTPM
Basal ganglia	21.6 nTPM
Hippocampus	20.7 nTPM

Deep-layer near-projecting	34.1 nTPM
Cerebral cortex	40.5 nTPM
Amygdala	39.4 nTPM
Hypothalamus	39.2 nTPM
Basal ganglia	28.1 nTPM
Hippocampus	23.4 nTPM

Eccentric medium spiny neuron	29.2 nTPM
Hypothalamus	31.4 nTPM
Thalamus	30.1 nTPM
Basal ganglia	29.4 nTPM
Amygdala	28.8 nTPM
Hippocampus	28.2 nTPM
Cerebral cortex	27.1 nTPM

Endothelial cell	11.9 nTPM
Midbrain	16.1 nTPM
Amygdala	15.6 nTPM
Cerebellum	13.2 nTPM
Hippocampus	13.1 nTPM
Pons	13.1 nTPM
Basal ganglia	12.1 nTPM
Spinal cord	12.1 nTPM
Cerebral cortex	10.9 nTPM
Hypothalamus	9.9 nTPM
Thalamus	8.5 nTPM
Medulla oblongata	6.2 nTPM

Ependymal cell	15.6 nTPM
Thalamus	19.8 nTPM
Hippocampus	19.5 nTPM
Amygdala	18.2 nTPM
Basal ganglia	17.6 nTPM
Hypothalamus	15.2 nTPM
Midbrain	14.6 nTPM
Medulla oblongata	13.6 nTPM
Pons	12.6 nTPM
Spinal cord	9.6 nTPM