Single cell type - LSG1 - The Human Protein Atlas

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.	LSG1
Gene descriptionⁱ Full gene name according to HGNC.	Large 60S subunit nuclear export GTPase 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Plasma proteins
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. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

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. Read more	Granulocytes - Receptor 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. Read more	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. Read more	Low immune cell specificity
Immune cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in all
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Low cell line specificity
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in all
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of 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 Group Expression Alphabetical RNA single cell type specificity: Low cell type specificity

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

LSG1 is part of cluster 60 Granulocytes - Receptor signaling with confidenceⁱ 0.99
79 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type 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. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
DHX38	DEAH-box helicase 38	0.6514	52
TTC4	Tetratricopeptide repeat domain 4	0.6130	59
ACIN1	Apoptotic chromatin condensation inducer 1	0.6100	60
NOP14	NOP14 nucleolar protein	0.5975	10
AC138969.1	Novel member of the nuclear pore complex interacting protein NPIP gene family	0.5787	60
CTR9	CTR9 homolog, Paf1/RNA polymerase II complex component	0.5705	60
SUPT6H	SPT6 homolog, histone chaperone and transcription elongation factor	0.5632	52
AL139300.1	Novel protein	0.5631	60
OR56A4	Olfactory receptor family 56 subfamily A member 4	0.5593	60
U2AF1L5	U2 small nuclear RNA auxiliary factor 1 like 5	0.5569	60
AL034430.1	Novel protein	0.5521	11
ZNF556	Zinc finger protein 556	0.5464	11
MAK16	MAK16 homolog	0.5401	10
NPIPA8	Nuclear pore complex interacting protein family member A8	0.5288	60
HEATR1	HEAT repeat containing 1	0.5211	59

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	25.0 nTPM
Adipose tissue	29.3 nTPM
Breast	20.7 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	29.6 nTPM
Lung	29.6 nTPM

Astrocytes	10.4 nTPM
Brain	10.4 nTPM

B-cells	22.5 nTPM
Adipose tissue	31.5 nTPM
Lymph node	30.5 nTPM
Bone marrow	28.6 nTPM
Stomach	27.3 nTPM
Spleen	26.9 nTPM
Breast	20.0 nTPM
Kidney	19.0 nTPM
Liver	16.0 nTPM
PBMC	14.3 nTPM
Colon	11.2 nTPM

Dendritic cells	21.2 nTPM
Adipose tissue	37.1 nTPM
Breast	18.6 nTPM
PBMC	8.0 nTPM

Endothelial cells	23.7 nTPM
Lung	53.0 nTPM
Endometrium	42.5 nTPM
Esophagus	30.0 nTPM
Skeletal muscle	29.0 nTPM
Testis	28.2 nTPM
Ovary	26.2 nTPM
Placenta	21.6 nTPM
Liver	15.6 nTPM
Skin	15.5 nTPM
Heart muscle	14.9 nTPM
Breast	14.8 nTPM
Eye	14.6 nTPM
Prostate	14.3 nTPM
Pancreas	11.6 nTPM

Fibroblasts	17.7 nTPM
Lung	38.0 nTPM
Stomach	20.8 nTPM
Adipose tissue	19.5 nTPM
Skeletal muscle	19.4 nTPM
Ovary	19.0 nTPM
Heart muscle	16.6 nTPM
Esophagus	15.3 nTPM
Breast	12.7 nTPM
Prostate	12.0 nTPM
Skin	10.9 nTPM
Placenta	10.6 nTPM

Intestinal goblet cells	14.2 nTPM
Colon	22.1 nTPM
Rectum	11.5 nTPM
Small intestine	8.9 nTPM

Macrophages	15.5 nTPM
Lung	42.8 nTPM
Esophagus	23.6 nTPM
Pancreas	17.8 nTPM
Breast	17.1 nTPM
Endometrium	16.7 nTPM
Bone marrow	16.3 nTPM
Adipose tissue	16.0 nTPM
Skeletal muscle	14.7 nTPM
Kidney	14.3 nTPM
Testis	13.4 nTPM
Ovary	10.7 nTPM
Spleen	10.4 nTPM
Prostate	10.3 nTPM
Stomach	8.8 nTPM
PBMC	0.0 nTPM

Paneth cells	8.0 nTPM
Colon	13.2 nTPM
Rectum	10.9 nTPM
Small intestine	0.0 nTPM

Plasma cells	23.8 nTPM
Adipose tissue	40.7 nTPM
Bone marrow	24.7 nTPM
Spleen	22.4 nTPM
Stomach	19.0 nTPM
Esophagus	12.3 nTPM

Respiratory ciliated cells	34.3 nTPM
Lung	54.0 nTPM
Bronchus	14.6 nTPM

Smooth muscle cells	14.6 nTPM
Esophagus	23.3 nTPM
Pancreas	19.1 nTPM
Endometrium	19.1 nTPM
Ovary	18.7 nTPM
Adipose tissue	18.1 nTPM
Skeletal muscle	13.9 nTPM
Breast	13.1 nTPM
Skin	11.9 nTPM
Prostate	11.0 nTPM
Bronchus	7.7 nTPM
Heart muscle	5.4 nTPM

T-cells	24.0 nTPM
Lung	53.2 nTPM
Endometrium	35.7 nTPM
Adipose tissue	33.9 nTPM
Bone marrow	30.5 nTPM
Lymph node	26.7 nTPM
Stomach	25.5 nTPM
Skeletal muscle	22.4 nTPM
Ovary	22.3 nTPM
Breast	20.5 nTPM
Kidney	19.8 nTPM
Esophagus	19.7 nTPM
Spleen	19.2 nTPM
Prostate	19.0 nTPM
Colon	18.5 nTPM
PBMC	17.5 nTPM
Liver	12.6 nTPM
Skin	11.6 nTPM

Basal keratinocytes	16.2 nTPM
Skin	16.2 nTPM

Collecting duct cells	9.2 nTPM
Kidney	9.2 nTPM

Cone photoreceptor cells	12.5 nTPM
Eye	12.5 nTPM

Cytotrophoblasts	25.1 nTPM
Placenta	25.1 nTPM

Undifferentiated cells	17.6 nTPM
Colon	22.3 nTPM
Small intestine	15.9 nTPM
Rectum	14.6 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC