Single cell type - LETM2 - 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.	LETM2
Gene descriptionⁱ Full gene name according to HGNC.	Leucine zipper and EF-hand containing transmembrane protein 2
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,Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	9

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	Spermatocytes - Spermatogenesis (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	Cell type enhanced (Early spermatids, Late spermatids, Spermatocytes, Pancreatic endocrine cells)
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	Immune cell enriched (neutrophil)
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 many
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	Cell line enhanced (HBEC3-KT, hTERT-HME1)
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 many
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: Cell type enhanced (Early spermatids, Late spermatids, Spermatocytes, Pancreatic endocrine cells)

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

LETM2 is part of cluster 66 Spermatocytes - Spermatogenesis with confidenceⁱ 1
507 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
CCDC110	Coiled-coil domain containing 110	0.5266	66
COX7B2	Cytochrome c oxidase subunit 7B2	0.5194	66
SULT6B1	Sulfotransferase family 6B member 1	0.5191	66
SLCO6A1	Solute carrier organic anion transporter family member 6A1	0.5180	66
DEFB121	Defensin beta 121	0.5108	66
CCDC87	Coiled-coil domain containing 87	0.5108	66
CCDC62	Coiled-coil domain containing 62	0.5089	66
MAP1LC3B	Microtubule associated protein 1 light chain 3 beta	0.5070	7
PRKACG	Protein kinase cAMP-activated catalytic subunit gamma	0.5015	66
BUD23	BUD23 rRNA methyltransferase and ribosome maturation factor	0.5005	7
ZPBP	Zona pellucida binding protein	0.4971	66
DBF4	DBF4 zinc finger	0.4948	66
PRKRIP1	PRKR interacting protein 1	0.4937	66
CTAGE9	CTAGE family member 9	0.4930	66
CDRT15	CMT1A duplicated region transcript 15	0.4918	66

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	3.0 nTPM
Breast	3.4 nTPM
Adipose tissue	2.7 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	6.4 nTPM
Lung	6.4 nTPM

Astrocytes	2.3 nTPM
Brain	2.3 nTPM

B-cells	10.3 nTPM
Breast	40.2 nTPM
Colon	17.6 nTPM
Stomach	13.2 nTPM
Adipose tissue	11.5 nTPM
Lymph node	7.8 nTPM
Spleen	4.9 nTPM
PBMC	4.3 nTPM
Bone marrow	2.5 nTPM
Liver	1.3 nTPM
Kidney	0.0 nTPM

Dendritic cells	10.1 nTPM
Breast	25.5 nTPM
Adipose tissue	4.7 nTPM
PBMC	0.0 nTPM

Endothelial cells	4.2 nTPM
Lung	18.7 nTPM
Eye	10.5 nTPM
Endometrium	5.1 nTPM
Esophagus	3.7 nTPM
Placenta	3.4 nTPM
Heart muscle	3.2 nTPM
Prostate	3.1 nTPM
Skeletal muscle	2.9 nTPM
Skin	2.7 nTPM
Testis	1.8 nTPM
Ovary	1.4 nTPM
Breast	1.4 nTPM
Liver	0.9 nTPM
Pancreas	0.0 nTPM

Fibroblasts	5.0 nTPM
Lung	19.0 nTPM
Heart muscle	6.1 nTPM
Prostate	5.9 nTPM
Esophagus	5.7 nTPM
Breast	4.3 nTPM
Skeletal muscle	4.2 nTPM
Stomach	3.0 nTPM
Placenta	2.2 nTPM
Skin	2.2 nTPM
Ovary	1.5 nTPM
Adipose tissue	1.2 nTPM

Intestinal goblet cells	1.9 nTPM
Colon	3.6 nTPM
Small intestine	1.1 nTPM
Rectum	1.1 nTPM

Macrophages	3.6 nTPM
Breast	17.1 nTPM
Endometrium	8.9 nTPM
Pancreas	5.1 nTPM
Spleen	4.2 nTPM
Testis	3.5 nTPM
Skeletal muscle	3.0 nTPM
Adipose tissue	3.0 nTPM
Stomach	2.9 nTPM
Lung	2.3 nTPM
Prostate	2.2 nTPM
Kidney	1.5 nTPM
Ovary	0.8 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Paneth cells	0.1 nTPM
Rectum	0.2 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	4.5 nTPM
Stomach	10.4 nTPM
Adipose tissue	7.0 nTPM
Spleen	3.5 nTPM
Bone marrow	1.7 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	4.9 nTPM
Bronchus	5.4 nTPM
Lung	4.4 nTPM

Smooth muscle cells	3.3 nTPM
Endometrium	8.7 nTPM
Breast	4.5 nTPM
Pancreas	4.2 nTPM
Heart muscle	3.2 nTPM
Prostate	3.2 nTPM
Bronchus	2.8 nTPM
Skeletal muscle	2.5 nTPM
Skin	2.1 nTPM
Adipose tissue	2.0 nTPM
Ovary	1.8 nTPM
Esophagus	1.5 nTPM

T-cells	9.1 nTPM
Breast	42.8 nTPM
Stomach	15.3 nTPM
Colon	13.8 nTPM
Endometrium	13.3 nTPM
Prostate	9.5 nTPM
Skeletal muscle	8.5 nTPM
Adipose tissue	8.2 nTPM
Spleen	7.9 nTPM
Skin	7.8 nTPM
Lung	7.6 nTPM
Lymph node	6.3 nTPM
Kidney	4.2 nTPM
Liver	4.1 nTPM
Bone marrow	2.9 nTPM
PBMC	2.3 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM

Basal keratinocytes	0.5 nTPM
Skin	0.5 nTPM

Basal prostatic cells	13.9 nTPM
Prostate	13.9 nTPM

Basal squamous epithelial cells	6.8 nTPM
Esophagus	6.8 nTPM

Collecting duct cells	5.5 nTPM
Kidney	5.5 nTPM

Undifferentiated cells	1.3 nTPM
Colon	1.7 nTPM
Small intestine	1.3 nTPM
Rectum	0.9 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