Single cell type - SECTM1 - 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.	SECTM1
Gene descriptionⁱ Full gene name according to HGNC.	Secreted and transmembrane 1
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	Membrane,Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	7

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	Intestinal epithelial cells - 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. Read more	Cell type enhanced (Distal enterocytes, Proximal enterocytes, Kupffer cells, Paneth cells, Macrophages)
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 enhanced (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 (ASC TERT1, BJ hTERT+, BJ hTERT+ SV40 Large T+, BJ hTERT+ SV40 Large T+ RasG12V, PC-3, SiHa, SK-BR-3, U-2197)
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data. Read more	Protein predicted to be secreted

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 (Distal enterocytes, Proximal enterocytes, Kupffer cells, Paneth cells, Macrophages)

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

SECTM1 is part of cluster 53 Intestinal epithelial cells - Unknown function with confidenceⁱ 1
611 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
MXD1	MAX dimerization protein 1	0.7038	53
CASP5	Caspase 5	0.6598	53
NAAA	N-acylethanolamine acid amidase	0.6527	45
SMPDL3A	Sphingomyelin phosphodiesterase acid like 3A	0.6438	45
RNF19B	Ring finger protein 19B	0.6347	41
TNFRSF1A	TNF receptor superfamily member 1A	0.6308	53
TRIM31	Tripartite motif containing 31	0.6203	53
OAS1	2'-5'-oligoadenylate synthetase 1	0.6165	53
C11orf86	Chromosome 11 open reading frame 86	0.6017	45
TMIGD1	Transmembrane and immunoglobulin domain containing 1	0.5909	45
CLCA4	Chloride channel accessory 4	0.5905	53
TMCC3	Transmembrane and coiled-coil domain family 3	0.5879	53
PTPRH	Protein tyrosine phosphatase receptor type H	0.5878	53
MYO15B	Myosin XVB	0.5849	53
CDA	Cytidine deaminase	0.5800	53

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	8.2 nTPM
Adipose tissue	11.2 nTPM
Breast	5.3 nTPM

Alveolar cells type 1	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	2.4 nTPM
Lung	2.4 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	1.0 nTPM
Colon	3.2 nTPM
Liver	2.8 nTPM
PBMC	1.4 nTPM
Breast	1.3 nTPM
Lymph node	0.6 nTPM
Adipose tissue	0.5 nTPM
Stomach	0.5 nTPM
Kidney	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Dendritic cells	1.8 nTPM
PBMC	4.0 nTPM
Adipose tissue	1.0 nTPM
Breast	0.4 nTPM

Endothelial cells	6.0 nTPM
Skin	35.1 nTPM
Skeletal muscle	10.8 nTPM
Esophagus	10.3 nTPM
Prostate	8.0 nTPM
Breast	6.5 nTPM
Liver	3.7 nTPM
Heart muscle	3.6 nTPM
Endometrium	2.2 nTPM
Placenta	1.7 nTPM
Testis	1.4 nTPM
Ovary	0.2 nTPM
Eye	0.0 nTPM
Lung	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	6.1 nTPM
Placenta	18.1 nTPM
Skin	12.5 nTPM
Esophagus	9.1 nTPM
Breast	7.2 nTPM
Adipose tissue	5.8 nTPM
Prostate	5.7 nTPM
Lung	4.5 nTPM
Skeletal muscle	3.0 nTPM
Stomach	1.5 nTPM
Heart muscle	0.3 nTPM
Ovary	0.1 nTPM

Intestinal goblet cells	8.7 nTPM
Small intestine	16.6 nTPM
Rectum	5.7 nTPM
Colon	3.6 nTPM

Macrophages	36.8 nTPM
Kidney	90.8 nTPM
Adipose tissue	69.7 nTPM
Spleen	69.5 nTPM
Bone marrow	52.4 nTPM
Skeletal muscle	52.2 nTPM
Stomach	49.8 nTPM
Prostate	41.3 nTPM
Esophagus	28.3 nTPM
Endometrium	27.3 nTPM
Testis	22.1 nTPM
Lung	17.5 nTPM
Ovary	14.6 nTPM
Breast	11.9 nTPM
Pancreas	5.1 nTPM
PBMC	0.0 nTPM

Paneth cells	48.2 nTPM
Colon	118.6 nTPM
Small intestine	18.8 nTPM
Rectum	7.1 nTPM

Plasma cells	1.1 nTPM
Adipose tissue	3.3 nTPM
Bone marrow	1.7 nTPM
Stomach	0.5 nTPM
Esophagus	0.0 nTPM
Spleen	0.0 nTPM

Respiratory ciliated cells	3.6 nTPM
Bronchus	4.3 nTPM
Lung	2.9 nTPM

Smooth muscle cells	1.8 nTPM
Prostate	7.5 nTPM
Skin	5.9 nTPM
Skeletal muscle	2.4 nTPM
Adipose tissue	1.6 nTPM
Breast	1.3 nTPM
Endometrium	0.8 nTPM
Heart muscle	0.2 nTPM
Pancreas	0.2 nTPM
Ovary	0.1 nTPM
Bronchus	0.0 nTPM
Esophagus	0.0 nTPM

T-cells	1.1 nTPM
Adipose tissue	2.4 nTPM
Skin	2.3 nTPM
Colon	1.9 nTPM
Lymph node	1.8 nTPM
Lung	1.5 nTPM
Breast	1.5 nTPM
Endometrium	1.4 nTPM
Skeletal muscle	1.3 nTPM
Stomach	1.1 nTPM
PBMC	1.0 nTPM
Liver	0.9 nTPM
Spleen	0.8 nTPM
Kidney	0.7 nTPM
Bone marrow	0.7 nTPM
Prostate	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM

Basal keratinocytes	9.4 nTPM
Skin	9.4 nTPM

Basal prostatic cells	4.6 nTPM
Prostate	4.6 nTPM

Distal enterocytes	63.4 nTPM
Rectum	86.1 nTPM
Colon	40.7 nTPM

Endometrial stromal cells	4.4 nTPM
Endometrium	4.4 nTPM

Undifferentiated cells	1.3 nTPM
Small intestine	2.0 nTPM
Colon	1.0 nTPM
Rectum	1.0 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