Single cell type - SEC61A1 - 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.	SEC61A1
Gene descriptionⁱ Full gene name according to HGNC.	SEC61 translocon subunit alpha 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes Potential drug targets Transporters
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
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	4

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	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

SEC61A1 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
TMEM214	Transmembrane protein 214	0.7781	55
SCYL1	SCY1 like pseudokinase 1	0.6467	55
LRRC59	Leucine rich repeat containing 59	0.6412	55
P4HB	Prolyl 4-hydroxylase subunit beta	0.6412	55
NCLN	Nicalin	0.6386	53
GMPPB	GDP-mannose pyrophosphorylase B	0.6331	55
SDF2L1	Stromal cell derived factor 2 like 1	0.6270	55
ARFGAP1	ADP ribosylation factor GTPase activating protein 1	0.6140	53
SLC52A2	Solute carrier family 52 member 2	0.6082	53
RABL6	RAB, member RAS oncogene family like 6	0.6056	53
RRBP1	Ribosome binding protein 1	0.6019	53
SLC39A7	Solute carrier family 39 member 7	0.6013	27
MED16	Mediator complex subunit 16	0.5972	53
ATP13A1	ATPase 13A1	0.5951	53
HM13	Histocompatibility minor 13	0.5867	55

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	31.9 nTPM
Adipose tissue	33.6 nTPM
Breast	30.2 nTPM

Alveolar cells type 1	32.1 nTPM
Lung	32.1 nTPM

Alveolar cells type 2	33.1 nTPM
Lung	33.1 nTPM

Astrocytes	18.6 nTPM
Brain	18.6 nTPM

B-cells	46.6 nTPM
Liver	177.8 nTPM
Breast	111.1 nTPM
Stomach	27.7 nTPM
Spleen	26.7 nTPM
Colon	25.5 nTPM
Kidney	23.8 nTPM
Bone marrow	23.7 nTPM
Lymph node	21.6 nTPM
PBMC	14.3 nTPM
Adipose tissue	13.5 nTPM

Dendritic cells	59.2 nTPM
PBMC	103.6 nTPM
Adipose tissue	39.5 nTPM
Breast	34.6 nTPM

Endothelial cells	45.9 nTPM
Ovary	91.1 nTPM
Pancreas	84.9 nTPM
Placenta	62.5 nTPM
Prostate	60.2 nTPM
Endometrium	57.4 nTPM
Eye	45.3 nTPM
Esophagus	40.2 nTPM
Skin	39.1 nTPM
Breast	35.9 nTPM
Liver	28.4 nTPM
Testis	27.5 nTPM
Heart muscle	26.3 nTPM
Skeletal muscle	25.2 nTPM
Lung	18.7 nTPM

Fibroblasts	57.4 nTPM
Placenta	109.5 nTPM
Ovary	86.9 nTPM
Prostate	71.8 nTPM
Stomach	60.9 nTPM
Adipose tissue	55.3 nTPM
Skin	48.2 nTPM
Esophagus	46.8 nTPM
Lung	45.8 nTPM
Breast	44.8 nTPM
Skeletal muscle	44.1 nTPM
Heart muscle	17.7 nTPM

Intestinal goblet cells	150.8 nTPM
Colon	280.9 nTPM
Small intestine	90.4 nTPM
Rectum	81.0 nTPM

Macrophages	38.2 nTPM
Ovary	76.9 nTPM
Pancreas	63.8 nTPM
Esophagus	48.7 nTPM
Endometrium	42.7 nTPM
Bone marrow	42.5 nTPM
Adipose tissue	38.5 nTPM
Spleen	38.4 nTPM
Prostate	36.7 nTPM
Breast	33.8 nTPM
Skeletal muscle	33.1 nTPM
Testis	28.4 nTPM
Kidney	28.0 nTPM
Lung	27.8 nTPM
Stomach	20.5 nTPM
PBMC	13.6 nTPM

Paneth cells	50.2 nTPM
Colon	69.2 nTPM
Rectum	58.9 nTPM
Small intestine	22.5 nTPM

Plasma cells	192.8 nTPM
Spleen	299.8 nTPM
Stomach	269.3 nTPM
Bone marrow	194.5 nTPM
Esophagus	135.4 nTPM
Adipose tissue	65.2 nTPM

Respiratory ciliated cells	31.0 nTPM
Bronchus	50.2 nTPM
Lung	11.7 nTPM

Smooth muscle cells	47.2 nTPM
Pancreas	193.3 nTPM
Ovary	53.2 nTPM
Endometrium	47.4 nTPM
Prostate	38.1 nTPM
Esophagus	35.7 nTPM
Adipose tissue	30.7 nTPM
Skin	29.6 nTPM
Skeletal muscle	27.2 nTPM
Breast	27.2 nTPM
Bronchus	23.5 nTPM
Heart muscle	13.5 nTPM

T-cells	32.4 nTPM
Colon	45.1 nTPM
Endometrium	43.4 nTPM
Stomach	41.6 nTPM
Bone marrow	41.3 nTPM
Liver	39.0 nTPM
Spleen	35.4 nTPM
Breast	34.1 nTPM
Ovary	33.3 nTPM
Adipose tissue	32.7 nTPM
PBMC	29.9 nTPM
Lymph node	29.3 nTPM
Prostate	28.4 nTPM
Skeletal muscle	26.8 nTPM
Kidney	26.7 nTPM
Lung	22.8 nTPM
Skin	21.2 nTPM
Esophagus	19.7 nTPM

Basal keratinocytes	37.0 nTPM
Skin	37.0 nTPM

Basal prostatic cells	25.7 nTPM
Prostate	25.7 nTPM

Basal respiratory cells	44.4 nTPM
Bronchus	44.4 nTPM

Cholangiocytes	37.1 nTPM
Liver	37.1 nTPM

Undifferentiated cells	100.4 nTPM
Colon	166.7 nTPM
Small intestine	70.0 nTPM
Rectum	64.3 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