Single cell type - COL3A1 - 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.	COL3A1
Gene descriptionⁱ Full gene name according to HGNC.	Collagen type III alpha 1 chain
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes FDA approved drug targets Human disease related genes 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,Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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	Fibroblasts - ECM organization (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 (Endometrial stromal cells, Fibroblasts, Smooth muscle cells, Theca 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	Not detected in immune cells
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	Not detected
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 (AF22, ASC diff, ASC TERT1, fHDF/TERT166, HHSteC, HSkMC)
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 (Endometrial stromal cells, Fibroblasts, Smooth muscle cells, Theca 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

COL3A1 is part of cluster 33 Fibroblasts - ECM organization with confidenceⁱ 1
171 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
COL5A1	Collagen type V alpha 1 chain	0.9669	33
COL1A1	Collagen type I alpha 1 chain	0.9546	33
COL6A1	Collagen type VI alpha 1 chain	0.8929	33
RCN3	Reticulocalbin 3	0.8729	33
LUM	Lumican	0.8676	33
OLFML3	Olfactomedin like 3	0.8321	33
LBHD2	LBH domain containing 2	0.8250	33
COL5A2	Collagen type V alpha 2 chain	0.8189	33
FKBP10	FKBP prolyl isomerase 10	0.8150	33
CTHRC1	Collagen triple helix repeat containing 1	0.8096	33
GPX7	Glutathione peroxidase 7	0.8033	33
COL1A2	Collagen type I alpha 2 chain	0.8015	33
MMP23B	Matrix metallopeptidase 23B	0.7980	33
ENPP1	Ectonucleotide pyrophosphatase/phosphodiesterase 1	0.7863	33
COL6A2	Collagen type VI alpha 2 chain	0.7730	33

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	111.8 nTPM
Adipose tissue	128.8 nTPM
Breast	94.8 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	13.7 nTPM
Lung	13.7 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	0.6 nTPM
Breast	2.6 nTPM
Liver	1.8 nTPM
Stomach	1.8 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Dendritic cells	1.6 nTPM
Breast	4.0 nTPM
Adipose tissue	0.7 nTPM
PBMC	0.0 nTPM

Endothelial cells	68.4 nTPM
Endometrium	248.4 nTPM
Skin	196.5 nTPM
Placenta	160.3 nTPM
Skeletal muscle	70.7 nTPM
Testis	57.8 nTPM
Lung	56.1 nTPM
Liver	48.6 nTPM
Breast	43.0 nTPM
Heart muscle	32.8 nTPM
Prostate	15.8 nTPM
Ovary	14.8 nTPM
Eye	8.9 nTPM
Esophagus	4.2 nTPM
Pancreas	0.0 nTPM

Fibroblasts	1764.2 nTPM
Placenta	6322.1 nTPM
Adipose tissue	3117.4 nTPM
Skin	2801.7 nTPM
Breast	1986.5 nTPM
Skeletal muscle	1981.3 nTPM
Ovary	1411.4 nTPM
Stomach	558.3 nTPM
Esophagus	467.9 nTPM
Lung	412.2 nTPM
Heart muscle	257.4 nTPM
Prostate	90.4 nTPM

Intestinal goblet cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Macrophages	17.5 nTPM
Endometrium	144.9 nTPM
Skeletal muscle	83.5 nTPM
Lung	7.3 nTPM
Breast	6.8 nTPM
Esophagus	6.3 nTPM
Testis	4.6 nTPM
Adipose tissue	4.3 nTPM
Pancreas	2.5 nTPM
Prostate	2.2 nTPM
Ovary	0.2 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

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

Plasma cells	1.5 nTPM
Adipose tissue	7.0 nTPM
Stomach	0.5 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Respiratory ciliated cells	1.6 nTPM
Lung	2.9 nTPM
Bronchus	0.2 nTPM

Smooth muscle cells	643.0 nTPM
Pancreas	2222.7 nTPM
Endometrium	2167.3 nTPM
Adipose tissue	1055.6 nTPM
Skin	349.4 nTPM
Ovary	325.1 nTPM
Skeletal muscle	306.7 nTPM
Heart muscle	237.2 nTPM
Breast	179.1 nTPM
Prostate	120.6 nTPM
Esophagus	65.2 nTPM
Bronchus	44.2 nTPM

T-cells	29.1 nTPM
Skin	221.0 nTPM
Endometrium	189.8 nTPM
Skeletal muscle	66.7 nTPM
Lung	9.1 nTPM
Breast	4.4 nTPM
Liver	2.1 nTPM
Stomach	0.6 nTPM
Adipose tissue	0.3 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Basal keratinocytes	171.6 nTPM
Skin	171.6 nTPM

Basal prostatic cells	0.4 nTPM
Prostate	0.4 nTPM

Basal respiratory cells	1.9 nTPM
Bronchus	1.9 nTPM

Basal squamous epithelial cells	3.4 nTPM
Esophagus	3.4 nTPM

Undifferentiated cells	0.0 nTPM
Rectum	0.1 nTPM
Colon	0.0 nTPM
Small intestine	0.0 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