Single cell type - SCAMP1 - 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.	SCAMP1
Gene descriptionⁱ Full gene name according to HGNC.	Secretory carrier membrane protein 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	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	Intracellular,Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	5

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	Bipolar cells - Visual perception (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

SCAMP1 is part of cluster 56 Bipolar cells - Visual perception with confidenceⁱ 1
199 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
ZNF229	Zinc finger protein 229	0.4944	52
GAL3ST3	Galactose-3-O-sulfotransferase 3	0.4920	46
DAAM1	Dishevelled associated activator of morphogenesis 1	0.4904	28
CALY	Calcyon neuron specific vesicular protein	0.4634	56
BSPH1	Binder of sperm protein homolog 1	0.4585	56
KIF21A	Kinesin family member 21A	0.4539	56
CLSTN1	Calsyntenin 1	0.4535	53
ZNF883	Zinc finger protein 883	0.4474	56
BTC	Betacellulin	0.4444	49
LAPTM4B	Lysosomal protein transmembrane 4 beta	0.4378	46
TCEAL2	Transcription elongation factor A like 2	0.4270	56
DGKE	Diacylglycerol kinase epsilon	0.4241	56
AMIGO1	Adhesion molecule with Ig like domain 1	0.4201	56
BEX1	Brain expressed X-linked 1	0.4198	5
UBE2QL1	Ubiquitin conjugating enzyme E2 Q family like 1	0.4148	46

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	59.5 nTPM
Adipose tissue	79.2 nTPM
Breast	39.8 nTPM

Alveolar cells type 1	25.6 nTPM
Lung	25.6 nTPM

Alveolar cells type 2	22.4 nTPM
Lung	22.4 nTPM

Astrocytes	45.7 nTPM
Brain	45.7 nTPM

B-cells	20.3 nTPM
Stomach	32.7 nTPM
Spleen	27.6 nTPM
Lymph node	27.4 nTPM
Bone marrow	24.5 nTPM
Breast	22.8 nTPM
Adipose tissue	21.6 nTPM
Liver	16.5 nTPM
PBMC	15.7 nTPM
Kidney	9.5 nTPM
Colon	4.8 nTPM

Dendritic cells	21.7 nTPM
PBMC	23.9 nTPM
Adipose tissue	23.6 nTPM
Breast	17.5 nTPM

Endothelial cells	31.4 nTPM
Lung	56.1 nTPM
Eye	51.8 nTPM
Heart muscle	35.6 nTPM
Breast	35.4 nTPM
Liver	33.9 nTPM
Skin	33.5 nTPM
Prostate	32.2 nTPM
Skeletal muscle	30.9 nTPM
Ovary	29.1 nTPM
Esophagus	27.3 nTPM
Testis	25.5 nTPM
Endometrium	24.0 nTPM
Placenta	17.0 nTPM
Pancreas	7.7 nTPM

Fibroblasts	34.3 nTPM
Adipose tissue	50.3 nTPM
Skin	42.1 nTPM
Lung	36.9 nTPM
Heart muscle	36.0 nTPM
Breast	36.0 nTPM
Esophagus	34.7 nTPM
Stomach	34.1 nTPM
Prostate	33.8 nTPM
Skeletal muscle	33.6 nTPM
Placenta	21.1 nTPM
Ovary	19.0 nTPM

Intestinal goblet cells	34.2 nTPM
Rectum	39.1 nTPM
Small intestine	35.6 nTPM
Colon	27.9 nTPM

Macrophages	25.1 nTPM
Spleen	39.4 nTPM
Ovary	37.8 nTPM
Stomach	35.1 nTPM
Adipose tissue	33.5 nTPM
Testis	32.0 nTPM
Lung	26.8 nTPM
Esophagus	25.2 nTPM
Kidney	24.2 nTPM
Skeletal muscle	22.2 nTPM
Bone marrow	20.0 nTPM
Endometrium	19.8 nTPM
Breast	17.5 nTPM
Prostate	16.0 nTPM
PBMC	13.6 nTPM
Pancreas	12.8 nTPM

Paneth cells	14.9 nTPM
Rectum	24.1 nTPM
Colon	13.2 nTPM
Small intestine	7.5 nTPM

Plasma cells	23.9 nTPM
Esophagus	30.7 nTPM
Stomach	26.9 nTPM
Adipose tissue	21.9 nTPM
Spleen	20.1 nTPM
Bone marrow	19.8 nTPM

Respiratory ciliated cells	65.4 nTPM
Lung	77.3 nTPM
Bronchus	53.5 nTPM

Smooth muscle cells	25.4 nTPM
Heart muscle	34.1 nTPM
Esophagus	32.5 nTPM
Adipose tissue	31.1 nTPM
Skin	30.3 nTPM
Endometrium	26.7 nTPM
Breast	26.0 nTPM
Ovary	25.7 nTPM
Pancreas	22.0 nTPM
Skeletal muscle	19.5 nTPM
Prostate	17.5 nTPM
Bronchus	14.2 nTPM

T-cells	21.2 nTPM
Adipose tissue	31.9 nTPM
Prostate	28.4 nTPM
Lymph node	28.0 nTPM
Spleen	25.8 nTPM
Skin	24.9 nTPM
Ovary	24.5 nTPM
Stomach	23.5 nTPM
Kidney	22.6 nTPM
Skeletal muscle	22.4 nTPM
Bone marrow	22.3 nTPM
Breast	22.0 nTPM
Endometrium	19.5 nTPM
Colon	18.5 nTPM
Lung	13.6 nTPM
Liver	12.9 nTPM
PBMC	12.1 nTPM
Esophagus	6.6 nTPM

Basal prostatic cells	31.5 nTPM
Prostate	31.5 nTPM

Basal squamous epithelial cells	38.7 nTPM
Esophagus	38.7 nTPM

Cholangiocytes	21.5 nTPM
Liver	21.5 nTPM

Collecting duct cells	40.5 nTPM
Kidney	40.5 nTPM

Undifferentiated cells	18.8 nTPM
Rectum	21.8 nTPM
Small intestine	19.0 nTPM
Colon	15.7 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