Single cell type - SCAMP5 - 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.	SCAMP5
Gene descriptionⁱ Full gene name according to HGNC.	Secretory carrier membrane protein 5
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.	11

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	Photoreceptor cells - Phototransduction (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 (Rod photoreceptor cells, Cone photoreceptor cells, Bipolar cells, Inhibitory neurons, Excitatory neurons, Horizontal cells, Enteroendocrine 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 (plasmacytoid DC)
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 single
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 (SCLC-21H, SH-SY5Y, THP-1)
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 (Rod photoreceptor cells, Cone photoreceptor cells, Bipolar cells, Inhibitory neurons, Excitatory neurons, Horizontal cells, Enteroendocrine 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

SCAMP5 is part of cluster 46 Photoreceptor cells - Phototransduction with confidenceⁱ 0.91
209 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
PACSIN1	Protein kinase C and casein kinase substrate in neurons 1	0.7623	9
SEZ6L2	Seizure related 6 homolog like 2	0.6079	56
SYP	Synaptophysin	0.5987	9
SRRM4	Serine/arginine repetitive matrix 4	0.5820	9
CDK5R2	Cyclin dependent kinase 5 regulatory subunit 2	0.5727	56
IGFL4	IGF like family member 4	0.5698	46
ZNF883	Zinc finger protein 883	0.5695	56
ELOVL4	ELOVL fatty acid elongase 4	0.5635	46
GAL3ST3	Galactose-3-O-sulfotransferase 3	0.5630	46
DRD4	Dopamine receptor D4	0.5624	56
SLC32A1	Solute carrier family 32 member 1	0.5612	65
AP3B2	Adaptor related protein complex 3 subunit beta 2	0.5588	46
FBXO16	F-box protein 16	0.5584	46
MANEAL	Mannosidase endo-alpha like	0.5568	17
SCG3	Secretogranin III	0.5553	62

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	2.2 nTPM
Breast	3.0 nTPM
Adipose tissue	1.3 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	1.1 nTPM
Lung	1.1 nTPM

Astrocytes	14.7 nTPM
Brain	14.7 nTPM

B-cells	2.5 nTPM
Breast	9.4 nTPM
Liver	8.8 nTPM
Kidney	4.8 nTPM
Stomach	0.9 nTPM
Bone marrow	0.8 nTPM
Spleen	0.3 nTPM
Colon	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Lymph node	0.0 nTPM

Dendritic cells	35.5 nTPM
PBMC	103.6 nTPM
Adipose tissue	2.5 nTPM
Breast	0.4 nTPM

Endothelial cells	3.6 nTPM
Ovary	14.6 nTPM
Eye	9.7 nTPM
Esophagus	6.2 nTPM
Endometrium	5.4 nTPM
Breast	4.2 nTPM
Placenta	4.0 nTPM
Skin	2.7 nTPM
Skeletal muscle	1.0 nTPM
Testis	0.9 nTPM
Prostate	0.7 nTPM
Heart muscle	0.6 nTPM
Liver	0.0 nTPM
Lung	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	1.9 nTPM
Stomach	7.4 nTPM
Ovary	4.4 nTPM
Heart muscle	2.8 nTPM
Esophagus	2.1 nTPM
Lung	1.2 nTPM
Breast	0.9 nTPM
Placenta	0.8 nTPM
Skeletal muscle	0.5 nTPM
Adipose tissue	0.5 nTPM
Prostate	0.2 nTPM
Skin	0.2 nTPM

Intestinal goblet cells	5.0 nTPM
Small intestine	13.5 nTPM
Rectum	1.4 nTPM
Colon	0.0 nTPM

Macrophages	2.0 nTPM
Ovary	8.4 nTPM
Breast	4.6 nTPM
Endometrium	4.4 nTPM
Kidney	2.3 nTPM
Skeletal muscle	2.3 nTPM
Spleen	2.1 nTPM
Esophagus	1.6 nTPM
Adipose tissue	1.3 nTPM
Prostate	1.2 nTPM
Bone marrow	1.2 nTPM
Testis	0.6 nTPM
Lung	0.3 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	5.3 nTPM
Small intestine	7.5 nTPM
Colon	6.5 nTPM
Rectum	1.9 nTPM

Plasma cells	8.9 nTPM
Stomach	18.9 nTPM
Spleen	12.3 nTPM
Bone marrow	11.5 nTPM
Adipose tissue	1.9 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	2.7 nTPM
Lung	2.9 nTPM
Bronchus	2.6 nTPM

Smooth muscle cells	2.8 nTPM
Bronchus	14.3 nTPM
Pancreas	4.7 nTPM
Esophagus	3.1 nTPM
Ovary	2.4 nTPM
Skin	1.4 nTPM
Breast	1.3 nTPM
Heart muscle	1.1 nTPM
Adipose tissue	0.9 nTPM
Endometrium	0.7 nTPM
Prostate	0.6 nTPM
Skeletal muscle	0.3 nTPM

T-cells	0.6 nTPM
Lung	4.5 nTPM
Kidney	1.4 nTPM
Breast	1.4 nTPM
Liver	0.7 nTPM
Colon	0.5 nTPM
PBMC	0.5 nTPM
Spleen	0.5 nTPM
Endometrium	0.3 nTPM
Adipose tissue	0.1 nTPM
Stomach	0.1 nTPM
Prostate	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM

Cholangiocytes	7.2 nTPM
Liver	7.2 nTPM

Collecting duct cells	5.5 nTPM
Kidney	5.5 nTPM

Exocrine glandular cells	43.3 nTPM
Pancreas	43.3 nTPM

Undifferentiated cells	2.7 nTPM
Small intestine	5.8 nTPM
Rectum	2.1 nTPM
Colon	0.3 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