Single cell type - CISD3 - 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.	CISD3
Gene descriptionⁱ Full gene name according to HGNC.	CDGSH iron sulfur domain 3
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
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	1

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	Enterocytes - Digestion (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 (Proximal enterocytes, Hepatocytes, Proximal tubular cells, Distal enterocytes, Paneth cells, Undifferentiated 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 (AN3-CA, U-138 MG)
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 (Proximal enterocytes, Hepatocytes, Proximal tubular cells, Distal enterocytes, Paneth cells, Undifferentiated 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

CISD3 is part of cluster 45 Enterocytes - Digestion with confidenceⁱ 1
268 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
SUCLG2	Succinate-CoA ligase GDP-forming subunit beta	0.6716	53
CDX1	Caudal type homeobox 1	0.6530	53
MRPL12	Mitochondrial ribosomal protein L12	0.6486	53
MPND	MPN domain containing	0.6308	53
NDUFB7	NADH:ubiquinone oxidoreductase subunit B7	0.6123	53
ACADS	Acyl-CoA dehydrogenase short chain	0.5987	45
ASL	Argininosuccinate lyase	0.5969	53
SLC39A5	Solute carrier family 39 member 5	0.5954	45
TONSL	Tonsoku like, DNA repair protein	0.5952	45
ISX	Intestine specific homeobox	0.5939	53
CHCHD10	Coiled-coil-helix-coiled-coil-helix domain containing 10	0.5910	39
CYC1	Cytochrome c1	0.5859	39
HNF4A	Hepatocyte nuclear factor 4 alpha	0.5782	53
SURF6	Surfeit 6	0.5752	53
VIL1	Villin 1	0.5709	45

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	58.6 nTPM
Breast	84.2 nTPM
Adipose tissue	33.0 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	23.6 nTPM
Lung	23.6 nTPM

Astrocytes	6.2 nTPM
Brain	6.2 nTPM

B-cells	21.4 nTPM
Liver	46.4 nTPM
Kidney	38.1 nTPM
Colon	27.1 nTPM
Breast	21.3 nTPM
PBMC	20.0 nTPM
Stomach	20.0 nTPM
Spleen	17.6 nTPM
Bone marrow	11.5 nTPM
Lymph node	7.0 nTPM
Adipose tissue	5.5 nTPM

Dendritic cells	44.7 nTPM
Breast	80.5 nTPM
PBMC	27.9 nTPM
Adipose tissue	25.7 nTPM

Endothelial cells	41.9 nTPM
Heart muscle	91.3 nTPM
Breast	75.2 nTPM
Liver	65.1 nTPM
Placenta	46.6 nTPM
Skin	44.3 nTPM
Skeletal muscle	35.7 nTPM
Testis	35.0 nTPM
Eye	33.2 nTPM
Esophagus	32.9 nTPM
Prostate	31.7 nTPM
Ovary	30.4 nTPM
Pancreas	23.1 nTPM
Lung	21.8 nTPM
Endometrium	20.0 nTPM

Enteroendocrine cells	129.0 nTPM
Rectum	140.8 nTPM
Colon	117.2 nTPM

Fibroblasts	41.8 nTPM
Heart muscle	123.3 nTPM
Skin	54.6 nTPM
Adipose tissue	44.5 nTPM
Ovary	42.3 nTPM
Breast	36.2 nTPM
Skeletal muscle	31.9 nTPM
Prostate	31.6 nTPM
Esophagus	28.9 nTPM
Placenta	25.5 nTPM
Stomach	22.3 nTPM
Lung	19.0 nTPM

Intestinal goblet cells	262.5 nTPM
Colon	299.4 nTPM
Small intestine	254.8 nTPM
Rectum	233.4 nTPM

Macrophages	58.3 nTPM
Pancreas	196.5 nTPM
Kidney	131.5 nTPM
Testis	73.2 nTPM
Ovary	59.2 nTPM
Esophagus	51.9 nTPM
Breast	48.8 nTPM
Bone marrow	48.7 nTPM
Prostate	48.2 nTPM
Spleen	46.7 nTPM
Stomach	38.1 nTPM
Skeletal muscle	37.8 nTPM
Endometrium	35.6 nTPM
Lung	34.0 nTPM
Adipose tissue	23.8 nTPM
PBMC	0.0 nTPM

Paneth cells	406.2 nTPM
Colon	467.7 nTPM
Small intestine	409.2 nTPM
Rectum	341.7 nTPM

Plasma cells	24.0 nTPM
Spleen	47.5 nTPM
Bone marrow	29.7 nTPM
Stomach	28.5 nTPM
Adipose tissue	14.2 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	21.5 nTPM
Bronchus	27.1 nTPM
Lung	16.0 nTPM

Smooth muscle cells	72.2 nTPM
Heart muscle	192.6 nTPM
Bronchus	144.8 nTPM
Pancreas	85.3 nTPM
Breast	77.1 nTPM
Esophagus	63.6 nTPM
Skin	49.8 nTPM
Adipose tissue	48.0 nTPM
Prostate	45.9 nTPM
Skeletal muscle	44.0 nTPM
Ovary	23.3 nTPM
Endometrium	19.7 nTPM

Basal keratinocytes	26.5 nTPM
Skin	26.5 nTPM

Basal prostatic cells	41.4 nTPM
Prostate	41.4 nTPM

Basal respiratory cells	27.3 nTPM
Bronchus	27.3 nTPM

Basal squamous epithelial cells	22.8 nTPM
Esophagus	22.8 nTPM

T-cells	47.2 nTPM
Kidney	131.4 nTPM
Liver	88.0 nTPM
Bone marrow	82.4 nTPM
Stomach	64.7 nTPM
Ovary	62.3 nTPM
Spleen	48.2 nTPM
PBMC	46.5 nTPM
Colon	45.6 nTPM
Skeletal muscle	39.1 nTPM
Skin	37.3 nTPM
Breast	36.0 nTPM
Endometrium	33.0 nTPM
Lung	22.8 nTPM
Esophagus	19.7 nTPM
Prostate	19.0 nTPM
Lymph node	14.7 nTPM
Adipose tissue	11.9 nTPM

Undifferentiated cells	398.5 nTPM
Colon	471.8 nTPM
Small intestine	374.5 nTPM
Rectum	349.1 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