Single cell type - VPS13D - 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.	VPS13D
Gene descriptionⁱ Full gene name according to HGNC.	Vacuolar protein sorting 13 homolog D
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes
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.	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	Neurons & Oligodendrocytes - Neuronal signaling (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 (Late spermatids, Excitatory neurons, Inhibitory neurons)
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 many
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: Cell type enhanced (Late spermatids, Excitatory neurons, Inhibitory neurons)

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

VPS13D is part of cluster 21 Neurons & Oligodendrocytes - Neuronal signaling with confidenceⁱ 1
589 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
MICAL2	Microtubule associated monooxygenase, calponin and LIM domain containing 2	0.7039	21
SUN1	Sad1 and UNC84 domain containing 1	0.6097	34
EFCAB6	EF-hand calcium binding domain 6	0.6039	31
SPIRE1	Spire type actin nucleation factor 1	0.5988	31
TIAM2	TIAM Rac1 associated GEF 2	0.5528	34
MAP2K5	Mitogen-activated protein kinase kinase 5	0.5360	21
TRPC5OS	TRPC5 opposite strand	0.5357	21
PNPLA5	Patatin like phospholipase domain containing 5	0.5306	31
CPNE9	Copine family member 9	0.5283	31
DLGAP2	DLG associated protein 2	0.5190	21
NPIPB8	Nuclear pore complex interacting protein family member B8	0.5174	34
ATP6V1A	ATPase H+ transporting V1 subunit A	0.5169	31
TRPC5	Transient receptor potential cation channel subfamily C member 5	0.5093	21
CEMIP	Cell migration inducing hyaluronidase 1	0.5092	21
MAST4	Microtubule associated serine/threonine kinase family member 4	0.5084	22

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	28.9 nTPM
Adipose tissue	34.6 nTPM
Breast	23.2 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	23.4 nTPM
Lung	23.4 nTPM

Astrocytes	111.0 nTPM
Brain	111.0 nTPM

B-cells	19.8 nTPM
Bone marrow	36.0 nTPM
Lymph node	26.3 nTPM
Stomach	24.5 nTPM
Spleen	23.6 nTPM
Adipose tissue	21.0 nTPM
PBMC	20.0 nTPM
Breast	14.7 nTPM
Liver	13.1 nTPM
Colon	9.6 nTPM
Kidney	9.5 nTPM

Dendritic cells	20.3 nTPM
Adipose tissue	27.4 nTPM
PBMC	20.0 nTPM
Breast	13.5 nTPM

Endothelial cells	23.0 nTPM
Heart muscle	62.6 nTPM
Skeletal muscle	29.4 nTPM
Liver	27.5 nTPM
Eye	25.1 nTPM
Testis	24.6 nTPM
Endometrium	24.6 nTPM
Ovary	23.0 nTPM
Esophagus	20.1 nTPM
Breast	19.9 nTPM
Prostate	19.8 nTPM
Pancreas	15.5 nTPM
Skin	12.0 nTPM
Lung	9.3 nTPM
Placenta	8.6 nTPM

Fibroblasts	19.4 nTPM
Heart muscle	38.7 nTPM
Skeletal muscle	28.7 nTPM
Prostate	25.6 nTPM
Adipose tissue	19.6 nTPM
Stomach	17.8 nTPM
Lung	16.8 nTPM
Esophagus	16.6 nTPM
Ovary	15.3 nTPM
Breast	14.3 nTPM
Skin	11.2 nTPM
Placenta	9.2 nTPM

Intestinal goblet cells	15.1 nTPM
Rectum	23.2 nTPM
Small intestine	11.4 nTPM
Colon	10.7 nTPM

Macrophages	17.5 nTPM
Skeletal muscle	29.6 nTPM
Bone marrow	28.7 nTPM
Endometrium	21.9 nTPM
Spleen	21.8 nTPM
Adipose tissue	20.5 nTPM
Testis	19.7 nTPM
Breast	19.2 nTPM
Ovary	19.1 nTPM
Esophagus	18.9 nTPM
Lung	18.8 nTPM
Pancreas	12.8 nTPM
Stomach	11.7 nTPM
Prostate	11.5 nTPM
Kidney	7.6 nTPM
PBMC	0.0 nTPM

Paneth cells	11.2 nTPM
Rectum	19.0 nTPM
Small intestine	11.3 nTPM
Colon	3.3 nTPM

Plasma cells	11.8 nTPM
Adipose tissue	31.0 nTPM
Spleen	11.4 nTPM
Stomach	8.9 nTPM
Esophagus	6.1 nTPM
Bone marrow	1.7 nTPM

Respiratory ciliated cells	32.0 nTPM
Bronchus	42.1 nTPM
Lung	21.9 nTPM

Smooth muscle cells	46.5 nTPM
Heart muscle	138.4 nTPM
Esophagus	66.7 nTPM
Endometrium	62.0 nTPM
Prostate	59.0 nTPM
Skeletal muscle	43.6 nTPM
Adipose tissue	41.0 nTPM
Skin	35.2 nTPM
Breast	26.0 nTPM
Ovary	16.8 nTPM
Bronchus	16.7 nTPM
Pancreas	6.6 nTPM

T-cells	21.4 nTPM
Skeletal muscle	34.3 nTPM
Adipose tissue	32.0 nTPM
Bone marrow	26.8 nTPM
Ovary	26.7 nTPM
Lymph node	24.2 nTPM
Endometrium	22.9 nTPM
PBMC	22.6 nTPM
Stomach	21.3 nTPM
Breast	21.3 nTPM
Spleen	20.6 nTPM
Esophagus	19.7 nTPM
Prostate	19.0 nTPM
Liver	17.3 nTPM
Lung	16.7 nTPM
Skin	14.3 nTPM
Colon	12.8 nTPM
Kidney	10.9 nTPM

Basal keratinocytes	21.7 nTPM
Skin	21.7 nTPM

Basal prostatic cells	45.1 nTPM
Prostate	45.1 nTPM

Collecting duct cells	18.4 nTPM
Kidney	18.4 nTPM

Cone photoreceptor cells	73.0 nTPM
Eye	73.0 nTPM

Undifferentiated cells	15.5 nTPM
Rectum	21.0 nTPM
Colon	15.1 nTPM
Small intestine	10.3 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