Single cell type - SNX13 - 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.	SNX13
Gene descriptionⁱ Full gene name according to HGNC.	Sorting nexin 13
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	Membrane
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	Early spermatids - Spermatogenesis (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 (Early spermatids, Late spermatids)
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 some
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 (Early spermatids, Late spermatids)

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

SNX13 is part of cluster 29 Early spermatids - Spermatogenesis with confidenceⁱ 1
337 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
LTN1	Listerin E3 ubiquitin protein ligase 1	0.6209	29
C19orf71	Chromosome 19 open reading frame 71	0.6104	29
CUL2	Cullin 2	0.6021	29
SPDYE1	Speedy/RINGO cell cycle regulator family member E1	0.5813	29
ISLR2	Immunoglobulin superfamily containing leucine rich repeat 2	0.5720	29
TANGO6	Transport and golgi organization 6 homolog	0.5583	29
ZNF705B	Zinc finger protein 705B	0.5566	29
SPDYE3	Speedy/RINGO cell cycle regulator family member E3	0.5489	29
CST8	Cystatin 8	0.5462	29
SLC25A41	Solute carrier family 25 member 41	0.5454	29
VN1R2	Vomeronasal 1 receptor 2	0.5399	29
PRSS37	Serine protease 37	0.5395	29
ARID2	AT-rich interaction domain 2	0.5394	29
TP53TG5	TP53 target 5	0.5376	29
SPATA31E1	SPATA31 subfamily E member 1	0.5363	29

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	29.9 nTPM
Adipose tissue	33.0 nTPM
Breast	26.9 nTPM

Alveolar cells type 1	22.4 nTPM
Lung	22.4 nTPM

Alveolar cells type 2	32.1 nTPM
Lung	32.1 nTPM

Astrocytes	65.6 nTPM
Brain	65.6 nTPM

B-cells	24.6 nTPM
Stomach	39.5 nTPM
PBMC	32.9 nTPM
Spleen	32.2 nTPM
Lymph node	28.5 nTPM
Adipose tissue	28.1 nTPM
Breast	20.0 nTPM
Bone marrow	18.8 nTPM
Colon	17.6 nTPM
Liver	14.5 nTPM
Kidney	14.3 nTPM

Dendritic cells	20.7 nTPM
PBMC	23.9 nTPM
Adipose tissue	23.9 nTPM
Breast	14.2 nTPM

Endothelial cells	22.9 nTPM
Heart muscle	52.5 nTPM
Endometrium	30.7 nTPM
Liver	28.4 nTPM
Skeletal muscle	26.8 nTPM
Ovary	23.6 nTPM
Prostate	22.3 nTPM
Esophagus	22.0 nTPM
Breast	21.8 nTPM
Testis	20.7 nTPM
Lung	18.7 nTPM
Eye	17.8 nTPM
Skin	14.3 nTPM
Placenta	13.1 nTPM
Pancreas	7.7 nTPM

Fibroblasts	25.6 nTPM
Heart muscle	41.6 nTPM
Stomach	29.7 nTPM
Adipose tissue	28.5 nTPM
Skeletal muscle	28.2 nTPM
Prostate	28.0 nTPM
Esophagus	27.2 nTPM
Breast	25.5 nTPM
Lung	21.2 nTPM
Placenta	17.5 nTPM
Ovary	17.2 nTPM
Skin	16.7 nTPM

Intestinal goblet cells	16.1 nTPM
Rectum	23.1 nTPM
Colon	13.6 nTPM
Small intestine	11.7 nTPM

Macrophages	31.5 nTPM
Esophagus	50.4 nTPM
Ovary	46.4 nTPM
Skeletal muscle	45.7 nTPM
Spleen	44.6 nTPM
Adipose tissue	43.2 nTPM
Testis	37.8 nTPM
Stomach	35.1 nTPM
Breast	30.7 nTPM
Lung	28.9 nTPM
Bone marrow	27.5 nTPM
Kidney	25.7 nTPM
Prostate	24.1 nTPM
Endometrium	22.9 nTPM
Pancreas	10.2 nTPM
PBMC	0.0 nTPM

Paneth cells	27.7 nTPM
Small intestine	33.8 nTPM
Colon	29.6 nTPM
Rectum	19.8 nTPM

Plasma cells	21.2 nTPM
Adipose tissue	36.7 nTPM
Stomach	26.5 nTPM
Spleen	15.7 nTPM
Bone marrow	14.8 nTPM
Esophagus	12.3 nTPM

Respiratory ciliated cells	31.3 nTPM
Bronchus	32.1 nTPM
Lung	30.6 nTPM

Smooth muscle cells	24.5 nTPM
Adipose tissue	38.8 nTPM
Endometrium	30.5 nTPM
Heart muscle	28.5 nTPM
Bronchus	27.7 nTPM
Prostate	25.4 nTPM
Esophagus	24.8 nTPM
Breast	24.4 nTPM
Skeletal muscle	23.6 nTPM
Ovary	18.4 nTPM
Skin	17.1 nTPM
Pancreas	10.6 nTPM

T-cells	18.5 nTPM
Lung	28.8 nTPM
Lymph node	23.8 nTPM
Stomach	23.3 nTPM
Adipose tissue	22.7 nTPM
Skeletal muscle	22.1 nTPM
Spleen	22.0 nTPM
Bone marrow	20.1 nTPM
Endometrium	18.6 nTPM
Breast	18.5 nTPM
Ovary	17.8 nTPM
Colon	16.6 nTPM
Liver	16.2 nTPM
PBMC	15.1 nTPM
Prostate	14.2 nTPM
Esophagus	13.1 nTPM
Skin	11.1 nTPM
Kidney	9.6 nTPM

Basal prostatic cells	14.0 nTPM
Prostate	14.0 nTPM

Basal respiratory cells	15.6 nTPM
Bronchus	15.6 nTPM

Basal squamous epithelial cells	21.1 nTPM
Esophagus	21.1 nTPM

Cholangiocytes	12.8 nTPM
Liver	12.8 nTPM

Undifferentiated cells	16.3 nTPM
Rectum	19.3 nTPM
Colon	15.8 nTPM
Small intestine	13.7 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