Single cell type - SYBU - 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.	SYBU
Gene descriptionⁱ Full gene name according to HGNC.	Syntabulin
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.	32

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 (Excitatory neurons, Inhibitory neurons, Horizontal 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	Group enriched (memory B-cell, naive B-cell)
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	Cell line enhanced (HaCaT, PC-3, SK-BR-3)
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 (Excitatory neurons, Inhibitory neurons, Horizontal 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

SYBU 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
ATP2B2	ATPase plasma membrane Ca2+ transporting 2	0.7604	21
KSR2	Kinase suppressor of ras 2	0.7465	21
ST6GALNAC5	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	0.7062	21
FSTL4	Follistatin like 4	0.7026	21
NDST3	N-deacetylase and N-sulfotransferase 3	0.7005	21
EPHX4	Epoxide hydrolase 4	0.6923	21
SLC4A10	Solute carrier family 4 member 10	0.6906	21
KHDRBS2	KH RNA binding domain containing, signal transduction associated 2	0.6875	21
C11orf87	Chromosome 11 open reading frame 87	0.6823	21
DRP2	Dystrophin related protein 2	0.6816	21
LRFN5	Leucine rich repeat and fibronectin type III domain containing 5	0.6785	21
LDB2	LIM domain binding 2	0.6783	21
SLC35F3	Solute carrier family 35 member F3	0.6782	21
FOCAD	Focadhesin	0.6689	21
DLGAP2	DLG associated protein 2	0.6686	21

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	39.3 nTPM
Adipose tissue	48.9 nTPM
Breast	29.7 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	7.7 nTPM
Lung	7.7 nTPM

Astrocytes	16.0 nTPM
Brain	16.0 nTPM

B-cells	4.3 nTPM
Kidney	9.5 nTPM
Bone marrow	7.4 nTPM
PBMC	5.7 nTPM
Spleen	4.5 nTPM
Adipose tissue	4.0 nTPM
Breast	4.0 nTPM
Colon	3.2 nTPM
Lymph node	2.6 nTPM
Stomach	1.4 nTPM
Liver	1.3 nTPM

Dendritic cells	0.1 nTPM
Breast	0.4 nTPM
Adipose tissue	0.1 nTPM
PBMC	0.0 nTPM

Endothelial cells	11.8 nTPM
Esophagus	42.0 nTPM
Skin	30.7 nTPM
Skeletal muscle	25.0 nTPM
Breast	19.0 nTPM
Prostate	13.0 nTPM
Heart muscle	9.5 nTPM
Testis	8.6 nTPM
Lung	6.2 nTPM
Eye	4.8 nTPM
Placenta	4.0 nTPM
Endometrium	1.9 nTPM
Ovary	1.2 nTPM
Liver	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	7.9 nTPM
Adipose tissue	23.6 nTPM
Skin	20.4 nTPM
Heart muscle	9.7 nTPM
Breast	9.3 nTPM
Skeletal muscle	6.8 nTPM
Esophagus	4.7 nTPM
Lung	4.5 nTPM
Stomach	4.4 nTPM
Prostate	2.9 nTPM
Placenta	0.3 nTPM
Ovary	0.2 nTPM

Intestinal goblet cells	22.2 nTPM
Rectum	26.6 nTPM
Small intestine	25.1 nTPM
Colon	15.0 nTPM

Macrophages	0.3 nTPM
Esophagus	1.6 nTPM
Skeletal muscle	1.2 nTPM
Endometrium	1.0 nTPM
Lung	0.8 nTPM
Breast	0.3 nTPM
Ovary	0.1 nTPM
Adipose tissue	0.1 nTPM
Kidney	0.0 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	9.8 nTPM
Small intestine	15.0 nTPM
Rectum	14.4 nTPM
Colon	0.0 nTPM

Plasma cells	0.1 nTPM
Adipose tissue	0.6 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Respiratory ciliated cells	15.6 nTPM
Lung	16.0 nTPM
Bronchus	15.2 nTPM

Smooth muscle cells	4.2 nTPM
Bronchus	7.5 nTPM
Skin	7.3 nTPM
Esophagus	6.2 nTPM
Adipose tissue	5.4 nTPM
Prostate	5.0 nTPM
Heart muscle	4.8 nTPM
Breast	4.1 nTPM
Skeletal muscle	2.9 nTPM
Pancreas	1.5 nTPM
Ovary	0.8 nTPM
Endometrium	0.4 nTPM

T-cells	0.6 nTPM
Skin	4.1 nTPM
Endometrium	2.1 nTPM
Breast	1.1 nTPM
Colon	1.0 nTPM
Kidney	0.7 nTPM
Skeletal muscle	0.5 nTPM
Stomach	0.4 nTPM
Liver	0.2 nTPM
Adipose tissue	0.2 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Basal prostatic cells	2.5 nTPM
Prostate	2.5 nTPM

Basal respiratory cells	8.3 nTPM
Bronchus	8.3 nTPM

Basal squamous epithelial cells	17.1 nTPM
Esophagus	17.1 nTPM

Cholangiocytes	30.0 nTPM
Liver	30.0 nTPM

Undifferentiated cells	13.7 nTPM
Small intestine	23.8 nTPM
Rectum	12.7 nTPM
Colon	4.5 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