Single cell type - SF3B3 - 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.	SF3B3
Gene descriptionⁱ Full gene name according to HGNC.	Splicing factor 3b subunit 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Plasma proteins
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.	6

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	Non-specific - Transcription (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	Low cell type specificity
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 all
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: Low cell type specificity

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

SF3B3 is part of cluster 59 Non-specific - Transcription with confidenceⁱ 0.98
354 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
POLR1A	RNA polymerase I subunit A	0.6554	59
LRRC14	Leucine rich repeat containing 14	0.5895	59
RPAP1	RNA polymerase II associated protein 1	0.5617	52
UTP20	UTP20 small subunit processome component	0.5491	59
KPNB1	Karyopherin subunit beta 1	0.5486	55
GEMIN5	Gem nuclear organelle associated protein 5	0.5429	59
KHDRBS1	KH RNA binding domain containing, signal transduction associated 1	0.5209	59
MEN1	Menin 1	0.5123	39
MCM3AP	Minichromosome maintenance complex component 3 associated protein	0.5006	59
GTF2H3	General transcription factor IIH subunit 3	0.4954	59
HEATR1	HEAT repeat containing 1	0.4944	59
PRKDC	Protein kinase, DNA-activated, catalytic subunit	0.4935	36
STAR	Steroidogenic acute regulatory protein	0.4867	52
YLPM1	YLP motif containing 1	0.4841	52
GART	Phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	0.4828	39

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	18.9 nTPM
Adipose tissue	19.2 nTPM
Breast	18.6 nTPM

Alveolar cells type 1	25.6 nTPM
Lung	25.6 nTPM

Alveolar cells type 2	25.7 nTPM
Lung	25.7 nTPM

Astrocytes	16.6 nTPM
Brain	16.6 nTPM

B-cells	33.0 nTPM
Bone marrow	46.6 nTPM
Stomach	39.1 nTPM
Spleen	38.7 nTPM
Lymph node	35.6 nTPM
Colon	35.1 nTPM
Liver	34.9 nTPM
Kidney	28.5 nTPM
PBMC	27.1 nTPM
Breast	26.8 nTPM
Adipose tissue	17.1 nTPM

Dendritic cells	21.6 nTPM
Breast	28.8 nTPM
Adipose tissue	23.9 nTPM
PBMC	12.0 nTPM

Endothelial cells	25.4 nTPM
Ovary	38.3 nTPM
Pancreas	34.7 nTPM
Placenta	33.5 nTPM
Endometrium	32.5 nTPM
Prostate	30.9 nTPM
Testis	24.9 nTPM
Liver	24.7 nTPM
Skeletal muscle	22.7 nTPM
Esophagus	21.7 nTPM
Eye	20.3 nTPM
Breast	19.1 nTPM
Lung	18.7 nTPM
Heart muscle	16.8 nTPM
Skin	16.3 nTPM

Fibroblasts	24.2 nTPM
Ovary	64.0 nTPM
Placenta	28.4 nTPM
Skeletal muscle	25.6 nTPM
Stomach	25.3 nTPM
Prostate	23.0 nTPM
Adipose tissue	21.6 nTPM
Esophagus	20.9 nTPM
Breast	20.1 nTPM
Skin	15.2 nTPM
Lung	13.4 nTPM
Heart muscle	9.0 nTPM

Intestinal goblet cells	21.8 nTPM
Rectum	27.0 nTPM
Small intestine	22.7 nTPM
Colon	15.7 nTPM

Macrophages	19.2 nTPM
Bone marrow	31.2 nTPM
Testis	28.4 nTPM
Ovary	25.7 nTPM
Esophagus	22.0 nTPM
Spleen	21.8 nTPM
Endometrium	20.9 nTPM
Stomach	20.5 nTPM
Lung	19.0 nTPM
Skeletal muscle	18.4 nTPM
Pancreas	17.8 nTPM
Breast	16.5 nTPM
Adipose tissue	16.1 nTPM
Kidney	15.8 nTPM
Prostate	13.8 nTPM
PBMC	0.0 nTPM

Paneth cells	14.0 nTPM
Rectum	23.7 nTPM
Small intestine	15.0 nTPM
Colon	3.3 nTPM

Plasma cells	25.1 nTPM
Spleen	40.6 nTPM
Bone marrow	36.2 nTPM
Esophagus	18.4 nTPM
Stomach	15.9 nTPM
Adipose tissue	14.2 nTPM

Respiratory ciliated cells	18.8 nTPM
Bronchus	23.1 nTPM
Lung	14.6 nTPM

Smooth muscle cells	18.8 nTPM
Ovary	32.2 nTPM
Pancreas	26.6 nTPM
Endometrium	24.6 nTPM
Skeletal muscle	22.6 nTPM
Prostate	19.6 nTPM
Breast	17.4 nTPM
Esophagus	14.0 nTPM
Adipose tissue	13.1 nTPM
Skin	12.9 nTPM
Bronchus	12.3 nTPM
Heart muscle	11.7 nTPM

T-cells	28.3 nTPM
Bone marrow	47.7 nTPM
Stomach	42.4 nTPM
Spleen	40.3 nTPM
Lymph node	39.5 nTPM
Kidney	32.9 nTPM
Esophagus	32.8 nTPM
Colon	28.0 nTPM
PBMC	27.9 nTPM
Skeletal muscle	27.6 nTPM
Liver	27.5 nTPM
Breast	26.9 nTPM
Endometrium	25.2 nTPM
Skin	24.4 nTPM
Adipose tissue	22.3 nTPM
Ovary	15.6 nTPM
Lung	15.2 nTPM
Prostate	4.7 nTPM

Basal keratinocytes	22.4 nTPM
Skin	22.4 nTPM

Basal prostatic cells	23.2 nTPM
Prostate	23.2 nTPM

Basal respiratory cells	23.4 nTPM
Bronchus	23.4 nTPM

Cholangiocytes	14.3 nTPM
Liver	14.3 nTPM

Undifferentiated cells	31.6 nTPM
Rectum	32.2 nTPM
Colon	31.7 nTPM
Small intestine	30.7 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