Single cell type - SF3A1 - 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.	SF3A1
Gene descriptionⁱ Full gene name according to HGNC.	Splicing factor 3a subunit 1
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.	2

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	Granulosa cells - Unknown function (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

SF3A1 is part of cluster 40 Granulosa cells - Unknown function with confidenceⁱ 1
316 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
ELK1	ETS transcription factor ELK1	0.5762	40
ZNF275	Zinc finger protein 275	0.5676	40
GATA4	GATA binding protein 4	0.5483	40
FOXL2	Forkhead box L2	0.5318	40
CEACAM21	CEA cell adhesion molecule 21	0.5296	40
AMH	Anti-Mullerian hormone	0.5296	40
CEP120	Centrosomal protein 120	0.5213	59
FNDC10	Fibronectin type III domain containing 10	0.5181	40
CRYGD	Crystallin gamma D	0.5117	40
CHST1	Carbohydrate sulfotransferase 1	0.5113	40
UBXN8	UBX domain protein 8	0.5027	40
ANXA6	Annexin A6	0.4971	40
RBP1	Retinol binding protein 1	0.4909	40
ADORA2A	Adenosine A2a receptor	0.4904	58
LCMT1	Leucine carboxyl methyltransferase 1	0.4883	40

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	32.4 nTPM
Adipose tissue	40.1 nTPM
Breast	24.8 nTPM

Alveolar cells type 1	57.7 nTPM
Lung	57.7 nTPM

Alveolar cells type 2	66.5 nTPM
Lung	66.5 nTPM

Astrocytes	12.1 nTPM
Brain	12.1 nTPM

B-cells	60.8 nTPM
Stomach	114.5 nTPM
Adipose tissue	86.7 nTPM
Spleen	80.0 nTPM
Lymph node	72.8 nTPM
Bone marrow	67.0 nTPM
Colon	59.1 nTPM
PBMC	51.3 nTPM
Liver	31.4 nTPM
Kidney	23.8 nTPM
Breast	21.3 nTPM

Dendritic cells	49.2 nTPM
Adipose tissue	74.6 nTPM
PBMC	43.8 nTPM
Breast	29.2 nTPM

Endothelial cells	32.6 nTPM
Lung	65.5 nTPM
Esophagus	39.8 nTPM
Heart muscle	39.6 nTPM
Skin	37.0 nTPM
Testis	34.4 nTPM
Liver	33.9 nTPM
Skeletal muscle	30.1 nTPM
Eye	29.9 nTPM
Prostate	29.9 nTPM
Ovary	28.3 nTPM
Endometrium	26.2 nTPM
Breast	23.6 nTPM
Pancreas	19.3 nTPM
Placenta	18.2 nTPM

Fibroblasts	29.1 nTPM
Lung	41.3 nTPM
Esophagus	40.1 nTPM
Ovary	32.3 nTPM
Stomach	31.2 nTPM
Adipose tissue	28.4 nTPM
Heart muscle	28.1 nTPM
Prostate	27.7 nTPM
Skin	27.6 nTPM
Skeletal muscle	23.3 nTPM
Placenta	21.8 nTPM
Breast	18.5 nTPM

Intestinal goblet cells	30.7 nTPM
Rectum	36.2 nTPM
Small intestine	35.6 nTPM
Colon	20.1 nTPM

Macrophages	39.8 nTPM
Adipose tissue	73.9 nTPM
PBMC	68.2 nTPM
Stomach	61.5 nTPM
Lung	45.1 nTPM
Ovary	42.4 nTPM
Spleen	39.4 nTPM
Skeletal muscle	36.9 nTPM
Testis	36.6 nTPM
Bone marrow	35.0 nTPM
Esophagus	33.1 nTPM
Endometrium	30.4 nTPM
Pancreas	28.0 nTPM
Kidney	22.7 nTPM
Breast	22.3 nTPM
Prostate	21.8 nTPM

Paneth cells	31.3 nTPM
Rectum	40.4 nTPM
Small intestine	33.8 nTPM
Colon	19.7 nTPM

Plasma cells	45.5 nTPM
Stomach	59.1 nTPM
Spleen	53.6 nTPM
Bone marrow	42.9 nTPM
Esophagus	36.9 nTPM
Adipose tissue	34.9 nTPM

Respiratory ciliated cells	39.4 nTPM
Lung	52.5 nTPM
Bronchus	26.2 nTPM

Smooth muscle cells	27.3 nTPM
Esophagus	43.4 nTPM
Adipose tissue	30.3 nTPM
Pancreas	29.3 nTPM
Skeletal muscle	29.1 nTPM
Ovary	28.8 nTPM
Skin	27.5 nTPM
Prostate	26.9 nTPM
Heart muscle	23.6 nTPM
Endometrium	22.7 nTPM
Breast	22.1 nTPM
Bronchus	16.1 nTPM

T-cells	55.8 nTPM
Stomach	121.6 nTPM
Spleen	96.2 nTPM
Adipose tissue	91.6 nTPM
Lymph node	76.1 nTPM
Bone marrow	74.5 nTPM
Colon	72.2 nTPM
Lung	47.1 nTPM
Breast	46.6 nTPM
PBMC	45.0 nTPM
Skin	42.8 nTPM
Skeletal muscle	42.8 nTPM
Liver	41.0 nTPM
Endometrium	37.4 nTPM
Prostate	33.1 nTPM
Esophagus	32.8 nTPM
Ovary	24.5 nTPM
Kidney	23.3 nTPM

Basal keratinocytes	26.1 nTPM
Skin	26.1 nTPM

Basal prostatic cells	25.4 nTPM
Prostate	25.4 nTPM

Basal respiratory cells	19.0 nTPM
Bronchus	19.0 nTPM

Cholangiocytes	34.3 nTPM
Liver	34.3 nTPM

Undifferentiated cells	33.9 nTPM
Rectum	39.2 nTPM
Small intestine	37.2 nTPM
Colon	25.2 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