Single cell type - PRPF40A - 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.	PRPF40A
Gene descriptionⁱ Full gene name according to HGNC.	Pre-mRNA processing factor 40 homolog A
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.	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	Non-specific - 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

PRPF40A is part of cluster 10 Non-specific - Unknown function with confidenceⁱ 0.99
482 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
SYNCRIP	Synaptotagmin binding cytoplasmic RNA interacting protein	0.7258	10
HNRNPR	Heterogeneous nuclear ribonucleoprotein R	0.6679	10
CCAR1	Cell division cycle and apoptosis regulator 1	0.6660	10
RBM17	RNA binding motif protein 17	0.6454	10
DNAJA2	DnaJ heat shock protein family (Hsp40) member A2	0.6308	10
NOP14	NOP14 nucleolar protein	0.6203	10
SERBP1	SERPINE1 mRNA binding protein 1	0.6106	10
SF3A3	Splicing factor 3a subunit 3	0.6075	10
GTPBP4	GTP binding protein 4	0.6047	44
SMU1	SMU1 DNA replication regulator and spliceosomal factor	0.6028	10
HNRNPA3	Heterogeneous nuclear ribonucleoprotein A3	0.5976	10
NCL	Nucleolin	0.5899	10
TCERG1	Transcription elongation regulator 1	0.5894	10
ABCE1	ATP binding cassette subfamily E member 1	0.5690	39
NIPBL	NIPBL cohesin loading factor	0.5673	10

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	98.5 nTPM
Adipose tissue	109.4 nTPM
Breast	87.7 nTPM

Alveolar cells type 1	112.2 nTPM
Lung	112.2 nTPM

Alveolar cells type 2	118.5 nTPM
Lung	118.5 nTPM

Astrocytes	48.3 nTPM
Brain	48.3 nTPM

B-cells	120.3 nTPM
Adipose tissue	175.9 nTPM
Lymph node	138.8 nTPM
Spleen	134.0 nTPM
Bone marrow	125.1 nTPM
Kidney	123.8 nTPM
Stomach	118.5 nTPM
Liver	103.0 nTPM
Colon	99.0 nTPM
Breast	99.0 nTPM
PBMC	85.6 nTPM

Basal squamous epithelial cells	101.3 nTPM
Esophagus	101.3 nTPM

Dendritic cells	123.7 nTPM
Adipose tissue	191.5 nTPM
Breast	103.9 nTPM
PBMC	75.7 nTPM

Endothelial cells	97.4 nTPM
Lung	156.0 nTPM
Pancreas	142.9 nTPM
Prostate	117.0 nTPM
Ovary	115.7 nTPM
Skeletal muscle	109.7 nTPM
Endometrium	104.3 nTPM
Heart muscle	95.3 nTPM
Testis	92.1 nTPM
Placenta	89.2 nTPM
Esophagus	82.2 nTPM
Breast	78.9 nTPM
Skin	72.7 nTPM
Eye	55.0 nTPM
Liver	53.2 nTPM

Erythroid cells	105.6 nTPM
Bone marrow	120.2 nTPM
Liver	90.9 nTPM

Fibroblasts	96.4 nTPM
Lung	215.5 nTPM
Ovary	116.5 nTPM
Prostate	109.8 nTPM
Heart muscle	102.9 nTPM
Adipose tissue	89.6 nTPM
Skeletal muscle	83.4 nTPM
Placenta	76.8 nTPM
Esophagus	68.9 nTPM
Skin	68.6 nTPM
Breast	65.1 nTPM
Stomach	63.9 nTPM

Intestinal goblet cells	81.5 nTPM
Colon	110.0 nTPM
Rectum	71.6 nTPM
Small intestine	63.0 nTPM

Macrophages	125.5 nTPM
Adipose tissue	218.2 nTPM
Lung	195.1 nTPM
Spleen	162.8 nTPM
Stomach	149.5 nTPM
Endometrium	139.0 nTPM
Skeletal muscle	137.6 nTPM
Bone marrow	121.2 nTPM
Breast	120.7 nTPM
Ovary	116.3 nTPM
Prostate	112.4 nTPM
Testis	112.1 nTPM
Kidney	102.0 nTPM
Pancreas	99.5 nTPM
Esophagus	96.0 nTPM
PBMC	0.0 nTPM

Paneth cells	86.8 nTPM
Small intestine	101.4 nTPM
Rectum	93.1 nTPM
Colon	65.8 nTPM

Plasma cells	112.1 nTPM
Adipose tissue	137.4 nTPM
Spleen	136.3 nTPM
Bone marrow	123.6 nTPM
Stomach	101.5 nTPM
Esophagus	61.7 nTPM

Respiratory ciliated cells	152.6 nTPM
Lung	206.9 nTPM
Bronchus	98.3 nTPM

Cholangiocytes	55.8 nTPM
Liver	55.8 nTPM

Collecting duct cells	53.3 nTPM
Kidney	53.3 nTPM

Cone photoreceptor cells	73.0 nTPM
Eye	73.0 nTPM

Cytotrophoblasts	123.1 nTPM
Placenta	123.1 nTPM

Smooth muscle cells	132.1 nTPM
Bronchus	465.3 nTPM
Ovary	157.8 nTPM
Heart muscle	110.6 nTPM
Pancreas	110.1 nTPM
Endometrium	105.1 nTPM
Skeletal muscle	103.5 nTPM
Prostate	92.6 nTPM
Adipose tissue	91.3 nTPM
Esophagus	86.8 nTPM
Breast	72.2 nTPM
Skin	57.6 nTPM

T-cells	119.9 nTPM
Lung	209.6 nTPM
Adipose tissue	191.7 nTPM
Endometrium	143.5 nTPM
Prostate	132.5 nTPM
Skeletal muscle	119.6 nTPM
Spleen	118.5 nTPM
Esophagus	117.9 nTPM
Stomach	116.4 nTPM
Colon	112.6 nTPM
Lymph node	108.2 nTPM
Bone marrow	105.0 nTPM
Breast	104.2 nTPM
PBMC	102.1 nTPM
Kidney	99.2 nTPM
Ovary	91.2 nTPM
Liver	85.0 nTPM
Skin	80.6 nTPM

Undifferentiated cells	103.7 nTPM
Colon	134.5 nTPM
Small intestine	92.4 nTPM
Rectum	84.3 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