Single cell type - RFFL - 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.	RFFL
Gene descriptionⁱ Full gene name according to HGNC.	Ring finger and FYVE like domain containing E3 ubiquitin protein ligase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes
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.	9

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	Epithelial cell types - Mixed 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	Cell type enhanced (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 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	Cell line enhanced (HDLM-2, Karpas-707)
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 (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

RFFL is part of cluster 22 Epithelial cell types - Mixed function with confidenceⁱ 1
298 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
NUP58	Nucleoporin 58	0.5082	25
ETNK2	Ethanolamine kinase 2	0.4965	25
HMOX2	Heme oxygenase 2	0.4902	31
ADAT1	Adenosine deaminase tRNA specific 1	0.4812	25
RNF6	Ring finger protein 6	0.4544	31
LYRM1	LYR motif containing 1	0.4480	25
OCLN	Occludin	0.4460	22
ECHDC2	Enoyl-CoA hydratase domain containing 2	0.4447	2
HGS	Hepatocyte growth factor-regulated tyrosine kinase substrate	0.4398	44
F11R	F11 receptor	0.4346	22
GGT2	Gamma-glutamyltransferase 2	0.4325	11
C12orf50	Chromosome 12 open reading frame 50	0.4269	31
MAD1L1	Mitotic arrest deficient 1 like 1	0.4235	31
LSMEM2	Leucine rich single-pass membrane protein 2	0.4226	25
BPIFB2	BPI fold containing family B member 2	0.4204	35

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	6.5 nTPM
Adipose tissue	8.5 nTPM
Breast	4.6 nTPM

Alveolar cells type 1	41.7 nTPM
Lung	41.7 nTPM

Alveolar cells type 2	27.4 nTPM
Lung	27.4 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	12.6 nTPM
Kidney	19.0 nTPM
PBMC	15.7 nTPM
Lymph node	14.6 nTPM
Colon	14.4 nTPM
Liver	13.1 nTPM
Spleen	12.8 nTPM
Stomach	12.3 nTPM
Bone marrow	11.5 nTPM
Adipose tissue	7.5 nTPM
Breast	5.3 nTPM

Dendritic cells	12.1 nTPM
Adipose tissue	20.9 nTPM
Breast	11.3 nTPM
PBMC	4.0 nTPM

Endothelial cells	6.6 nTPM
Lung	18.7 nTPM
Prostate	9.8 nTPM
Skin	7.8 nTPM
Skeletal muscle	7.4 nTPM
Eye	7.3 nTPM
Placenta	6.2 nTPM
Testis	5.7 nTPM
Esophagus	5.2 nTPM
Breast	5.2 nTPM
Endometrium	5.0 nTPM
Ovary	4.3 nTPM
Pancreas	3.9 nTPM
Liver	3.7 nTPM
Heart muscle	1.9 nTPM

Fibroblasts	9.3 nTPM
Lung	38.0 nTPM
Prostate	11.8 nTPM
Skin	8.8 nTPM
Esophagus	8.7 nTPM
Skeletal muscle	8.0 nTPM
Stomach	6.0 nTPM
Placenta	5.9 nTPM
Adipose tissue	5.7 nTPM
Breast	4.5 nTPM
Ovary	3.8 nTPM
Heart muscle	1.3 nTPM

Intestinal goblet cells	26.4 nTPM
Small intestine	34.1 nTPM
Colon	23.5 nTPM
Rectum	21.7 nTPM

Macrophages	16.1 nTPM
Stomach	32.2 nTPM
Lung	28.8 nTPM
Esophagus	25.2 nTPM
Spleen	23.9 nTPM
Bone marrow	18.8 nTPM
Testis	16.3 nTPM
Adipose tissue	15.1 nTPM
Skeletal muscle	14.0 nTPM
Prostate	13.8 nTPM
Ovary	13.4 nTPM
Breast	11.7 nTPM
Endometrium	10.9 nTPM
Kidney	9.9 nTPM
Pancreas	7.7 nTPM
PBMC	0.0 nTPM

Paneth cells	19.3 nTPM
Rectum	23.2 nTPM
Colon	19.7 nTPM
Small intestine	15.0 nTPM

Plasma cells	12.9 nTPM
Esophagus	18.4 nTPM
Adipose tissue	14.9 nTPM
Bone marrow	11.5 nTPM
Stomach	10.8 nTPM
Spleen	8.8 nTPM

Respiratory ciliated cells	11.7 nTPM
Lung	11.7 nTPM
Bronchus	11.7 nTPM

Smooth muscle cells	5.7 nTPM
Skeletal muscle	9.8 nTPM
Adipose tissue	9.7 nTPM
Prostate	9.4 nTPM
Breast	7.5 nTPM
Skin	7.0 nTPM
Endometrium	6.8 nTPM
Ovary	4.8 nTPM
Esophagus	3.1 nTPM
Bronchus	2.8 nTPM
Pancreas	2.2 nTPM
Heart muscle	0.2 nTPM

T-cells	23.7 nTPM
Lung	34.9 nTPM
Ovary	33.3 nTPM
Stomach	32.3 nTPM
Bone marrow	30.4 nTPM
Liver	28.8 nTPM
Spleen	27.7 nTPM
Esophagus	26.2 nTPM
Lymph node	25.9 nTPM
Skeletal muscle	23.4 nTPM
PBMC	22.6 nTPM
Colon	21.9 nTPM
Skin	21.2 nTPM
Kidney	18.5 nTPM
Endometrium	17.5 nTPM
Adipose tissue	17.3 nTPM
Breast	16.3 nTPM
Prostate	4.7 nTPM

Basal prostatic cells	11.9 nTPM
Prostate	11.9 nTPM

Cholangiocytes	20.0 nTPM
Liver	20.0 nTPM

Distal enterocytes	33.7 nTPM
Colon	36.1 nTPM
Rectum	31.2 nTPM

Early spermatids	41.0 nTPM
Testis	41.0 nTPM

Undifferentiated cells	18.9 nTPM
Rectum	21.4 nTPM
Small intestine	20.9 nTPM
Colon	14.3 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