Single cell type - RAB11FIP3 - 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.	RAB11FIP3
Gene descriptionⁱ Full gene name according to HGNC.	RAB11 family interacting protein 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes
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	Proximal tubular cells - Tubular reabsorption (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 enriched (Proximal tubular 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	Not detected in immune cells
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	Not detected
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: Cell type enriched (Proximal tubular 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

RAB11FIP3 is part of cluster 67 Proximal tubular cells - Tubular reabsorption with confidenceⁱ 1
499 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
SLC22A13	Solute carrier family 22 member 13	0.9238	67
GLYAT	Glycine-N-acyltransferase	0.9201	67
SLC6A13	Solute carrier family 6 member 13	0.9139	67
AGMAT	Agmatinase	0.9120	67
AGXT2	Alanine--glyoxylate aminotransferase 2	0.9102	67
TMEM174	Transmembrane protein 174	0.9096	67
CTXN3	Cortexin 3	0.9094	67
CLEC18A	C-type lectin domain family 18 member A	0.9088	67
ASPDH	Aspartate dehydrogenase domain containing	0.9021	67
ACMSD	Aminocarboxymuconate semialdehyde decarboxylase	0.9015	67
RIDA	Reactive intermediate imine deaminase A homolog	0.9005	67
RBP5	Retinol binding protein 5	0.9003	67
BHMT2	Betaine--homocysteine S-methyltransferase 2	0.8983	67
UGT2A1	UDP glucuronosyltransferase family 2 member A1 complex locus	0.8956	67
BBOX1	Gamma-butyrobetaine hydroxylase 1	0.8927	67

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	9.4 nTPM
Adipose tissue	11.8 nTPM
Breast	7.0 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	1.7 nTPM
Lung	1.7 nTPM

Astrocytes	36.9 nTPM
Brain	36.9 nTPM

B-cells	3.8 nTPM
Kidney	14.3 nTPM
Breast	6.6 nTPM
Adipose tissue	3.5 nTPM
Colon	3.2 nTPM
Bone marrow	2.5 nTPM
Lymph node	2.4 nTPM
Liver	2.0 nTPM
PBMC	1.4 nTPM
Spleen	1.4 nTPM
Stomach	0.9 nTPM

Dendritic cells	5.7 nTPM
Adipose tissue	11.0 nTPM
Breast	6.2 nTPM
PBMC	0.0 nTPM

Endothelial cells	7.1 nTPM
Liver	22.9 nTPM
Heart muscle	14.8 nTPM
Endometrium	13.8 nTPM
Lung	12.5 nTPM
Ovary	7.5 nTPM
Breast	6.8 nTPM
Skeletal muscle	6.5 nTPM
Esophagus	4.1 nTPM
Skin	3.0 nTPM
Eye	2.4 nTPM
Placenta	2.2 nTPM
Prostate	2.0 nTPM
Testis	1.4 nTPM
Pancreas	0.0 nTPM

Fibroblasts	5.5 nTPM
Heart muscle	12.4 nTPM
Lung	11.1 nTPM
Adipose tissue	7.9 nTPM
Skeletal muscle	6.3 nTPM
Breast	5.0 nTPM
Ovary	4.5 nTPM
Esophagus	3.6 nTPM
Skin	3.5 nTPM
Stomach	3.0 nTPM
Placenta	1.6 nTPM
Prostate	1.5 nTPM

Intestinal goblet cells	3.0 nTPM
Small intestine	3.2 nTPM
Rectum	3.0 nTPM
Colon	2.9 nTPM

Macrophages	4.7 nTPM
Kidney	43.2 nTPM
Adipose tissue	4.5 nTPM
Breast	4.3 nTPM
Endometrium	3.8 nTPM
Esophagus	3.1 nTPM
Bone marrow	2.5 nTPM
Ovary	2.4 nTPM
Lung	1.7 nTPM
Skeletal muscle	1.4 nTPM
Prostate	1.2 nTPM
Testis	1.2 nTPM
Spleen	1.0 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	3.9 nTPM
Colon	9.9 nTPM
Rectum	1.9 nTPM
Small intestine	0.0 nTPM

Plasma cells	3.4 nTPM
Adipose tissue	14.2 nTPM
Spleen	1.6 nTPM
Stomach	1.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Respiratory ciliated cells	3.1 nTPM
Lung	4.4 nTPM
Bronchus	1.9 nTPM

Smooth muscle cells	5.4 nTPM
Heart muscle	13.2 nTPM
Endometrium	13.1 nTPM
Adipose tissue	8.5 nTPM
Ovary	7.8 nTPM
Breast	6.9 nTPM
Skeletal muscle	5.0 nTPM
Skin	2.5 nTPM
Bronchus	0.9 nTPM
Pancreas	0.7 nTPM
Prostate	0.4 nTPM
Esophagus	0.0 nTPM

T-cells	4.4 nTPM
Kidney	14.4 nTPM
Adipose tissue	9.2 nTPM
Breast	8.8 nTPM
Skeletal muscle	8.7 nTPM
Endometrium	8.2 nTPM
Skin	4.1 nTPM
Lung	3.0 nTPM
Colon	2.9 nTPM
Bone marrow	2.6 nTPM
Spleen	2.5 nTPM
Liver	2.2 nTPM
Ovary	2.2 nTPM
Stomach	1.9 nTPM
Lymph node	1.8 nTPM
PBMC	1.6 nTPM
Prostate	0.0 nTPM
Esophagus	0.0 nTPM

Basal keratinocytes	3.7 nTPM
Skin	3.7 nTPM

Basal respiratory cells	1.1 nTPM
Bronchus	1.1 nTPM

Cholangiocytes	7.2 nTPM
Liver	7.2 nTPM

Excitatory neurons	73.5 nTPM
Brain	73.5 nTPM

Undifferentiated cells	5.9 nTPM
Small intestine	9.6 nTPM
Colon	5.3 nTPM
Rectum	2.7 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