Single cell type - RALY - 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.	RALY
Gene descriptionⁱ Full gene name according to HGNC.	RALY heterogeneous nuclear ribonucleoprotein
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	Intestinal epithelial 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

RALY is part of cluster 53 Intestinal epithelial cells - Unknown function with confidenceⁱ 1
611 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
PRELID1	PRELI domain containing 1	0.7042	16
TICAM1	Toll like receptor adaptor molecule 1	0.6355	53
POLR2J	RNA polymerase II subunit J	0.6241	53
CEACAM1	CEA cell adhesion molecule 1	0.6056	53
PLCD3	Phospholipase C delta 3	0.6014	53
ARHGDIA	Rho GDP dissociation inhibitor alpha	0.5943	16
RHOF	Ras homolog family member F, filopodia associated	0.5844	53
MALL	Mal, T cell differentiation protein like	0.5808	53
CLDN23	Claudin 23	0.5769	53
MIER3	MIER family member 3	0.5733	53
CLCA4	Chloride channel accessory 4	0.5711	53
SIRT6	Sirtuin 6	0.5707	53
TRIM31	Tripartite motif containing 31	0.5676	53
ABHD3	Abhydrolase domain containing 3, phospholipase	0.5665	53
TNIP1	TNFAIP3 interacting protein 1	0.5654	53

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	91.8 nTPM
Breast	96.3 nTPM
Adipose tissue	87.4 nTPM

Alveolar cells type 1	54.5 nTPM
Lung	54.5 nTPM

Alveolar cells type 2	61.3 nTPM
Lung	61.3 nTPM

Astrocytes	23.2 nTPM
Brain	23.2 nTPM

B-cells	98.3 nTPM
Liver	187.2 nTPM
Colon	115.0 nTPM
Breast	115.0 nTPM
Stomach	103.1 nTPM
Lymph node	90.7 nTPM
Spleen	89.7 nTPM
PBMC	72.9 nTPM
Kidney	71.4 nTPM
Adipose tissue	69.7 nTPM
Bone marrow	68.7 nTPM

Dendritic cells	118.3 nTPM
Breast	150.1 nTPM
Adipose tissue	129.2 nTPM
PBMC	75.7 nTPM

Endothelial cells	92.1 nTPM
Prostate	155.3 nTPM
Pancreas	131.3 nTPM
Placenta	119.4 nTPM
Breast	106.0 nTPM
Liver	104.6 nTPM
Testis	104.6 nTPM
Skin	98.5 nTPM
Esophagus	95.0 nTPM
Ovary	94.9 nTPM
Skeletal muscle	71.1 nTPM
Endometrium	63.7 nTPM
Eye	58.2 nTPM
Heart muscle	49.8 nTPM
Lung	37.4 nTPM

Enteroendocrine cells	93.0 nTPM
Colon	135.0 nTPM
Rectum	51.0 nTPM

Fibroblasts	78.2 nTPM
Placenta	120.5 nTPM
Ovary	106.2 nTPM
Skin	93.3 nTPM
Adipose tissue	89.0 nTPM
Esophagus	88.0 nTPM
Prostate	80.6 nTPM
Breast	73.3 nTPM
Stomach	71.3 nTPM
Heart muscle	53.9 nTPM
Skeletal muscle	51.4 nTPM
Lung	32.4 nTPM

Intestinal goblet cells	143.2 nTPM
Colon	175.1 nTPM
Small intestine	140.9 nTPM
Rectum	113.7 nTPM

Macrophages	96.9 nTPM
Prostate	145.6 nTPM
Pancreas	135.2 nTPM
Kidney	127.8 nTPM
Ovary	112.6 nTPM
Adipose tissue	106.2 nTPM
Bone marrow	103.7 nTPM
Breast	101.9 nTPM
PBMC	95.5 nTPM
Stomach	93.7 nTPM
Spleen	85.0 nTPM
Testis	82.5 nTPM
Skeletal muscle	75.3 nTPM
Esophagus	73.9 nTPM
Endometrium	69.0 nTPM
Lung	44.9 nTPM

Paneth cells	270.7 nTPM
Colon	480.9 nTPM
Small intestine	168.9 nTPM
Rectum	162.2 nTPM

Plasma cells	206.4 nTPM
Stomach	287.9 nTPM
Esophagus	246.5 nTPM
Spleen	246.5 nTPM
Bone marrow	168.1 nTPM
Adipose tissue	83.2 nTPM

Respiratory ciliated cells	38.8 nTPM
Bronchus	49.8 nTPM
Lung	27.7 nTPM

Smooth muscle cells	97.7 nTPM
Ovary	164.2 nTPM
Pancreas	159.0 nTPM
Breast	128.1 nTPM
Esophagus	122.5 nTPM
Prostate	119.7 nTPM
Skin	95.2 nTPM
Adipose tissue	74.3 nTPM
Skeletal muscle	70.5 nTPM
Endometrium	66.9 nTPM
Heart muscle	40.7 nTPM
Bronchus	33.6 nTPM

Basal keratinocytes	79.2 nTPM
Skin	79.2 nTPM

Basal prostatic cells	126.9 nTPM
Prostate	126.9 nTPM

Basal respiratory cells	102.3 nTPM
Bronchus	102.3 nTPM

Cholangiocytes	58.6 nTPM
Liver	58.6 nTPM

T-cells	117.2 nTPM
Ovary	166.8 nTPM
Colon	164.9 nTPM
Liver	145.3 nTPM
Stomach	143.0 nTPM
Spleen	136.8 nTPM
Kidney	134.1 nTPM
Esophagus	131.0 nTPM
Breast	123.7 nTPM
Bone marrow	121.6 nTPM
Skin	113.3 nTPM
PBMC	105.8 nTPM
Adipose tissue	105.8 nTPM
Lymph node	103.3 nTPM
Skeletal muscle	84.3 nTPM
Endometrium	72.2 nTPM
Prostate	71.1 nTPM
Lung	69.8 nTPM

Undifferentiated cells	178.6 nTPM
Colon	226.6 nTPM
Small intestine	161.7 nTPM
Rectum	147.4 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