Single cell type - XRN1 - 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.	XRN1
Gene descriptionⁱ Full gene name according to HGNC.	5'-3' exoribonuclease 1
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.	5

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 - Transcription (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	Cell line enriched (RH-30)
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

XRN1 is part of cluster 59 Non-specific - Transcription with confidenceⁱ 1
354 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
UBR2	Ubiquitin protein ligase E3 component n-recognin 2	0.6091	6
ANKRD36B	Ankyrin repeat domain 36B	0.5658	59
FNDC3A	Fibronectin type III domain containing 3A	0.5288	55
PRDM1	PR/SET domain 1	0.5168	55
ATG5	Autophagy related 5	0.5122	21
PRPF39	Pre-mRNA processing factor 39	0.5068	59
CAPN7	Calpain 7	0.5018	46
ALG11	ALG11 alpha-1,2-mannosyltransferase	0.4969	59
DNAJC1	DnaJ heat shock protein family (Hsp40) member C1	0.4965	13
ZBTB49	Zinc finger and BTB domain containing 49	0.4940	63
ZNF805	Zinc finger protein 805	0.4912	52
UBE4A	Ubiquitination factor E4A	0.4828	59
ANKRD28	Ankyrin repeat domain 28	0.4805	55
RBM33	RNA binding motif protein 33	0.4765	52
SEL1L	SEL1L adaptor subunit of ERAD E3 ubiquitin ligase	0.4700	55

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	66.1 nTPM
Adipose tissue	75.4 nTPM
Breast	56.8 nTPM

Alveolar cells type 1	54.5 nTPM
Lung	54.5 nTPM

Alveolar cells type 2	33.3 nTPM
Lung	33.3 nTPM

Astrocytes	74.7 nTPM
Brain	74.7 nTPM

B-cells	55.9 nTPM
Adipose tissue	90.2 nTPM
Stomach	79.1 nTPM
Lymph node	71.1 nTPM
Spleen	67.2 nTPM
Bone marrow	64.6 nTPM
Breast	53.6 nTPM
Colon	43.2 nTPM
PBMC	37.1 nTPM
Liver	29.6 nTPM
Kidney	23.8 nTPM

Dendritic cells	80.8 nTPM
Adipose tissue	121.7 nTPM
Breast	76.9 nTPM
PBMC	43.8 nTPM

Endothelial cells	40.6 nTPM
Lung	87.4 nTPM
Heart muscle	86.9 nTPM
Skeletal muscle	63.8 nTPM
Endometrium	42.5 nTPM
Prostate	41.9 nTPM
Esophagus	38.7 nTPM
Breast	37.7 nTPM
Ovary	34.4 nTPM
Testis	30.5 nTPM
Liver	26.6 nTPM
Skin	26.4 nTPM
Eye	21.0 nTPM
Pancreas	19.3 nTPM
Placenta	10.8 nTPM

Fibroblasts	41.8 nTPM
Heart muscle	68.3 nTPM
Adipose tissue	55.3 nTPM
Skeletal muscle	51.2 nTPM
Lung	49.2 nTPM
Prostate	45.6 nTPM
Breast	45.6 nTPM
Esophagus	42.3 nTPM
Stomach	31.2 nTPM
Skin	25.2 nTPM
Ovary	23.4 nTPM
Placenta	22.0 nTPM

Intestinal goblet cells	22.5 nTPM
Small intestine	23.2 nTPM
Rectum	22.8 nTPM
Colon	21.5 nTPM

Macrophages	38.8 nTPM
Bone marrow	67.5 nTPM
Adipose tissue	66.7 nTPM
Stomach	58.6 nTPM
Skeletal muscle	53.8 nTPM
Spleen	47.7 nTPM
Lung	45.2 nTPM
Ovary	39.8 nTPM
Esophagus	37.7 nTPM
Breast	36.7 nTPM
Kidney	35.6 nTPM
Endometrium	32.4 nTPM
Prostate	26.3 nTPM
Testis	23.8 nTPM
Pancreas	10.2 nTPM
PBMC	0.0 nTPM

Paneth cells	41.9 nTPM
Colon	79.0 nTPM
Small intestine	26.3 nTPM
Rectum	20.4 nTPM

Plasma cells	111.7 nTPM
Stomach	178.0 nTPM
Adipose tissue	138.7 nTPM
Esophagus	104.7 nTPM
Spleen	87.5 nTPM
Bone marrow	49.4 nTPM

Respiratory ciliated cells	34.2 nTPM
Bronchus	39.2 nTPM
Lung	29.1 nTPM

Smooth muscle cells	39.9 nTPM
Heart muscle	82.5 nTPM
Adipose tissue	52.5 nTPM
Esophagus	51.2 nTPM
Breast	45.4 nTPM
Skeletal muscle	45.2 nTPM
Endometrium	41.7 nTPM
Prostate	33.4 nTPM
Ovary	28.2 nTPM
Bronchus	26.6 nTPM
Skin	17.1 nTPM
Pancreas	14.8 nTPM

T-cells	69.8 nTPM
Adipose tissue	123.2 nTPM
Spleen	103.7 nTPM
Bone marrow	95.8 nTPM
Skeletal muscle	90.5 nTPM
Stomach	87.7 nTPM
Esophagus	78.6 nTPM
Endometrium	77.7 nTPM
Lymph node	77.7 nTPM
Lung	74.4 nTPM
Breast	67.3 nTPM
PBMC	55.5 nTPM
Colon	54.6 nTPM
Kidney	54.0 nTPM
Ovary	48.9 nTPM
Prostate	37.9 nTPM
Liver	34.8 nTPM
Skin	24.9 nTPM

Basal keratinocytes	25.6 nTPM
Skin	25.6 nTPM

Basal prostatic cells	33.7 nTPM
Prostate	33.7 nTPM

Basal respiratory cells	22.7 nTPM
Bronchus	22.7 nTPM

Basal squamous epithelial cells	33.6 nTPM
Esophagus	33.6 nTPM

Undifferentiated cells	15.0 nTPM
Small intestine	15.8 nTPM
Colon	15.0 nTPM
Rectum	14.1 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