Single cell type - ALYREF - 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.	ALYREF
Gene descriptionⁱ Full gene name according to HGNC.	Aly/REF export factor
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.	1

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 - Mitochondria (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 many
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

ALYREF is part of cluster 7 Non-specific - Mitochondria with confidenceⁱ 1
481 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
UBE2M	Ubiquitin conjugating enzyme E2 M	0.7240	7
KMT5A	Lysine methyltransferase 5A	0.6913	7
NUDT4B	Nudix hydrolase 4B	0.6556	7
RFLNB	Refilin B	0.6389	14
UBALD2	UBA like domain containing 2	0.6285	7
MBD2	Methyl-CpG binding domain protein 2	0.6271	41
SPINDOC	Spindlin interactor and repressor of chromatin binding	0.6264	7
GNAI2	G protein subunit alpha i2	0.6234	7
THAP12	THAP domain containing 12	0.5911	7
ZFPM1	Zinc finger protein, FOG family member 1	0.5794	7
RRP36	Ribosomal RNA processing 36	0.5787	7
MAZ	MYC associated zinc finger protein	0.5688	53
JUND	JunD proto-oncogene, AP-1 transcription factor subunit	0.5648	7
TENT4A	Terminal nucleotidyltransferase 4A	0.5608	65
MOSMO	Modulator of smoothened	0.5601	7

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	68.4 nTPM
Adipose tissue	73.8 nTPM
Breast	63.1 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	16.0 nTPM
Lung	16.0 nTPM

Astrocytes	1.3 nTPM
Brain	1.3 nTPM

B-cells	22.9 nTPM
Adipose tissue	57.2 nTPM
Liver	51.6 nTPM
Breast	44.1 nTPM
Colon	30.3 nTPM
Stomach	11.3 nTPM
Lymph node	11.2 nTPM
Spleen	10.0 nTPM
PBMC	8.5 nTPM
Bone marrow	4.9 nTPM
Kidney	0.0 nTPM

Dendritic cells	59.0 nTPM
Adipose tissue	87.7 nTPM
Breast	61.2 nTPM
PBMC	27.9 nTPM

Endothelial cells	23.4 nTPM
Ovary	74.0 nTPM
Endometrium	63.4 nTPM
Prostate	35.7 nTPM
Breast	29.8 nTPM
Skeletal muscle	29.6 nTPM
Skin	20.3 nTPM
Lung	15.6 nTPM
Placenta	14.2 nTPM
Eye	10.5 nTPM
Esophagus	8.8 nTPM
Heart muscle	7.8 nTPM
Pancreas	7.7 nTPM
Liver	6.4 nTPM
Testis	4.1 nTPM

Fibroblasts	24.9 nTPM
Ovary	88.2 nTPM
Adipose tissue	58.9 nTPM
Breast	26.5 nTPM
Skeletal muscle	24.5 nTPM
Prostate	22.8 nTPM
Skin	15.9 nTPM
Stomach	10.4 nTPM
Placenta	9.5 nTPM
Lung	6.7 nTPM
Heart muscle	6.1 nTPM
Esophagus	4.9 nTPM

Intestinal goblet cells	24.3 nTPM
Colon	40.0 nTPM
Rectum	16.5 nTPM
Small intestine	16.3 nTPM

Macrophages	31.3 nTPM
Adipose tissue	90.5 nTPM
Endometrium	89.9 nTPM
Breast	59.9 nTPM
Skeletal muscle	42.7 nTPM
Spleen	36.3 nTPM
Stomach	35.1 nTPM
Ovary	33.3 nTPM
Bone marrow	16.3 nTPM
Prostate	16.0 nTPM
Kidney	15.8 nTPM
Lung	14.6 nTPM
Esophagus	11.0 nTPM
Testis	5.2 nTPM
Pancreas	2.5 nTPM
PBMC	0.0 nTPM

Paneth cells	10.1 nTPM
Colon	16.5 nTPM
Rectum	10.1 nTPM
Small intestine	3.7 nTPM

Plasma cells	46.4 nTPM
Spleen	81.3 nTPM
Bone marrow	69.2 nTPM
Adipose tissue	41.3 nTPM
Stomach	28.0 nTPM
Esophagus	12.3 nTPM

Respiratory ciliated cells	8.4 nTPM
Lung	8.7 nTPM
Bronchus	8.1 nTPM

Smooth muscle cells	30.6 nTPM
Ovary	77.5 nTPM
Endometrium	53.6 nTPM
Adipose tissue	46.7 nTPM
Breast	45.4 nTPM
Bronchus	38.3 nTPM
Skeletal muscle	21.7 nTPM
Prostate	16.6 nTPM
Heart muscle	12.8 nTPM
Pancreas	11.2 nTPM
Skin	11.1 nTPM
Esophagus	1.5 nTPM

T-cells	27.6 nTPM
Adipose tissue	83.1 nTPM
Endometrium	75.0 nTPM
Breast	60.3 nTPM
Ovary	55.6 nTPM
Skeletal muscle	41.3 nTPM
Colon	24.7 nTPM
Skin	20.2 nTPM
Stomach	19.3 nTPM
Lung	13.6 nTPM
Spleen	12.7 nTPM
PBMC	9.7 nTPM
Lymph node	9.7 nTPM
Liver	9.6 nTPM
Prostate	9.5 nTPM
Kidney	8.9 nTPM
Bone marrow	8.9 nTPM
Esophagus	6.6 nTPM

Basal keratinocytes	34.9 nTPM
Skin	34.9 nTPM

Basal respiratory cells	7.5 nTPM
Bronchus	7.5 nTPM

Basal squamous epithelial cells	9.1 nTPM
Esophagus	9.1 nTPM

Cholangiocytes	11.5 nTPM
Liver	11.5 nTPM

Undifferentiated cells	21.9 nTPM
Colon	26.2 nTPM
Rectum	20.2 nTPM
Small intestine	19.3 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