Single cell type - ISY1 - 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.	ISY1
Gene descriptionⁱ Full gene name according to HGNC.	ISY1 splicing factor homolog
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.	4

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	Spermatocytes & Spermatogonia - Spermatogenesis (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

ISY1 is part of cluster 13 Spermatocytes & Spermatogonia - Spermatogenesis with confidenceⁱ 1
231 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
HUS1B	HUS1 checkpoint clamp component B	0.5646	13
RPA2	Replication protein A2	0.5138	20
SAE1	SUMO1 activating enzyme subunit 1	0.4910	12
PRIM1	DNA primase subunit 1	0.4836	13
DDX23	DEAD-box helicase 23	0.4822	63
OTUD6A	OTU deubiquitinase 6A	0.4807	13
CHST12	Carbohydrate sulfotransferase 12	0.4804	63
MRPL10	Mitochondrial ribosomal protein L10	0.4772	63
PITHD1	PITH domain containing 1	0.4770	6
TAF12	TATA-box binding protein associated factor 12	0.4766	13
SLF1	SMC5-SMC6 complex localization factor 1	0.4761	13
SMC3	Structural maintenance of chromosomes 3	0.4730	13
TAF11	TATA-box binding protein associated factor 11	0.4724	13
RIC8A	RIC8 guanine nucleotide exchange factor A	0.4721	55
CSTF2T	Cleavage stimulation factor subunit 2 tau variant	0.4704	63

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	26.5 nTPM
Adipose tissue	29.7 nTPM
Breast	23.3 nTPM

Alveolar cells type 1	25.6 nTPM
Lung	25.6 nTPM

Alveolar cells type 2	23.4 nTPM
Lung	23.4 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	27.4 nTPM
PBMC	48.5 nTPM
Spleen	31.1 nTPM
Liver	31.0 nTPM
Stomach	30.0 nTPM
Colon	25.5 nTPM
Adipose tissue	24.6 nTPM
Bone marrow	22.9 nTPM
Breast	22.8 nTPM
Kidney	19.0 nTPM
Lymph node	18.9 nTPM

Dendritic cells	38.5 nTPM
Adipose tissue	47.5 nTPM
Breast	44.1 nTPM
PBMC	23.9 nTPM

Endothelial cells	25.3 nTPM
Pancreas	38.6 nTPM
Liver	32.1 nTPM
Placenta	31.3 nTPM
Testis	31.2 nTPM
Endometrium	27.9 nTPM
Prostate	26.2 nTPM
Lung	24.9 nTPM
Ovary	24.0 nTPM
Breast	24.0 nTPM
Skeletal muscle	22.9 nTPM
Skin	22.6 nTPM
Esophagus	20.5 nTPM
Heart muscle	14.0 nTPM
Eye	13.7 nTPM

Fibroblasts	21.8 nTPM
Lung	34.7 nTPM
Placenta	30.0 nTPM
Ovary	26.6 nTPM
Adipose tissue	24.6 nTPM
Esophagus	20.7 nTPM
Breast	20.2 nTPM
Prostate	19.8 nTPM
Skin	19.6 nTPM
Skeletal muscle	17.9 nTPM
Stomach	17.8 nTPM
Heart muscle	7.9 nTPM

Intestinal goblet cells	16.7 nTPM
Colon	18.6 nTPM
Rectum	16.8 nTPM
Small intestine	14.6 nTPM

Macrophages	23.9 nTPM
Lung	39.9 nTPM
Kidney	34.0 nTPM
Pancreas	30.7 nTPM
Stomach	29.4 nTPM
Breast	25.8 nTPM
Prostate	25.3 nTPM
Ovary	25.0 nTPM
Endometrium	24.3 nTPM
Adipose tissue	24.2 nTPM
Skeletal muscle	21.6 nTPM
Testis	20.3 nTPM
Esophagus	17.3 nTPM
Spleen	16.5 nTPM
PBMC	13.6 nTPM
Bone marrow	10.0 nTPM

Paneth cells	15.3 nTPM
Rectum	17.8 nTPM
Small intestine	15.0 nTPM
Colon	13.2 nTPM

Plasma cells	24.1 nTPM
Spleen	29.6 nTPM
Stomach	27.1 nTPM
Esophagus	24.6 nTPM
Bone marrow	19.8 nTPM
Adipose tissue	19.4 nTPM

Respiratory ciliated cells	14.8 nTPM
Lung	16.0 nTPM
Bronchus	13.6 nTPM

Smooth muscle cells	20.9 nTPM
Pancreas	32.4 nTPM
Esophagus	31.0 nTPM
Ovary	25.7 nTPM
Breast	24.4 nTPM
Endometrium	21.5 nTPM
Skin	21.3 nTPM
Skeletal muscle	19.2 nTPM
Heart muscle	18.5 nTPM
Prostate	16.8 nTPM
Adipose tissue	14.5 nTPM
Bronchus	4.6 nTPM

T-cells	32.9 nTPM
Colon	44.2 nTPM
Liver	42.6 nTPM
Ovary	42.2 nTPM
Kidney	41.1 nTPM
Breast	39.9 nTPM
Adipose tissue	37.6 nTPM
PBMC	36.6 nTPM
Bone marrow	34.6 nTPM
Prostate	33.1 nTPM
Skeletal muscle	32.9 nTPM
Skin	32.3 nTPM
Stomach	31.5 nTPM
Endometrium	31.4 nTPM
Lung	28.8 nTPM
Spleen	28.0 nTPM
Lymph node	22.7 nTPM
Esophagus	0.0 nTPM

Collecting duct cells	9.2 nTPM
Kidney	9.2 nTPM

Distal enterocytes	15.8 nTPM
Rectum	17.1 nTPM
Colon	14.4 nTPM

Distal tubular cells	23.5 nTPM
Kidney	23.5 nTPM

Early spermatids	2.8 nTPM
Testis	2.8 nTPM

Undifferentiated cells	20.5 nTPM
Small intestine	24.9 nTPM
Colon	18.8 nTPM
Rectum	17.9 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