Single cell type - SPTY2D1 - 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.	SPTY2D1
Gene descriptionⁱ Full gene name according to HGNC.	SPT2 chromatin protein domain containing 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.	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 - Transcription regulation (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

SPTY2D1 is part of cluster 24 Non-specific - Transcription regulation with confidenceⁱ 1
415 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
SUPT5H	SPT5 homolog, DSIF elongation factor subunit	0.6871	65
GCNA	Germ cell nuclear acidic peptidase	0.6204	7
ZC3HAV1	Zinc finger CCCH-type containing, antiviral 1	0.6068	65
SMAD7	SMAD family member 7	0.5926	24
JMY	Junction mediating and regulatory protein, p53 cofactor	0.5917	24
LYSMD3	LysM domain containing 3	0.5873	24
TSPYL2	TSPY like 2	0.5872	7
BRD1	Bromodomain containing 1	0.5793	24
WHRN	Whirlin	0.5763	24
USP36	Ubiquitin specific peptidase 36	0.5723	24
MPZL3	Myelin protein zero like 3	0.5582	24
IKZF5	IKAROS family zinc finger 5	0.5560	35
MCL1	MCL1 apoptosis regulator, BCL2 family member	0.5538	41
TMEM238	Transmembrane protein 238	0.5481	35
SLC35E1	Solute carrier family 35 member E1	0.5442	65

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	42.3 nTPM
Adipose tissue	54.1 nTPM
Breast	30.5 nTPM

Alveolar cells type 1	25.6 nTPM
Lung	25.6 nTPM

Alveolar cells type 2	47.7 nTPM
Lung	47.7 nTPM

Astrocytes	5.2 nTPM
Brain	5.2 nTPM

B-cells	38.0 nTPM
Adipose tissue	68.2 nTPM
Lymph node	49.0 nTPM
Breast	45.4 nTPM
Spleen	43.6 nTPM
Liver	37.3 nTPM
Stomach	37.3 nTPM
Colon	36.7 nTPM
Bone marrow	29.4 nTPM
PBMC	18.6 nTPM
Kidney	14.3 nTPM

Dendritic cells	75.3 nTPM
Adipose tissue	127.7 nTPM
Breast	70.3 nTPM
PBMC	27.9 nTPM

Endothelial cells	29.1 nTPM
Endometrium	58.6 nTPM
Lung	53.0 nTPM
Breast	42.7 nTPM
Esophagus	40.8 nTPM
Skeletal muscle	34.2 nTPM
Skin	29.6 nTPM
Prostate	25.4 nTPM
Liver	24.7 nTPM
Ovary	22.9 nTPM
Heart muscle	18.6 nTPM
Placenta	16.5 nTPM
Eye	15.4 nTPM
Testis	13.0 nTPM
Pancreas	11.6 nTPM

Fibroblasts	35.3 nTPM
Lung	65.9 nTPM
Adipose tissue	46.8 nTPM
Heart muscle	40.1 nTPM
Esophagus	37.8 nTPM
Skin	36.9 nTPM
Skeletal muscle	36.4 nTPM
Breast	35.2 nTPM
Prostate	35.0 nTPM
Stomach	25.3 nTPM
Ovary	15.0 nTPM
Placenta	14.6 nTPM

Intestinal goblet cells	39.4 nTPM
Colon	70.0 nTPM
Rectum	26.0 nTPM
Small intestine	22.1 nTPM

Macrophages	44.3 nTPM
Adipose tissue	110.2 nTPM
Endometrium	99.1 nTPM
Breast	60.5 nTPM
Spleen	49.7 nTPM
Skeletal muscle	48.6 nTPM
Stomach	46.9 nTPM
Lung	42.3 nTPM
Prostate	41.3 nTPM
Esophagus	37.7 nTPM
Ovary	33.6 nTPM
Pancreas	33.2 nTPM
Bone marrow	22.5 nTPM
Kidney	19.6 nTPM
Testis	19.2 nTPM
PBMC	0.0 nTPM

Paneth cells	29.8 nTPM
Colon	46.1 nTPM
Rectum	24.5 nTPM
Small intestine	18.8 nTPM

Plasma cells	83.6 nTPM
Esophagus	110.8 nTPM
Stomach	106.5 nTPM
Spleen	70.6 nTPM
Adipose tissue	69.0 nTPM
Bone marrow	61.0 nTPM

Respiratory ciliated cells	47.5 nTPM
Lung	67.0 nTPM
Bronchus	28.0 nTPM

Smooth muscle cells	28.2 nTPM
Endometrium	54.2 nTPM
Adipose tissue	47.9 nTPM
Skeletal muscle	32.0 nTPM
Heart muscle	30.0 nTPM
Skin	26.5 nTPM
Prostate	25.9 nTPM
Breast	24.1 nTPM
Esophagus	21.7 nTPM
Ovary	19.9 nTPM
Pancreas	15.7 nTPM
Bronchus	12.2 nTPM

T-cells	69.7 nTPM
Adipose tissue	180.4 nTPM
Endometrium	120.2 nTPM
Breast	102.5 nTPM
Colon	87.4 nTPM
Prostate	85.2 nTPM
Lymph node	73.7 nTPM
Lung	72.9 nTPM
Skeletal muscle	69.9 nTPM
Esophagus	65.5 nTPM
Spleen	63.1 nTPM
Skin	61.3 nTPM
Stomach	58.3 nTPM
Bone marrow	37.5 nTPM
Liver	36.4 nTPM
PBMC	28.4 nTPM
Ovary	24.5 nTPM
Kidney	18.5 nTPM

Basal keratinocytes	55.8 nTPM
Skin	55.8 nTPM

Basal respiratory cells	17.1 nTPM
Bronchus	17.1 nTPM

Basal squamous epithelial cells	32.5 nTPM
Esophagus	32.5 nTPM

Collecting duct cells	27.6 nTPM
Kidney	27.6 nTPM

Undifferentiated cells	24.4 nTPM
Colon	34.7 nTPM
Rectum	20.5 nTPM
Small intestine	18.1 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