Single cell type - RPUSD3 - The Human Protein Atlas

RPUSD3

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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.	RPUSD3
Gene descriptionⁱ Full gene name according to HGNC.	RNA pseudouridine synthase D3
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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	8

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.	Spermatocytes - 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.	Cell type enhanced (Early spermatids)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.34
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	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.	Low immune cell specificity
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized 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 RNA single cell type specificity: Cell type enhanced (Early spermatids)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Low cell type specificity

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Low immune cell specificity
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

RPUSD3 is part of cluster 31 Spermatocytes - Spermatogenesis with confidenceⁱ 1
240 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
SAC3D1	SAC3 domain containing 1	0.6243	31
C9orf57	Chromosome 9 open reading frame 57	0.6231	31
FAAP24	FA core complex associated protein 24	0.6053	31
RPL39L	Ribosomal protein L39 like	0.6032	31
ZWILCH	Zwilch kinetochore protein	0.5708	31
DNAJC5G	DnaJ heat shock protein family (Hsp40) member C5 gamma	0.5695	31
OXLD1	Oxidoreductase like domain containing 1	0.5672	39
GMCL2	Germ cell-less 2, spermatogenesis associated	0.5642	31
GOLGA8F	Golgin A8 family member F	0.5637	31
EXD1	Exonuclease 3'-5' domain containing 1	0.5618	31
KRBOX1	KRAB box domain containing 1	0.5588	31
ADAD2	Adenosine deaminase domain containing 2	0.5543	31
SLC2A14	Solute carrier family 2 member 14	0.5538	31
MGAT4D	MGAT4 family member D	0.5513	31
TERB2	Telomere repeat binding bouquet formation protein 2	0.5457	31

IMMUNE CELLS

RPUSD3 is part of cluster 12 Non-specific - Mitochondrial translation with confidenceⁱ 0.47
566 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
TEX264	Testis expressed 264, ER-phagy receptor	1.0000	12
EIF3I	Eukaryotic translation initiation factor 3 subunit I	0.9762	12
CEP128	Centrosomal protein 128	0.9762	12
ALG1	ALG1 chitobiosyldiphosphodolichol beta-mannosyltransferase	0.9524	12
XRCC6	X-ray repair cross complementing 6	0.9524	12
TMEM126A	Transmembrane protein 126A	0.9524	13
MRPL58	Mitochondrial ribosomal protein L58	0.9524	13
GTF3C6	General transcription factor IIIC subunit 6	0.9524	12
HIKESHI	Heat shock protein nuclear import factor hikeshi	0.9524	13
RARS2	Arginyl-tRNA synthetase 2, mitochondrial	0.9524	12
CPSF3	Cleavage and polyadenylation specific factor 3	0.9524	13
PFDN4	Prefoldin subunit 4	0.9524	12
ABCF2	ATP binding cassette subfamily F member 2	0.9524	13
ACOT2	Acyl-CoA thioesterase 2	0.9286	33
PPM1G	Protein phosphatase, Mg2+/Mn2+ dependent 1G	0.9286	12

Adipocytes	11.7 nTPM
Breast	17.1 nTPM
Adipose tissue	6.3 nTPM

Alveolar cells type 1	21.9 nTPM
Lung	21.9 nTPM

Alveolar cells type 2	18.7 nTPM
Lung	18.7 nTPM

Astrocytes	9.6 nTPM
Brain	9.6 nTPM

B-cells	18.4 nTPM
PBMC	33.9 nTPM
Kidney	31.2 nTPM
Liver	24.2 nTPM
Lung	24.1 nTPM
Thymus	21.8 nTPM
Salivary gland	19.2 nTPM
Bone marrow	18.8 nTPM
Stomach	13.9 nTPM
Spleen	13.3 nTPM
Esophagus	11.8 nTPM
Skin	10.2 nTPM
Lymph node	9.0 nTPM
Adipose tissue	7.4 nTPM

Ciliated cells	9.5 nTPM
Lung	11.2 nTPM
Bronchus	10.4 nTPM
Fallopian tube	9.5 nTPM
Endometrium	6.9 nTPM

Club cells	19.1 nTPM
Bronchus	23.3 nTPM
Prostate	17.6 nTPM
Lung	16.3 nTPM

Endothelial cells	15.9 nTPM
Placenta	32.4 nTPM
Ovary	22.7 nTPM
Heart muscle	22.6 nTPM
Testis	22.0 nTPM
Breast	21.1 nTPM
Lung	17.0 nTPM
Tongue	16.8 nTPM
Liver	15.1 nTPM
Thymus	14.1 nTPM
Salivary gland	13.7 nTPM
Prostate	13.3 nTPM
Pancreas	12.9 nTPM
Vascular	11.7 nTPM
Skin	11.6 nTPM
Endometrium	10.6 nTPM
Skeletal muscle	10.2 nTPM
Fallopian tube	9.6 nTPM
Esophagus	8.7 nTPM

Enteroendocrine cells	26.4 nTPM
Colon	31.7 nTPM
Small intestine	30.9 nTPM
Rectum	16.8 nTPM

Fibroblasts	18.8 nTPM
Placenta	38.2 nTPM
Pancreas	33.4 nTPM
Liver	27.3 nTPM
Heart muscle	24.2 nTPM
Thymus	23.1 nTPM
Prostate	20.5 nTPM
Salivary gland	19.9 nTPM
Breast	18.9 nTPM
Vascular	16.0 nTPM
Skeletal muscle	13.9 nTPM
Lung	13.4 nTPM
Adipose tissue	13.1 nTPM
Esophagus	10.8 nTPM
Fallopian tube	10.1 nTPM
Skin	8.6 nTPM
Stomach	8.6 nTPM

Granulocytes	13.0 nTPM
Lung	22.2 nTPM
Fallopian tube	12.1 nTPM
Tongue	4.9 nTPM

Intestinal goblet cells	14.5 nTPM
Rectum	18.9 nTPM
Colon	16.0 nTPM
Small intestine	8.5 nTPM

Lymphatic endothelial cells	25.0 nTPM
Ovary	38.2 nTPM
Fallopian tube	11.8 nTPM

Macrophages	14.1 nTPM
Pancreas	24.7 nTPM
Kidney	22.1 nTPM
Testis	21.1 nTPM
Lung	20.6 nTPM
Bone marrow	18.2 nTPM
Breast	16.6 nTPM
Prostate	15.5 nTPM
Thymus	15.4 nTPM
Endometrium	14.1 nTPM
Salivary gland	14.1 nTPM
Vascular	12.6 nTPM
Skeletal muscle	11.4 nTPM
Tongue	11.4 nTPM
Fallopian tube	11.2 nTPM
Spleen	11.0 nTPM
Esophagus	7.7 nTPM
Stomach	7.7 nTPM
Adipose tissue	7.0 nTPM
Skin	4.5 nTPM

Paneth cells	22.2 nTPM
Rectum	31.3 nTPM
Colon	18.1 nTPM
Small intestine	17.3 nTPM

Basal respiratory cells	25.9 nTPM
Bronchus	25.9 nTPM

Basal squamous epithelial cells	14.4 nTPM
Esophagus	14.4 nTPM

Bipolar cells	21.3 nTPM
Eye	21.3 nTPM

Collecting duct cells	9.7 nTPM
Kidney	9.7 nTPM

Plasma cells	22.9 nTPM
Thymus	39.1 nTPM
Liver	34.0 nTPM
Spleen	27.7 nTPM
Bone marrow	24.2 nTPM
Stomach	18.4 nTPM
Salivary gland	17.5 nTPM
Fallopian tube	12.2 nTPM
Esophagus	10.4 nTPM

Schwann cells	10.2 nTPM
Vascular	20.4 nTPM
Adipose tissue	10.1 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	17.5 nTPM
Tongue	17.7 nTPM
Salivary gland	17.4 nTPM

Smooth muscle cells	19.5 nTPM
Placenta	34.1 nTPM
Ovary	26.1 nTPM
Fallopian tube	25.4 nTPM
Thymus	24.9 nTPM
Breast	24.4 nTPM
Vascular	21.9 nTPM
Lung	20.0 nTPM
Salivary gland	19.3 nTPM
Prostate	18.9 nTPM
Liver	18.7 nTPM
Tongue	18.3 nTPM
Skin	15.5 nTPM
Endometrium	13.9 nTPM
Adipose tissue	10.9 nTPM
Skeletal muscle	10.8 nTPM
Esophagus	8.4 nTPM

Suprabasal keratinocytes	27.0 nTPM
Tongue	42.0 nTPM
Skin	12.0 nTPM

T-cells	18.4 nTPM
PBMC	37.4 nTPM
Kidney	30.1 nTPM
Liver	27.9 nTPM
Thymus	24.6 nTPM
Colon	23.4 nTPM
Lung	23.0 nTPM
Bone marrow	22.6 nTPM
Prostate	20.2 nTPM
Breast	19.6 nTPM
Salivary gland	18.5 nTPM
Tongue	17.3 nTPM
Skeletal muscle	15.1 nTPM
Vascular	14.5 nTPM
Stomach	14.4 nTPM
Spleen	13.9 nTPM
Fallopian tube	13.8 nTPM
Endometrium	13.3 nTPM
Skin	12.6 nTPM
Adipose tissue	8.6 nTPM
Lymph node	8.3 nTPM
Esophagus	7.3 nTPM

Undifferentiated cells	33.4 nTPM
Colon	36.8 nTPM
Rectum	32.8 nTPM
Small intestine	30.7 nTPM

Amygdala excitatory	13.7 nTPM
Hippocampus	14.8 nTPM
Cerebral cortex	14.7 nTPM
Basal ganglia	14.4 nTPM
Thalamus	13.6 nTPM
Amygdala	13.5 nTPM
Hypothalamus	11.1 nTPM

Astrocyte	12.9 nTPM
Thalamus	16.6 nTPM
Cerebellum	15.7 nTPM
Cerebral cortex	15.2 nTPM
Pons	14.3 nTPM
Midbrain	13.8 nTPM
Hippocampus	12.9 nTPM
Amygdala	11.6 nTPM
Basal ganglia	11.2 nTPM
Hypothalamus	10.3 nTPM
Spinal cord	10.2 nTPM
Medulla oblongata	10.0 nTPM

Bergmann glia	12.2 nTPM
Cerebellum	12.9 nTPM
Pons	12.9 nTPM
Medulla oblongata	10.7 nTPM

Central nervous system macrophage	12.5 nTPM
Cerebral cortex	15.5 nTPM
Cerebellum	14.3 nTPM
Hippocampus	13.5 nTPM
Pons	13.3 nTPM
Midbrain	13.1 nTPM
Thalamus	12.5 nTPM
Amygdala	12.3 nTPM
Hypothalamus	11.9 nTPM
Medulla oblongata	11.7 nTPM
Basal ganglia	10.4 nTPM
Spinal cord	9.1 nTPM

Cerebellar inhibitory	15.6 nTPM
Pons	18.5 nTPM
Medulla oblongata	16.6 nTPM
Cerebellum	15.5 nTPM
Midbrain	13.7 nTPM
Spinal cord	13.7 nTPM

Cge interneuron	16.3 nTPM
Thalamus	18.9 nTPM
Basal ganglia	18.3 nTPM
Cerebral cortex	17.7 nTPM
Hippocampus	17.7 nTPM
Amygdala	14.6 nTPM
Hypothalamus	13.7 nTPM
Midbrain	13.0 nTPM

Choroid plexus epithelial cell	6.2 nTPM
Basal ganglia	8.3 nTPM
Hippocampus	8.3 nTPM
Medulla oblongata	5.5 nTPM
Thalamus	2.7 nTPM

Committed oligodendrocyte precursor	11.7 nTPM
Cerebellum	19.0 nTPM
Spinal cord	14.7 nTPM
Hippocampus	13.2 nTPM
Amygdala	13.0 nTPM
Midbrain	12.6 nTPM
Pons	11.5 nTPM
Thalamus	11.3 nTPM
Cerebral cortex	10.1 nTPM
Basal ganglia	9.9 nTPM
Medulla oblongata	7.7 nTPM
Hypothalamus	6.1 nTPM

Deep-layer corticothalamic and 6b	14.7 nTPM
Basal ganglia	18.2 nTPM
Cerebral cortex	17.7 nTPM
Hippocampus	16.7 nTPM
Amygdala	16.5 nTPM
Midbrain	10.0 nTPM
Hypothalamus	9.2 nTPM

Deep-layer intratelencephalic	14.5 nTPM
Basal ganglia	16.8 nTPM
Hippocampus	16.5 nTPM
Cerebral cortex	16.3 nTPM
Amygdala	14.1 nTPM
Hypothalamus	8.9 nTPM

Deep-layer near-projecting	15.9 nTPM
Amygdala	18.2 nTPM
Hippocampus	18.2 nTPM
Cerebral cortex	17.5 nTPM
Basal ganglia	16.4 nTPM
Hypothalamus	9.0 nTPM

Eccentric medium spiny neuron	13.9 nTPM
Hippocampus	14.9 nTPM
Hypothalamus	14.3 nTPM
Thalamus	14.0 nTPM
Basal ganglia	13.7 nTPM
Amygdala	13.5 nTPM
Cerebral cortex	13.1 nTPM

Endothelial cell	11.1 nTPM
Thalamus	16.4 nTPM
Cerebellum	16.3 nTPM
Amygdala	14.5 nTPM
Hippocampus	14.1 nTPM
Midbrain	11.3 nTPM
Basal ganglia	10.3 nTPM
Medulla oblongata	10.3 nTPM
Pons	10.0 nTPM
Hypothalamus	9.9 nTPM
Cerebral cortex	7.7 nTPM
Spinal cord	1.7 nTPM