Single cell type - RPRD1B - The Human Protein Atlas

RPRD1B

Search result

Field

Term

Cluster

Pathway

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.	RPRD1B
Gene descriptionⁱ Full gene name according to HGNC.	Regulation of nuclear pre-mRNA domain containing 1B
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.	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.	Hepatocytes - Metabolism (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 (Hepatocytes)
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.	0.36
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 (Hepatocytes)

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

RPRD1B is part of cluster 62 Hepatocytes - Metabolism with confidenceⁱ 1
159 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.
SLC22A9	Solute carrier family 22 member 9	0.6446	62
F9	Coagulation factor IX	0.6376	62
SPRN	Shadow of prion protein	0.6263	62
ELOVL6	ELOVL fatty acid elongase 6	0.6199	62
PLGLB1	Plasminogen like B1	0.6188	62
INHBE	Inhibin subunit beta E	0.6097	62
LPA	Lipoprotein(a)	0.6096	62
APOF	Apolipoprotein F	0.6070	62
SERPINF2	Serpin family F member 2	0.6069	62
SERPINA6	Serpin family A member 6	0.6066	62
ITIH3	Inter-alpha-trypsin inhibitor heavy chain 3	0.6038	62
TFR2	Transferrin receptor 2	0.6034	62
UROC1	Urocanate hydratase 1	0.5962	62
SLC22A25	Solute carrier family 22 member 25	0.5961	62
SCD	Stearoyl-CoA desaturase	0.5955	62

IMMUNE CELLS

RPRD1B is part of cluster 7 Non-specific - Innate immune response with confidenceⁱ 0.99
237 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.
KIF9	Kinesin family member 9	0.9048	38
POLR2A	RNA polymerase II subunit A	0.9048	38
YEATS2	YEATS domain containing 2	0.9048	38
FUS	FUS RNA binding protein	0.8810	33
GTF2H4	General transcription factor IIH subunit 4	0.8810	30
ATG10	Autophagy related 10	0.8810	7
CACNA2D4	Calcium voltage-gated channel auxiliary subunit alpha2delta 4	0.8571	38
ENSG00000272980	Novel protein	0.8571	7
ERCC6	ERCC excision repair 6, chromatin remodeling factor	0.8571	7
NISCH	Nischarin	0.8571	30
CPSF7	Cleavage and polyadenylation specific factor 7	0.8571	7
PIP5K1A	Phosphatidylinositol-4-phosphate 5-kinase type 1 alpha	0.8571	7
MFSD13A	Major facilitator superfamily domain containing 13A	0.8571	21
THBS1	Thrombospondin 1	0.8571	7
HOOK3	Hook microtubule tethering protein 3	0.8333	7

Adipocytes	14.5 nTPM
Adipose tissue	16.0 nTPM
Breast	13.1 nTPM

Alveolar cells type 1	16.0 nTPM
Lung	16.0 nTPM

Alveolar cells type 2	15.9 nTPM
Lung	15.9 nTPM

Astrocytes	19.5 nTPM
Brain	19.5 nTPM

B-cells	13.7 nTPM
Kidney	26.0 nTPM
Lymph node	23.3 nTPM
Stomach	20.7 nTPM
Spleen	15.0 nTPM
Adipose tissue	14.0 nTPM
Salivary gland	13.4 nTPM
Thymus	11.9 nTPM
Esophagus	11.8 nTPM
Bone marrow	10.2 nTPM
Liver	9.7 nTPM
PBMC	9.2 nTPM
Skin	6.8 nTPM
Lung	6.7 nTPM

Ciliated cells	18.3 nTPM
Bronchus	20.9 nTPM
Lung	20.9 nTPM
Fallopian tube	19.4 nTPM
Endometrium	12.1 nTPM

Club cells	14.5 nTPM
Prostate	15.3 nTPM
Bronchus	14.2 nTPM
Lung	14.0 nTPM

Endothelial cells	14.9 nTPM
Liver	25.2 nTPM
Esophagus	24.2 nTPM
Skin	18.6 nTPM
Fallopian tube	18.6 nTPM
Heart muscle	18.0 nTPM
Endometrium	15.6 nTPM
Skeletal muscle	15.6 nTPM
Thymus	15.5 nTPM
Prostate	13.7 nTPM
Salivary gland	13.7 nTPM
Vascular	13.6 nTPM
Lung	13.5 nTPM
Placenta	13.1 nTPM
Ovary	11.0 nTPM
Pancreas	10.3 nTPM
Tongue	9.8 nTPM
Breast	9.7 nTPM
Testis	8.9 nTPM

Enteroendocrine cells	14.7 nTPM
Rectum	21.8 nTPM
Colon	15.4 nTPM
Small intestine	6.9 nTPM

Fibroblasts	17.0 nTPM
Liver	39.1 nTPM
Heart muscle	35.3 nTPM
Placenta	22.0 nTPM
Esophagus	19.4 nTPM
Fallopian tube	18.1 nTPM
Skin	15.1 nTPM
Skeletal muscle	14.7 nTPM
Breast	14.2 nTPM
Adipose tissue	13.2 nTPM
Lung	13.1 nTPM
Stomach	13.0 nTPM
Thymus	12.6 nTPM
Salivary gland	12.3 nTPM
Vascular	12.3 nTPM
Prostate	9.9 nTPM
Pancreas	6.9 nTPM

Granulocytes	19.8 nTPM
Fallopian tube	28.1 nTPM
Lung	16.6 nTPM
Tongue	14.6 nTPM

Intestinal goblet cells	23.4 nTPM
Small intestine	26.6 nTPM
Rectum	25.2 nTPM
Colon	18.2 nTPM

Lymphatic endothelial cells	14.5 nTPM
Fallopian tube	18.1 nTPM
Ovary	10.9 nTPM

Macrophages	17.1 nTPM
Adipose tissue	27.8 nTPM
Spleen	24.1 nTPM
Stomach	23.1 nTPM
Fallopian tube	23.1 nTPM
Kidney	23.0 nTPM
Skeletal muscle	21.9 nTPM
Esophagus	20.6 nTPM
Lung	19.4 nTPM
Skin	18.9 nTPM
Bone marrow	18.2 nTPM
Endometrium	13.5 nTPM
Thymus	13.0 nTPM
Prostate	12.6 nTPM
Tongue	12.2 nTPM
Vascular	12.0 nTPM
Salivary gland	11.6 nTPM
Breast	10.4 nTPM
Pancreas	10.3 nTPM
Testis	9.3 nTPM

Paneth cells	15.9 nTPM
Colon	18.1 nTPM
Rectum	15.8 nTPM
Small intestine	13.8 nTPM

Basal keratinocytes	14.3 nTPM
Skin	17.3 nTPM
Tongue	11.3 nTPM

Basal squamous epithelial cells	17.5 nTPM
Esophagus	17.5 nTPM

Bipolar cells	16.1 nTPM
Eye	16.1 nTPM

Cholangiocytes	17.2 nTPM
Liver	17.2 nTPM

Plasma cells	15.0 nTPM
Liver	21.5 nTPM
Fallopian tube	20.9 nTPM
Spleen	19.5 nTPM
Thymus	16.1 nTPM
Salivary gland	13.0 nTPM
Stomach	11.3 nTPM
Esophagus	10.4 nTPM
Bone marrow	7.6 nTPM

Schwann cells	22.1 nTPM
Adipose tissue	32.4 nTPM
Esophagus	24.0 nTPM
Vascular	9.9 nTPM

Serous glandular cells	6.6 nTPM
Salivary gland	13.1 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	11.9 nTPM
Liver	18.3 nTPM
Esophagus	15.6 nTPM
Placenta	14.4 nTPM
Skeletal muscle	13.9 nTPM
Adipose tissue	12.9 nTPM
Fallopian tube	12.7 nTPM
Breast	12.0 nTPM
Lung	11.8 nTPM
Endometrium	11.4 nTPM
Salivary gland	11.1 nTPM
Tongue	10.2 nTPM
Vascular	9.9 nTPM
Prostate	9.7 nTPM
Skin	9.2 nTPM
Thymus	9.2 nTPM
Ovary	8.4 nTPM

Suprabasal keratinocytes	17.7 nTPM
Skin	21.7 nTPM
Tongue	13.7 nTPM

T-cells	14.4 nTPM
Adipose tissue	23.6 nTPM
Endometrium	21.5 nTPM
Fallopian tube	21.3 nTPM
Stomach	20.5 nTPM
Skeletal muscle	17.8 nTPM
Lymph node	16.6 nTPM
Spleen	16.4 nTPM
Liver	15.9 nTPM
Salivary gland	14.5 nTPM
Bone marrow	14.4 nTPM
Thymus	14.0 nTPM
Breast	13.1 nTPM
Vascular	12.9 nTPM
Esophagus	12.2 nTPM
Lung	11.8 nTPM
Prostate	11.8 nTPM
Colon	11.7 nTPM
Tongue	10.9 nTPM
Skin	10.2 nTPM
PBMC	8.8 nTPM
Kidney	3.5 nTPM

Undifferentiated cells	15.2 nTPM
Rectum	18.0 nTPM
Small intestine	15.0 nTPM
Colon	12.5 nTPM

Amygdala excitatory	45.0 nTPM
Thalamus	50.4 nTPM
Hypothalamus	48.5 nTPM
Amygdala	47.1 nTPM
Cerebral cortex	43.6 nTPM
Basal ganglia	40.4 nTPM
Hippocampus	40.0 nTPM

Astrocyte	42.0 nTPM
Amygdala	58.3 nTPM
Cerebral cortex	46.5 nTPM
Hippocampus	45.6 nTPM
Hypothalamus	44.4 nTPM
Basal ganglia	42.8 nTPM
Medulla oblongata	40.0 nTPM
Spinal cord	40.0 nTPM
Thalamus	39.7 nTPM
Pons	36.7 nTPM
Midbrain	36.1 nTPM
Cerebellum	32.1 nTPM

Bergmann glia	52.2 nTPM
Pons	59.0 nTPM
Cerebellum	57.1 nTPM
Medulla oblongata	40.5 nTPM

Central nervous system macrophage	59.1 nTPM
Amygdala	76.7 nTPM
Hypothalamus	66.6 nTPM
Basal ganglia	61.5 nTPM
Thalamus	60.8 nTPM
Midbrain	60.1 nTPM
Hippocampus	59.6 nTPM
Cerebellum	57.3 nTPM
Cerebral cortex	55.3 nTPM
Pons	54.8 nTPM
Spinal cord	49.2 nTPM
Medulla oblongata	48.8 nTPM

Cerebellar inhibitory	42.2 nTPM
Medulla oblongata	49.0 nTPM
Spinal cord	44.0 nTPM
Cerebellum	41.8 nTPM
Midbrain	38.9 nTPM
Pons	37.2 nTPM

Cge interneuron	37.8 nTPM
Hypothalamus	45.2 nTPM
Amygdala	40.7 nTPM
Basal ganglia	36.8 nTPM
Midbrain	36.3 nTPM
Thalamus	36.0 nTPM
Cerebral cortex	34.9 nTPM
Hippocampus	34.6 nTPM

Choroid plexus epithelial cell	56.0 nTPM
Thalamus	60.3 nTPM
Basal ganglia	59.0 nTPM
Hippocampus	52.7 nTPM
Medulla oblongata	52.0 nTPM

Committed oligodendrocyte precursor	42.3 nTPM
Hypothalamus	53.3 nTPM
Hippocampus	48.9 nTPM
Cerebral cortex	48.1 nTPM
Amygdala	46.2 nTPM
Basal ganglia	43.3 nTPM
Thalamus	43.2 nTPM
Cerebellum	39.6 nTPM
Midbrain	38.6 nTPM
Medulla oblongata	37.4 nTPM
Pons	33.6 nTPM
Spinal cord	33.1 nTPM

Deep-layer corticothalamic and 6b	38.8 nTPM
Hypothalamus	43.8 nTPM
Amygdala	43.2 nTPM
Cerebral cortex	40.9 nTPM
Hippocampus	38.8 nTPM
Basal ganglia	37.2 nTPM
Midbrain	28.8 nTPM

Deep-layer intratelencephalic	44.3 nTPM
Amygdala	49.8 nTPM
Hypothalamus	47.9 nTPM
Cerebral cortex	41.9 nTPM
Basal ganglia	41.6 nTPM
Hippocampus	40.4 nTPM

Deep-layer near-projecting	35.9 nTPM
Amygdala	43.5 nTPM
Hypothalamus	39.6 nTPM
Basal ganglia	33.4 nTPM
Cerebral cortex	33.4 nTPM
Hippocampus	29.6 nTPM

Eccentric medium spiny neuron	47.7 nTPM
Thalamus	54.5 nTPM
Basal ganglia	50.9 nTPM
Hypothalamus	48.2 nTPM
Amygdala	47.1 nTPM
Cerebral cortex	45.9 nTPM
Hippocampus	39.8 nTPM

Endothelial cell	61.8 nTPM
Hippocampus	76.3 nTPM
Basal ganglia	75.5 nTPM
Cerebellum	72.8 nTPM
Amygdala	65.9 nTPM
Midbrain	63.3 nTPM
Spinal cord	58.7 nTPM
Hypothalamus	57.1 nTPM
Thalamus	56.5 nTPM
Cerebral cortex	54.3 nTPM
Pons	52.4 nTPM
Medulla oblongata	47.2 nTPM