Single cell type - PRPF38B - The Human Protein Atlas

PRPF38B

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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.	PRPF38B
Gene descriptionⁱ Full gene name according to HGNC.	Pre-mRNA processing factor 38B
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.	3

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.	NK-cells & T-cells - Immune system & Transcription (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.	Low cell type specificity
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.	0.23
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: Low cell type specificity

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

PRPF38B is part of cluster 78 NK-cells & T-cells - Immune system & Transcription with confidenceⁱ 1
392 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.
SLFN12L	Schlafen family member 12 like	0.6622	19
PPP2R5C	Protein phosphatase 2 regulatory subunit B'gamma	0.5983	78
TRGC2	T cell receptor gamma constant 2	0.5915	19
CLEC2D	C-type lectin domain family 2 member D	0.5756	78
TRAC	T cell receptor alpha constant	0.5652	19
TRBC1	T cell receptor beta constant 1	0.5595	19
GZMK	Granzyme K	0.5486	78
RUNX3	RUNX family transcription factor 3	0.5463	78
TRBC2	T cell receptor beta constant 2	0.5462	78
CASP8	Caspase 8	0.5284	78
C16orf54	Chromosome 16 open reading frame 54	0.5272	78
KLRC4	Killer cell lectin like receptor C4	0.5265	19
IL4	Interleukin 4	0.5239	78
RNF125	Ring finger protein 125	0.5217	78
CD226	CD226 molecule	0.5177	78

IMMUNE CELLS

PRPF38B is part of cluster 22 Eosinophils - Transcription with confidenceⁱ 0.81
357 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.
RALGAPA2	Ral GTPase activating protein catalytic subunit alpha 2	0.9524	29
ZNF516	Zinc finger protein 516	0.9048	36
FNDC3B	Fibronectin type III domain containing 3B	0.8810	22
CNOT3	CCR4-NOT transcription complex subunit 3	0.8810	29
MLF2	Myeloid leukemia factor 2	0.8810	29
C11orf54	Chromosome 11 open reading frame 54	0.8810	21
RBM7	RNA binding motif protein 7	0.8571	21
ZBTB48	Zinc finger and BTB domain containing 48	0.8571	22
UBL5	Ubiquitin like 5	0.8571	36
IL17RA	Interleukin 17 receptor A	0.8571	21
RUNX1	RUNX family transcription factor 1	0.8571	22
PIGM	Phosphatidylinositol glycan anchor biosynthesis class M	0.8571	22
CD63	CD63 molecule	0.8571	22
MBOAT7	Membrane bound O-acyltransferase domain containing 7	0.8571	21
MRGBP	MRG domain binding protein	0.8571	22

Adipocytes	84.7 nTPM
Adipose tissue	86.4 nTPM
Breast	83.0 nTPM

Alveolar cells type 1	67.5 nTPM
Lung	67.5 nTPM

Alveolar cells type 2	84.0 nTPM
Lung	84.0 nTPM

Astrocytes	36.5 nTPM
Brain	36.5 nTPM

B-cells	156.6 nTPM
Adipose tissue	214.0 nTPM
Salivary gland	185.9 nTPM
Liver	183.5 nTPM
Skin	172.8 nTPM
PBMC	170.9 nTPM
Lymph node	159.6 nTPM
Kidney	156.0 nTPM
Stomach	153.1 nTPM
Lung	136.8 nTPM
Esophagus	135.7 nTPM
Thymus	131.8 nTPM
Spleen	129.5 nTPM
Bone marrow	105.7 nTPM

Ciliated cells	56.5 nTPM
Fallopian tube	60.3 nTPM
Endometrium	59.7 nTPM
Lung	57.9 nTPM
Bronchus	48.0 nTPM

Club cells	74.2 nTPM
Prostate	76.6 nTPM
Bronchus	74.8 nTPM
Lung	71.2 nTPM

Dendritic cells	183.6 nTPM
Adipose tissue	237.7 nTPM
PBMC	129.5 nTPM

Endothelial cells	89.0 nTPM
Heart muscle	126.9 nTPM
Placenta	115.8 nTPM
Skin	109.1 nTPM
Ovary	109.0 nTPM
Endometrium	104.0 nTPM
Fallopian tube	100.3 nTPM
Salivary gland	99.1 nTPM
Skeletal muscle	89.7 nTPM
Liver	85.7 nTPM
Testis	84.9 nTPM
Vascular	82.7 nTPM
Breast	82.6 nTPM
Lung	75.5 nTPM
Prostate	75.5 nTPM
Esophagus	69.4 nTPM
Thymus	69.2 nTPM
Pancreas	62.0 nTPM
Tongue	59.9 nTPM

Enteroendocrine cells	95.5 nTPM
Colon	125.4 nTPM
Small intestine	82.4 nTPM
Rectum	78.8 nTPM

Fibroblasts	70.6 nTPM
Liver	106.7 nTPM
Skin	97.2 nTPM
Fallopian tube	88.5 nTPM
Lung	75.0 nTPM
Placenta	74.3 nTPM
Skeletal muscle	73.3 nTPM
Breast	71.5 nTPM
Prostate	70.6 nTPM
Adipose tissue	66.4 nTPM
Salivary gland	64.1 nTPM
Pancreas	63.4 nTPM
Vascular	62.3 nTPM
Stomach	62.0 nTPM
Heart muscle	56.0 nTPM
Thymus	52.5 nTPM
Esophagus	45.5 nTPM

Granulocytes	80.9 nTPM
Fallopian tube	100.5 nTPM
Lung	88.7 nTPM
Tongue	53.4 nTPM

Intestinal goblet cells	99.0 nTPM
Colon	128.7 nTPM
Small intestine	107.2 nTPM
Rectum	61.0 nTPM

Lymphatic endothelial cells	102.9 nTPM
Ovary	114.6 nTPM
Fallopian tube	91.2 nTPM

Macrophages	135.2 nTPM
Adipose tissue	230.5 nTPM
Prostate	210.0 nTPM
Skin	206.1 nTPM
Testis	184.7 nTPM
Breast	170.3 nTPM
Salivary gland	160.2 nTPM
Endometrium	159.3 nTPM
Tongue	152.0 nTPM
Fallopian tube	147.7 nTPM
Skeletal muscle	138.7 nTPM
Lung	123.3 nTPM
Esophagus	105.3 nTPM
Vascular	98.1 nTPM
Spleen	86.2 nTPM
Thymus	85.5 nTPM
Stomach	84.9 nTPM
Kidney	79.7 nTPM
Pancreas	74.0 nTPM
Bone marrow	72.0 nTPM

Basal keratinocytes	181.2 nTPM
Skin	272.9 nTPM
Tongue	89.4 nTPM

Basal prostatic cells	88.1 nTPM
Prostate	88.1 nTPM

Basal respiratory cells	79.2 nTPM
Bronchus	79.2 nTPM

Basal squamous epithelial cells	93.5 nTPM
Esophagus	93.5 nTPM

Paneth cells	81.0 nTPM
Small intestine	103.6 nTPM
Rectum	81.6 nTPM
Colon	57.9 nTPM

Plasma cells	96.8 nTPM
Liver	124.2 nTPM
Stomach	116.4 nTPM
Salivary gland	114.6 nTPM
Spleen	109.7 nTPM
Thymus	91.4 nTPM
Fallopian tube	87.2 nTPM
Esophagus	67.6 nTPM
Bone marrow	63.4 nTPM

Schwann cells	77.4 nTPM
Adipose tissue	160.1 nTPM
Vascular	60.1 nTPM
Esophagus	12.0 nTPM

Serous glandular cells	57.0 nTPM
Salivary gland	69.8 nTPM
Tongue	44.2 nTPM

Smooth muscle cells	80.7 nTPM
Endometrium	121.9 nTPM
Skin	114.9 nTPM
Skeletal muscle	100.6 nTPM
Lung	97.6 nTPM
Liver	93.4 nTPM
Ovary	84.0 nTPM
Placenta	83.1 nTPM
Adipose tissue	79.7 nTPM
Vascular	77.5 nTPM
Salivary gland	71.3 nTPM
Breast	69.3 nTPM
Fallopian tube	68.3 nTPM
Tongue	67.1 nTPM
Esophagus	54.1 nTPM
Prostate	54.1 nTPM
Thymus	53.8 nTPM

Suprabasal keratinocytes	174.9 nTPM
Skin	277.2 nTPM
Tongue	72.5 nTPM

T-cells	221.0 nTPM
Adipose tissue	385.3 nTPM
Skin	358.5 nTPM
Colon	337.3 nTPM
Endometrium	258.0 nTPM
Skeletal muscle	249.5 nTPM
Tongue	249.0 nTPM
Breast	244.6 nTPM
Liver	233.6 nTPM
PBMC	228.8 nTPM
Lung	218.6 nTPM
Salivary gland	216.1 nTPM
Vascular	195.8 nTPM
Fallopian tube	186.5 nTPM
Prostate	184.8 nTPM
Thymus	177.8 nTPM
Esophagus	170.4 nTPM
Spleen	158.2 nTPM
Lymph node	158.0 nTPM
Kidney	157.8 nTPM
Stomach	140.3 nTPM
Bone marrow	131.5 nTPM

Undifferentiated cells	101.2 nTPM
Colon	135.5 nTPM
Small intestine	86.9 nTPM
Rectum	81.3 nTPM

Amygdala excitatory	51.3 nTPM
Hypothalamus	67.4 nTPM
Basal ganglia	56.2 nTPM
Amygdala	55.6 nTPM
Hippocampus	49.6 nTPM
Cerebral cortex	44.8 nTPM
Thalamus	34.0 nTPM

Astrocyte	53.0 nTPM
Amygdala	83.1 nTPM
Cerebral cortex	71.4 nTPM
Hippocampus	70.4 nTPM
Hypothalamus	53.8 nTPM
Thalamus	53.5 nTPM
Basal ganglia	51.2 nTPM
Midbrain	45.7 nTPM
Pons	44.8 nTPM
Medulla oblongata	38.4 nTPM
Cerebellum	38.0 nTPM
Spinal cord	33.3 nTPM

Bergmann glia	57.3 nTPM
Cerebellum	74.6 nTPM
Pons	50.3 nTPM
Medulla oblongata	46.9 nTPM

Central nervous system macrophage	210.0 nTPM
Amygdala	307.1 nTPM
Cerebral cortex	233.5 nTPM
Hippocampus	230.9 nTPM
Thalamus	215.8 nTPM
Hypothalamus	215.6 nTPM
Midbrain	210.6 nTPM
Cerebellum	193.8 nTPM
Basal ganglia	184.8 nTPM
Pons	183.1 nTPM
Spinal cord	172.5 nTPM
Medulla oblongata	162.2 nTPM

Cerebellar inhibitory	53.8 nTPM
Spinal cord	63.2 nTPM
Cerebellum	63.0 nTPM
Midbrain	55.7 nTPM
Medulla oblongata	44.9 nTPM
Pons	42.0 nTPM

Cge interneuron	40.5 nTPM
Amygdala	43.7 nTPM
Hypothalamus	43.4 nTPM
Thalamus	41.6 nTPM
Cerebral cortex	39.7 nTPM
Basal ganglia	39.0 nTPM
Midbrain	38.3 nTPM
Hippocampus	37.9 nTPM

Choroid plexus epithelial cell	43.0 nTPM
Hippocampus	49.9 nTPM
Basal ganglia	47.6 nTPM
Medulla oblongata	38.9 nTPM
Thalamus	35.6 nTPM

Committed oligodendrocyte precursor	64.3 nTPM
Amygdala	93.0 nTPM
Hypothalamus	77.8 nTPM
Thalamus	76.8 nTPM
Cerebral cortex	70.9 nTPM
Midbrain	68.0 nTPM
Hippocampus	65.5 nTPM
Cerebellum	58.7 nTPM
Pons	58.4 nTPM
Basal ganglia	58.0 nTPM
Spinal cord	55.2 nTPM
Medulla oblongata	24.5 nTPM

Deep-layer corticothalamic and 6b	44.6 nTPM
Hypothalamus	61.2 nTPM
Amygdala	44.4 nTPM
Midbrain	43.3 nTPM
Cerebral cortex	41.2 nTPM
Hippocampus	38.9 nTPM
Basal ganglia	38.8 nTPM

Deep-layer intratelencephalic	39.6 nTPM
Amygdala	45.0 nTPM
Hypothalamus	43.8 nTPM
Cerebral cortex	36.6 nTPM
Hippocampus	36.6 nTPM
Basal ganglia	36.3 nTPM

Deep-layer near-projecting	31.3 nTPM
Hypothalamus	39.4 nTPM
Basal ganglia	33.2 nTPM
Cerebral cortex	32.9 nTPM
Amygdala	29.8 nTPM
Hippocampus	21.5 nTPM

Eccentric medium spiny neuron	47.6 nTPM
Hypothalamus	58.0 nTPM
Amygdala	48.6 nTPM
Cerebral cortex	47.0 nTPM
Basal ganglia	46.4 nTPM
Thalamus	42.9 nTPM
Hippocampus	42.7 nTPM