Single cell type - PACRGL - The Human Protein Atlas

PACRGL

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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.	PACRGL
Gene descriptionⁱ Full gene name according to HGNC.	Parkin coregulated like
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.	24

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.	Spermatids - 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.	Cell type enhanced (Early spermatids, Late spermatids, Spermatocytes)
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.	0.57
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, Late spermatids, Spermatocytes)

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

PACRGL is part of cluster 13 Spermatids - Transcription with confidenceⁱ 1
116 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.
NPIPA1	Nuclear pore complex interacting protein family member A1	0.6484	13
NBPF4	NBPF member 4	0.6127	13
MRRF	Mitochondrial ribosome recycling factor	0.6002	11
NPIPB4	Nuclear pore complex interacting protein family member B4	0.5969	13
CEP76	Centrosomal protein 76	0.5968	21
NPIPA2	Nuclear pore complex interacting protein family member A2	0.5957	13
AGAP4	ArfGAP with GTPase domain, ankyrin repeat and PH domain 4	0.5829	13
PEX5	Peroxisomal biogenesis factor 5	0.5804	21
CCDC90B	Coiled-coil domain containing 90B	0.5782	13
TANGO6	Transport and golgi organization 6 homolog	0.5732	21
AGAP5	ArfGAP with GTPase domain, ankyrin repeat and PH domain 5	0.5721	13
ASNS	Asparagine synthetase (glutamine-hydrolyzing)	0.5686	13
EFCAB11	EF-hand calcium binding domain 11	0.5576	11
SPATA31C1	SPATA31 subfamily C member 1	0.5551	13
SPDYE17	Speedy/RINGO cell cycle regulator family member E17	0.5536	13

IMMUNE CELLS

PACRGL is part of cluster 13 Non-specific - Mitochondria with confidenceⁱ 0.62
458 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.
POLD1	DNA polymerase delta 1, catalytic subunit	0.9762	18
DNAAF4	Dynein axonemal assembly factor 4	0.9762	13
ZNF846	Zinc finger protein 846	0.9762	18
PIP5K1C	Phosphatidylinositol-4-phosphate 5-kinase type 1 gamma	0.9762	13
OTULIN	OTU deubiquitinase with linear linkage specificity	0.9762	13
PPRC1	PPARG related coactivator 1	0.9762	13
POLR3H	RNA polymerase III subunit H	0.9762	13
TOP3B	DNA topoisomerase III beta	0.9762	13
PRMT5	Protein arginine methyltransferase 5	0.9524	13
STK16	Serine/threonine kinase 16	0.9524	13
BRCA2	BRCA2 DNA repair associated	0.9524	13
TP53	Tumor protein p53	0.9524	13
ANKMY1	Ankyrin repeat and MYND domain containing 1	0.9524	18
MYO1E	Myosin IE	0.9524	13
RFNG	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	0.9524	13

Adipocytes	7.6 nTPM
Adipose tissue	8.7 nTPM
Breast	6.5 nTPM

Alveolar cells type 1	6.8 nTPM
Lung	6.8 nTPM

Alveolar cells type 2	7.8 nTPM
Lung	7.8 nTPM

Astrocytes	35.9 nTPM
Brain	35.9 nTPM

B-cells	4.8 nTPM
PBMC	10.8 nTPM
Adipose tissue	7.4 nTPM
Bone marrow	7.2 nTPM
Spleen	6.9 nTPM
Stomach	5.9 nTPM
Salivary gland	5.7 nTPM
Liver	4.8 nTPM
Lymph node	4.7 nTPM
Thymus	4.3 nTPM
Lung	2.7 nTPM
Skin	1.7 nTPM
Kidney	0.0 nTPM
Esophagus	0.0 nTPM

Ciliated cells	19.4 nTPM
Lung	21.4 nTPM
Bronchus	19.9 nTPM
Fallopian tube	18.6 nTPM
Endometrium	17.8 nTPM

Club cells	6.4 nTPM
Bronchus	7.5 nTPM
Prostate	6.6 nTPM
Lung	5.2 nTPM

Endothelial cells	7.3 nTPM
Pancreas	12.9 nTPM
Skin	12.5 nTPM
Testis	11.0 nTPM
Esophagus	10.3 nTPM
Prostate	9.9 nTPM
Fallopian tube	8.8 nTPM
Ovary	8.3 nTPM
Vascular	7.3 nTPM
Thymus	7.1 nTPM
Salivary gland	6.3 nTPM
Tongue	5.8 nTPM
Lung	5.7 nTPM
Endometrium	5.5 nTPM
Breast	5.3 nTPM
Placenta	5.1 nTPM
Skeletal muscle	4.7 nTPM
Heart muscle	4.2 nTPM
Liver	1.3 nTPM

Enteroendocrine cells	6.8 nTPM
Colon	10.2 nTPM
Rectum	6.7 nTPM
Small intestine	3.4 nTPM

Fibroblasts	9.1 nTPM
Liver	13.0 nTPM
Adipose tissue	13.0 nTPM
Skin	12.4 nTPM
Esophagus	11.7 nTPM
Skeletal muscle	11.2 nTPM
Lung	11.1 nTPM
Breast	9.0 nTPM
Stomach	8.6 nTPM
Vascular	8.5 nTPM
Fallopian tube	8.2 nTPM
Prostate	7.9 nTPM
Salivary gland	7.7 nTPM
Thymus	7.6 nTPM
Pancreas	6.9 nTPM
Placenta	4.4 nTPM
Heart muscle	3.7 nTPM

Granulocytes	4.5 nTPM
Tongue	4.9 nTPM
Fallopian tube	4.6 nTPM
Lung	4.0 nTPM

Intestinal goblet cells	7.0 nTPM
Small intestine	7.8 nTPM
Rectum	6.9 nTPM
Colon	6.2 nTPM

Lymphatic endothelial cells	6.0 nTPM
Fallopian tube	6.6 nTPM
Ovary	5.5 nTPM

Macrophages	5.1 nTPM
Bone marrow	10.1 nTPM
Breast	9.6 nTPM
Testis	9.3 nTPM
Kidney	8.9 nTPM
Pancreas	6.2 nTPM
Vascular	5.5 nTPM
Adipose tissue	5.2 nTPM
Skeletal muscle	5.1 nTPM
Salivary gland	4.5 nTPM
Lung	4.3 nTPM
Prostate	4.3 nTPM
Fallopian tube	4.1 nTPM
Esophagus	3.9 nTPM
Skin	3.3 nTPM
Spleen	3.0 nTPM
Tongue	3.0 nTPM
Stomach	2.6 nTPM
Endometrium	2.5 nTPM
Thymus	2.1 nTPM

Paneth cells	12.6 nTPM
Small intestine	20.7 nTPM
Rectum	10.0 nTPM
Colon	7.2 nTPM

Basal prostatic cells	8.0 nTPM
Prostate	8.0 nTPM

Basal squamous epithelial cells	10.4 nTPM
Esophagus	10.4 nTPM

Collecting duct cells	9.7 nTPM
Kidney	9.7 nTPM

Cone photoreceptor cells	13.6 nTPM
Eye	13.6 nTPM

Plasma cells	1.9 nTPM
Fallopian tube	3.5 nTPM
Liver	3.0 nTPM
Spleen	2.4 nTPM
Thymus	2.4 nTPM
Stomach	1.7 nTPM
Bone marrow	1.5 nTPM
Salivary gland	0.9 nTPM
Esophagus	0.0 nTPM

Schwann cells	4.3 nTPM
Vascular	7.8 nTPM
Adipose tissue	5.1 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	4.7 nTPM
Salivary gland	4.9 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	7.6 nTPM
Placenta	11.9 nTPM
Lung	10.6 nTPM
Adipose tissue	10.2 nTPM
Fallopian tube	9.7 nTPM
Skin	8.7 nTPM
Vascular	8.6 nTPM
Ovary	8.1 nTPM
Skeletal muscle	7.9 nTPM
Liver	7.6 nTPM
Breast	7.5 nTPM
Thymus	7.0 nTPM
Endometrium	6.7 nTPM
Prostate	5.5 nTPM
Tongue	4.5 nTPM
Salivary gland	4.1 nTPM
Esophagus	3.6 nTPM

T-cells	4.1 nTPM
Kidney	7.1 nTPM
Lymph node	5.8 nTPM
Stomach	5.7 nTPM
Skin	5.6 nTPM
Adipose tissue	5.1 nTPM
Breast	5.0 nTPM
Endometrium	4.6 nTPM
PBMC	4.4 nTPM
Fallopian tube	4.1 nTPM
Bone marrow	4.0 nTPM
Prostate	3.9 nTPM
Salivary gland	3.9 nTPM
Tongue	3.7 nTPM
Spleen	3.6 nTPM
Vascular	3.6 nTPM
Thymus	3.2 nTPM
Skeletal muscle	3.0 nTPM
Lung	2.9 nTPM
Esophagus	2.4 nTPM
Liver	2.2 nTPM
Colon	1.9 nTPM

Undifferentiated cells	10.7 nTPM
Colon	11.3 nTPM
Small intestine	10.7 nTPM
Rectum	10.0 nTPM

Amygdala excitatory	74.3 nTPM
Hypothalamus	85.4 nTPM
Thalamus	78.5 nTPM
Hippocampus	75.8 nTPM
Cerebral cortex	71.8 nTPM
Amygdala	70.2 nTPM
Basal ganglia	64.0 nTPM

Astrocyte	68.5 nTPM
Amygdala	93.5 nTPM
Hypothalamus	76.7 nTPM
Hippocampus	72.8 nTPM
Thalamus	70.7 nTPM
Basal ganglia	69.7 nTPM
Cerebral cortex	66.8 nTPM
Midbrain	65.3 nTPM
Pons	60.4 nTPM
Medulla oblongata	60.0 nTPM
Spinal cord	59.2 nTPM
Cerebellum	57.9 nTPM

Bergmann glia	73.0 nTPM
Medulla oblongata	85.2 nTPM
Cerebellum	73.2 nTPM
Pons	60.4 nTPM

Central nervous system macrophage	63.9 nTPM
Amygdala	97.3 nTPM
Hippocampus	69.0 nTPM
Hypothalamus	67.4 nTPM
Thalamus	66.1 nTPM
Midbrain	65.9 nTPM
Basal ganglia	64.1 nTPM
Cerebellum	62.3 nTPM
Cerebral cortex	58.6 nTPM
Pons	58.2 nTPM
Medulla oblongata	49.6 nTPM
Spinal cord	44.5 nTPM

Cerebellar inhibitory	67.4 nTPM
Spinal cord	74.2 nTPM
Cerebellum	67.9 nTPM
Medulla oblongata	66.1 nTPM
Pons	64.9 nTPM
Midbrain	64.1 nTPM

Cge interneuron	50.7 nTPM
Hypothalamus	58.0 nTPM
Amygdala	55.6 nTPM
Midbrain	53.9 nTPM
Thalamus	48.5 nTPM
Basal ganglia	47.9 nTPM
Hippocampus	46.9 nTPM
Cerebral cortex	44.0 nTPM

Choroid plexus epithelial cell	110.3 nTPM
Basal ganglia	168.6 nTPM
Hippocampus	94.3 nTPM
Thalamus	90.4 nTPM
Medulla oblongata	88.0 nTPM

Committed oligodendrocyte precursor	61.6 nTPM
Hypothalamus	92.9 nTPM
Cerebellum	77.7 nTPM
Basal ganglia	65.7 nTPM
Thalamus	65.3 nTPM
Amygdala	63.2 nTPM
Cerebral cortex	62.7 nTPM
Hippocampus	62.6 nTPM
Medulla oblongata	55.5 nTPM
Midbrain	54.6 nTPM
Pons	44.3 nTPM
Spinal cord	33.1 nTPM

Deep-layer corticothalamic and 6b	69.1 nTPM
Amygdala	76.2 nTPM
Hypothalamus	75.6 nTPM
Cerebral cortex	69.0 nTPM
Hippocampus	65.9 nTPM
Midbrain	64.3 nTPM
Basal ganglia	63.3 nTPM

Deep-layer intratelencephalic	58.8 nTPM
Hypothalamus	66.4 nTPM
Amygdala	61.3 nTPM
Hippocampus	60.4 nTPM
Basal ganglia	53.2 nTPM
Cerebral cortex	53.0 nTPM

Deep-layer near-projecting	65.1 nTPM
Hypothalamus	74.1 nTPM
Amygdala	68.2 nTPM
Basal ganglia	67.0 nTPM
Cerebral cortex	62.1 nTPM
Hippocampus	54.3 nTPM

Eccentric medium spiny neuron	70.3 nTPM
Basal ganglia	75.6 nTPM
Thalamus	74.8 nTPM
Amygdala	73.6 nTPM
Hypothalamus	71.5 nTPM
Cerebral cortex	68.0 nTPM
Hippocampus	58.4 nTPM

Endothelial cell	46.3 nTPM
Hypothalamus	72.0 nTPM
Amygdala	61.5 nTPM
Basal ganglia	49.4 nTPM
Cerebral cortex	48.6 nTPM
Hippocampus	46.2 nTPM
Spinal cord	44.9 nTPM
Cerebellum	41.0 nTPM
Pons	40.6 nTPM
Midbrain	39.7 nTPM
Medulla oblongata	33.8 nTPM
Thalamus	31.6 nTPM

Ependymal cell	124.6 nTPM
Amygdala	143.9 nTPM
Hypothalamus	139.2 nTPM
Hippocampus	139.0 nTPM
Basal ganglia	131.4 nTPM
Midbrain	130.8 nTPM
Thalamus	120.3 nTPM
Pons	108.0 nTPM
Medulla oblongata	105.6 nTPM
Spinal cord	103.5 nTPM