Single cell type - PCBP3 - 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.	PCBP3
Gene descriptionⁱ Full gene name according to HGNC.	Poly(rC) binding protein 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Plasma proteins
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.	9

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.	Bipolar cells - Visual perception (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 (Bipolar cells, Horizontal cells, Late spermatids, Rod photoreceptor cells, Cone photoreceptor cells, Muller glia cells, Early 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.	0.81
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.	Cell type enhanced (Midbrain-derived inhibitory, Pericyte)
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.	Immune cell enhanced (eosinophil)
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 type

Cell type enrichment

Single nuclei - Brain

Immune cells

Expression clustering

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 (Bipolar cells, Horizontal cells, Late spermatids, Rod photoreceptor cells, Cone photoreceptor cells, Muller glia cells, Early 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: Cell type enhanced (Midbrain-derived inhibitory, Pericyte)

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: Immune cell enhanced (eosinophil)
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

PCBP3 is part of cluster 25 Bipolar cells - Visual perception with confidenceⁱ 1
152 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.
GABRR2	Gamma-aminobutyric acid type A receptor subunit rho2	0.7723	25
NEUROD4	Neuronal differentiation 4	0.7627	25
GABRR3	Gamma-aminobutyric acid type A receptor subunit rho3	0.7612	25
VSX1	Visual system homeobox 1	0.7557	25
PCDHA13	Protocadherin alpha 13	0.7433	25
TMEM215	Transmembrane protein 215	0.7400	25
TRPM1	Transient receptor potential cation channel subfamily M member 1	0.7400	25
GPR179	G protein-coupled receptor 179	0.7373	25
GRM6	Glutamate metabotropic receptor 6	0.7319	25
PLCD4	Phospholipase C delta 4	0.7250	25
AANAT	Aralkylamine N-acetyltransferase	0.7228	25
ATP6V1G2	ATPase H+ transporting V1 subunit G2	0.7215	25
VSX2	Visual system homeobox 2	0.7144	25
GABRR1	Gamma-aminobutyric acid type A receptor subunit rho1	0.7117	25
CCDC177	Coiled-coil domain containing 177	0.7073	25

IMMUNE CELLS

PCBP3 is part of cluster 41 Basophils - Unknown function with confidenceⁱ 0.67
293 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.
CASP9	Caspase 9	1.0000	41
RNF103	Ring finger protein 103	1.0000	41
PSME3IP1	Proteasome activator subunit 3 interacting protein 1	1.0000	41
C19orf47	Chromosome 19 open reading frame 47	1.0000	41
DCLRE1C	DNA cross-link repair 1C	1.0000	41
GPR107	G protein-coupled receptor 107	1.0000	41
PAPSS1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	1.0000	41
ADAM19	ADAM metallopeptidase domain 19	1.0000	41
CTNNBL1	Catenin beta like 1	1.0000	41
CD9	CD9 molecule	0.9762	41
DPF2	Double PHD fingers 2	0.9762	41
HEATR5A	HEAT repeat containing 5A	0.9762	41
SPDYE1	Speedy/RINGO cell cycle regulator family member E1	0.9762	32
IL1RL1	Interleukin 1 receptor like 1	0.9762	41
PLD3	Phospholipase D family member 3	0.9762	41