Single cell type - CPSF3 - 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.	CPSF3
Gene descriptionⁱ Full gene name according to HGNC.	Cleavage and polyadenylation specific factor 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes
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.	Non-specific - Mixed function (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, 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.	0.51
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 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 (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: 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

CPSF3 is part of cluster 15 Non-specific - Mixed function with confidenceⁱ 1
295 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.
H3-5	H3.5 histone	0.6744	70
GMPS	Guanine monophosphate synthase	0.6536	70
UBL7	Ubiquitin like 7	0.6208	15
ACTL6A	Actin like 6A	0.6082	15
CCT4	Chaperonin containing TCP1 subunit 4	0.6034	15
NACA2	Nascent polypeptide associated complex subunit alpha 2	0.6031	70
PSMD6	Proteasome 26S subunit, non-ATPase 6	0.5974	15
PSMD11	Proteasome 26S subunit, non-ATPase 11	0.5922	15
CDC45	Cell division cycle 45	0.5846	52
CCT5	Chaperonin containing TCP1 subunit 5	0.5813	15
HSPA14	Heat shock protein family A (Hsp70) member 14	0.5801	15
HMGA2	High mobility group AT-hook 2	0.5587	15
WDR12	WD repeat domain 12	0.5471	15
HTRA2	HtrA serine peptidase 2	0.5470	1
UBE2K	Ubiquitin conjugating enzyme E2 K	0.5428	15

IMMUNE CELLS

CPSF3 is part of cluster 13 Non-specific - Mitochondria with confidenceⁱ 0.48
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.
EIF3I	Eukaryotic translation initiation factor 3 subunit I	0.9762	12
TMTC4	Transmembrane O-mannosyltransferase targeting cadherins 4	0.9762	13
DUS3L	Dihydrouridine synthase 3 like	0.9762	13
SMIM15	Small integral membrane protein 15	0.9762	13
FLAD1	Flavin adenine dinucleotide synthetase 1	0.9762	13
PCBD1	Pterin-4 alpha-carbinolamine dehydratase 1	0.9762	13
RPUSD3	RNA pseudouridine synthase D3	0.9524	12
UHRF1	Ubiquitin like with PHD and ring finger domains 1	0.9524	13
ATP5MF-PTCD1	ATP5MF-PTCD1 readthrough	0.9524	13
TMEM126A	Transmembrane protein 126A	0.9524	13
ATG4B	Autophagy related 4B cysteine peptidase	0.9524	13
TRAPPC2L	Trafficking protein particle complex subunit 2L	0.9524	13
TEX264	Testis expressed 264, ER-phagy receptor	0.9524	12
ALG1	ALG1 chitobiosyldiphosphodolichol beta-mannosyltransferase	0.9524	12
PIGF	Phosphatidylinositol glycan anchor biosynthesis class F	0.9524	13