Single cell type - TVP23C-CDRT4 - 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.	TVP23C-CDRT4
Gene descriptionⁱ Full gene name according to HGNC.	TVP23C-CDRT4 readthrough
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.	Membrane, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

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.	Neurons - Neuronal signaling (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.	Group enriched (Oligodendrocytes, Oligodendrocyte precursor cells, Inhibitory neurons, Microglial cells, Excitatory neurons, Astrocytes)
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.	0.91
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.	Not available
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 transcript level

ASSAYSⁱ

Single cell type

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: Group enriched (Oligodendrocytes, Oligodendrocyte precursor cells, Inhibitory neurons, Microglial cells, Excitatory neurons, Astrocytes)

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

TVP23C-CDRT4 is part of cluster 69 Neurons - Neuronal signaling with confidenceⁱ 1
331 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.
NLGN1	Neuroligin 1	0.8715	76
RFX7	Regulatory factor X7	0.8345	69
ZNF782	Zinc finger protein 782	0.8285	69
TRPC1	Transient receptor potential cation channel subfamily C member 1	0.8146	69
GPR137C	G protein-coupled receptor 137C	0.7973	69
GALNT13	Polypeptide N-acetylgalactosaminyltransferase 13	0.7825	69
NALCN	Sodium leak channel, non-selective	0.7496	69
ZSWIM5	Zinc finger SWIM-type containing 5	0.7474	69
ZC3H12B	Zinc finger CCCH-type containing 12B	0.7450	69
VPS13B	Vacuolar protein sorting 13 homolog B	0.7445	69
ZNF559-ZNF177	ZNF559-ZNF177 readthrough	0.7368	69
SLC24A3	Solute carrier family 24 member 3	0.7284	69
GPHN	Gephyrin	0.7267	69
KCNK2	Potassium two pore domain channel subfamily K member 2	0.7198	69
GLRA2	Glycine receptor alpha 2	0.7156	69

IMMUNE CELLS

TVP23C-CDRT4 is part of cluster 22 Eosinophils - Transcription with confidenceⁱ 1
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.
ZNF582	Zinc finger protein 582	0.9762	22
WIPI1	WD repeat domain, phosphoinositide interacting 1	0.9762	22
LSM3	LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated	0.9762	22
CDKN2D	Cyclin dependent kinase inhibitor 2D	0.9762	22
NCOR2	Nuclear receptor corepressor 2	0.9524	22
NFATC2IP	Nuclear factor of activated T cells 2 interacting protein	0.9524	22
USP48	Ubiquitin specific peptidase 48	0.9524	22
SCAPER	S-phase cyclin A associated protein in the ER	0.9524	22
CHPT1	Choline phosphotransferase 1	0.9286	22
ERVK3-1	Endogenous retrovirus group K3 member 1	0.9286	42
CUTC	CutC copper transporter	0.9286	22
BBX	BBX high mobility group box domain containing	0.9286	22
XRN1	5'-3' exoribonuclease 1	0.9286	22
ST3GAL1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	0.9286	22
FZR1	Fizzy and cell division cycle 20 related 1	0.9286	22