Single cell type - RPH3AL - 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.	RPH3AL
Gene descriptionⁱ Full gene name according to HGNC.	Rabphilin 3A like (without C2 domains)
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.	15

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.	Alveolar cells - Lung 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 (Hepatocytes, Alveolar cells type 2, Alveolar cells type 1)
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.	0.52
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 (Endothelial cell)
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 (Hepatocytes, Alveolar cells type 2, Alveolar cells type 1)

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 (Endothelial cell)

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

RPH3AL is part of cluster 72 Alveolar cells - Lung function with confidenceⁱ 1
121 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.
EMP2	Epithelial membrane protein 2	0.5089	72
FOXA2	Forkhead box A2	0.4927	16
FZD5	Frizzled class receptor 5	0.4859	16
GPX2	Glutathione peroxidase 2	0.4733	43
TDGF1	Teratocarcinoma-derived growth factor 1	0.4731	6
EPHX1	Epoxide hydrolase 1	0.4704	53
MYO1B	Myosin IB	0.4680	48
LDLR	Low density lipoprotein receptor	0.4468	72
ENSG00000282218	Novel protein, GOPC-ROS1 readthrough	0.4454	72
SFTPC	Surfactant protein C	0.4333	72
HYAL1	Hyaluronidase 1	0.4330	56
SFTPA1	Surfactant protein A1	0.4329	72
ADH1C	Alcohol dehydrogenase 1C (class I), gamma polypeptide	0.4324	43
DOCK6	Dedicator of cytokinesis 6	0.4320	41
ADGRF5	Adhesion G protein-coupled receptor F5	0.4290	41

IMMUNE CELLS

RPH3AL is part of cluster 30 Non-specific - DNA binding with confidenceⁱ 1
263 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.
C2orf81	Chromosome 2 open reading frame 81	0.9762	13
ACBD6	Acyl-CoA binding domain containing 6	0.9762	30
APP	Amyloid beta precursor protein	0.9762	2
NREP	Neuronal regeneration related protein	0.9762	2
ABL1	ABL proto-oncogene 1, non-receptor tyrosine kinase	0.9762	30
SH3BP4	SH3 domain binding protein 4	0.9762	2
PTCH2	Patched 2	0.9762	30
OSCP1	Organic solute carrier partner 1	0.9762	30
PTGR1	Prostaglandin reductase 1	0.9762	2
UBFD1	Ubiquitin family domain containing 1	0.9524	30
RECQL5	RecQ like helicase 5	0.9524	30
LIG3	DNA ligase 3	0.9524	30
DHODH	Dihydroorotate dehydrogenase (quinone)	0.9524	30
APEX1	Apurinic/apyrimidinic endodeoxyribonuclease 1	0.9524	30
MCAT	Malonyl-CoA-acyl carrier protein transacylase	0.9524	30