Single cell type - RFPL4AL1 - 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.	RFPL4AL1
Gene descriptionⁱ Full gene name according to HGNC.	Ret finger protein like 4A like 1
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.	1

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.	Mononuclear phagocytes - Antigen presentation (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.	Not detected
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.	Not detected
Brain cell type 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.	Immune cell enhanced (classical monocyte)
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

Cell type summary (DVP)

Cell type enrichment

Expression clustering

SINGLE CELL TYPESⁱ A summary of normalized single cell RNA (nCPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. * Single nuclei
Single cell type groups RNA single cell type group specificity: Not detected

DVP - RNA AND PROTEIN ABUNDANCE COMPARISON

RNA cell type specificity:	Not detected	Agreement detection:	N/A
Protein cell type specificity:	Not detected	Agreement expression:	N/A
RNA tau score:	Not detected	Overlap:	Not detected - Both
Protein tau score:	Not detected

BULK RNA DECONVOLUTIONⁱ 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.

EXPRESSION CLUSTERING & CORRELATIONⁱ

RFPL4AL1 is part of cluster 57 Mononuclear phagocytes - Antigen presentation with confidenceⁱ 1
199 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.
RFPL4A	Ret finger protein like 4A	0.7282	57
TIFAB	TIFA inhibitor	0.6372	57
HLA-DPA1	Major histocompatibility complex, class II, DP alpha 1	0.6344	57
HLA-DPB1	Major histocompatibility complex, class II, DP beta 1	0.6323	57
HLA-DQA1	Major histocompatibility complex, class II, DQ alpha 1	0.5985	57
CD1C	CD1c molecule	0.5967	57
GPR31	G protein-coupled receptor 31	0.5946	57
HLA-DRB1	Major histocompatibility complex, class II, DR beta 1	0.5820	57
HLA-DMA	Major histocompatibility complex, class II, DM alpha	0.5791	57
HLA-DQB1	Major histocompatibility complex, class II, DQ beta 1	0.5771	57
HLA-DRA	Major histocompatibility complex, class II, DR alpha	0.5740	57
C1orf54	Chromosome 1 open reading frame 54	0.5649	57
UTF1	Undifferentiated embryonic cell transcription factor 1	0.5632	57
CD74	CD74 molecule	0.5621	57
CLEC10A	C-type lectin domain containing 10A	0.5542	57