Single cell type - USE1 - 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.	USE1
Gene descriptionⁱ Full gene name according to HGNC.	Unconventional SNARE in the ER 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Essential 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.	Membrane, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	4

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.	Late spermatids - Spermiogenesis: Maturation (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 (Late spermatids)
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.	0.43
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 (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 Read more
Single cell type groups RNA single cell type group specificity: Cell type enhanced (Spermatogenic cell types)

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

USE1 is part of cluster 56 Late spermatids - Spermiogenesis: Maturation with confidenceⁱ 1
234 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.
EIF3G	Eukaryotic translation initiation factor 3 subunit G	0.5679	56
CZIB	CXXC motif containing zinc binding protein	0.5463	56
ALKBH7	AlkB homolog 7	0.5458	56
TMEM120A	Transmembrane protein 120A	0.5402	56
ELOB	Elongin B	0.5186	56
DNAJC30	DnaJ heat shock protein family (Hsp40) member C30	0.5116	56
TMEM53	Transmembrane protein 53	0.4940	56
NELFE	Negative elongation factor complex member E	0.4888	56
IFT22	Intraflagellar transport 22	0.4834	56
TCEA2	Transcription elongation factor A2	0.4721	56
MZT2B	Mitotic spindle organizing protein 2B	0.4691	15
CIB3	Calcium and integrin binding family member 3	0.4641	56
SPEM1	Spermatid maturation 1	0.4605	56
HSPB9	Heat shock protein family B (small) member 9	0.4600	56
RPL29	Ribosomal protein L29	0.4595	15

IMMUNE CELLS

USE1 is part of cluster 12 Non-specific - Mitochondrial translation with confidenceⁱ 0.94
566 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.
TIMM10	Translocase of inner mitochondrial membrane 10	0.9762	12
PPIAL4C	Peptidylprolyl isomerase A like 4C	0.9762	12
TMEM256	Transmembrane protein 256	0.9762	12
HID1	HID1 domain containing	0.9762	12
UXT	Ubiquitously expressed prefoldin like chaperone	0.9762	18
PEBP1	Phosphatidylethanolamine binding protein 1	0.9524	18
NUFIP1	Nuclear FMR1 interacting protein 1	0.9524	18
RPL35	Ribosomal protein L35	0.9524	18
HMGA1	High mobility group AT-hook 1	0.9524	12
RPS11	Ribosomal protein S11	0.9524	18
RPS8	Ribosomal protein S8	0.9524	18
ELP5	Elongator acetyltransferase complex subunit 5	0.9524	12
TOP1MT	DNA topoisomerase I mitochondrial	0.9524	18
NOP16	NOP16 nucleolar protein	0.9524	12
ATP5F1D	ATP synthase F1 subunit delta	0.9286	12