Single cell type - ENSG00000273047 - 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.	ENSG00000273047
Gene descriptionⁱ Full gene name according to HGNC.	Novel transcript, LIME1-SLC2A4RG 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.	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.	Plasma cells - Plasma cell differentiation (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 (Gastric chief cells, Tuft cells, Plasma cells, Foveolar cells, Mucous neck cells, Paneth cells, Enterocytes, T-cells, Hepatocytes, Enteric stem cells, Colonocytes)
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.	Cell type enhanced (Leukocyte)
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 (plasmacytoid DC)
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

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 (Gastric glandular cells, Secretory gland support, Plasma cells)

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Cell type enhanced (Leukocyte)

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: Immune cell enhanced (plasmacytoid DC)
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

ENSG00000273047 is part of cluster 67 Plasma cells - Plasma cell differentiation with confidenceⁱ 1
116 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.
KRTCAP2	Keratinocyte associated protein 2	0.9376	67
IGHV4-34	Immunoglobulin heavy variable 4-34	0.9315	67
IGLV5-45	Immunoglobulin lambda variable 5-45	0.9216	67
IGLV7-43	Immunoglobulin lambda variable 7-43	0.9183	67
IGLV1-40	Immunoglobulin lambda variable 1-40	0.9131	67
IGHV7-4-1	Immunoglobulin heavy variable 7-4-1	0.9105	67
IGHV4-28	Immunoglobulin heavy variable 4-28	0.9041	67
JCHAIN	Joining chain of multimeric IgA and IgM	0.9030	67
IGHV1-24	Immunoglobulin heavy variable 1-24	0.9015	67
IGHA1	Immunoglobulin heavy constant alpha 1	0.8974	67
IGLL5	Immunoglobulin lambda like polypeptide 5	0.8943	67
IGHA2	Immunoglobulin heavy constant alpha 2 (A2m marker)	0.8901	67
BGLAP	Bone gamma-carboxyglutamate protein	0.8810	67
IGHV3-13	Immunoglobulin heavy variable 3-13	0.8753	67
IGLV3-9	Immunoglobulin lambda variable 3-9	0.8647	67

IMMUNE CELLS

ENSG00000273047 is part of cluster 13 Non-specific - Mitochondria with confidenceⁱ 0.7
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.
ATP2A1	ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1	0.9762	13
TRAM1	Translocation associated membrane protein 1	0.9762	13
PSMD14	Proteasome 26S subunit, non-ATPase 14	0.9762	13
BCCIP	BRCA2 and CDKN1A interacting protein	0.9524	13
RPL7L1	Ribosomal protein L7 like 1	0.9524	13
HNRNPL	Heterogeneous nuclear ribonucleoprotein L	0.9524	13
PSMA3	Proteasome 20S subunit alpha 3	0.9524	13
XPO1	Exportin 1	0.9286	13
PRPF31	Pre-mRNA processing factor 31	0.9286	13
CKS2	CDC28 protein kinase regulatory subunit 2	0.9286	13
PRMT7	Protein arginine methyltransferase 7	0.9286	12
HS3ST3A1	Heparan sulfate-glucosamine 3-sulfotransferase 3A1	0.9286	13
CCDC107	Coiled-coil domain containing 107	0.9286	8
RELL2	RELT like 2	0.9286	13
COQ4	Coenzyme Q4	0.9286	13