Single cell type - H3C3 - 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.	H3C3
Gene descriptionⁱ Full gene name according to HGNC.	H3 clustered histone 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes
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 - Immunoglobulins & histones (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 mucus-secreting cells, Plasma cells, Erythroid cells, Squamous epithelial cells)
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.	0.88
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 detected
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

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 (Gastric mucus-secreting cells, Plasma cells, Erythroid cells, Squamous epithelial cells)

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Not detected

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ

HPA datasetⁱ

Lineage

Expression

Alphabetical

Immune cell type specificity: Low immune cell specificity

Monaco datasetⁱ

Lineage

Expression

Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

H3C3 is part of cluster 61 Plasma cells - Immunoglobulins & histones with confidenceⁱ 1
169 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.
H4C6	H4 clustered histone 6	0.9571	61
TXNDC5	Thioredoxin domain containing 5	0.9345	61
IGKV2D-29	Immunoglobulin kappa variable 2D-29	0.9331	61
IGHV3-35	Immunoglobulin heavy variable 3-35 (non-functional)	0.9301	61
IGHV3-16	Immunoglobulin heavy variable 3-16 (non-functional)	0.9271	61
IGLV1-36	Immunoglobulin lambda variable 1-36	0.9264	61
IGHV1OR21-1	Immunoglobulin heavy variable 1/OR21-1 (non-functional)	0.9258	61
IGLV1-47	Immunoglobulin lambda variable 1-47	0.9229	61
IGHV3OR16-8	Immunoglobulin heavy variable 3/OR16-8 (non-functional)	0.9220	61
IGHV3OR16-12	Immunoglobulin heavy variable 3/OR16-12 (non-functional)	0.9216	61
IGHV1OR15-9	Immunoglobulin heavy variable 1/OR15-9 (non-functional)	0.9215	61
IGLV3-9	Immunoglobulin lambda variable 3-9	0.9212	61
IGHV2-26	Immunoglobulin heavy variable 2-26	0.9205	61
IGHV3OR16-17	Immunoglobulin heavy variable 3/OR16-17 (non-functional)	0.9196	61
IGHV3OR16-9	Immunoglobulin heavy variable 3/OR16-9 (non-functional)	0.9180	61

IMMUNE CELLS

H3C3 is part of cluster 43 Non-specific - Transcription & Translation with confidenceⁱ 0.98
433 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.
CHMP7	Charged multivesicular body protein 7	0.9762	43
ENSG00000281179	Novel gene identicle to IGHV1OR15-1	0.9762	43
IGHV1OR15-1	Immunoglobulin heavy variable 1/OR15-1 (non-functional)	0.9762	43
IGSF8	Immunoglobulin superfamily member 8	0.9762	43
GRAP	GRB2 related adaptor protein	0.9762	43
ID3	Inhibitor of DNA binding 3	0.9762	43
GNB5	G protein subunit beta 5	0.9762	43
SNX25	Sorting nexin 25	0.9524	43
GJB6	Gap junction protein beta 6	0.9524	43
PRPSAP2	Phosphoribosyl pyrophosphate synthetase associated protein 2	0.9524	43
FCMR	Fc mu receptor	0.9524	43
PDE4DIP	Phosphodiesterase 4D interacting protein	0.9524	43
H2AC11	H2A clustered histone 11	0.9524	43
ZNF607	Zinc finger protein 607	0.9524	43
RPL41	Ribosomal protein L41	0.9524	43