Single cell type - ZC3H7A - The Human Protein Atlas

ZC3H7A

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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.	ZC3H7A
Gene descriptionⁱ Full gene name according to HGNC.	Zinc finger CCCH-type containing 7A
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.	9

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.	Non-specific - Transcription (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.	Low cell type specificity
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.	0.26
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 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: Low cell type specificity

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

ZC3H7A is part of cluster 55 Non-specific - Transcription with confidenceⁱ 1
709 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.
MIA3	MIA SH3 domain ER export factor 3	0.6071	55
SKIC3	SKI3 subunit of superkiller complex	0.5561	55
GOLGB1	Golgin B1	0.5393	55
ERCC6	ERCC excision repair 6, chromatin remodeling factor	0.5381	55
VPS13C	Vacuolar protein sorting 13 homolog C	0.5126	55
STAG2	Stromal antigen 2	0.5088	55
LYSMD3	LysM domain containing 3	0.5021	55
PJA2	Praja ring finger ubiquitin ligase 2	0.5021	55
RBM33	RNA binding motif protein 33	0.4944	78
ARCN1	Archain 1	0.4884	77
SETD2	SET domain containing 2, histone lysine methyltransferase	0.4822	55
SCFD1	Sec1 family domain containing 1	0.4760	55
SETD7	SET domain containing 7, histone lysine methyltransferase	0.4691	32
PHF3	PHD finger protein 3	0.4689	55
BPTF	Bromodomain PHD finger transcription factor	0.4662	55

IMMUNE CELLS

ZC3H7A is part of cluster 42 Non-specific - Vesicular transport with confidenceⁱ 1
519 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.
SPECC1L	Sperm antigen with calponin homology and coiled-coil domains 1 like	1.0000	42
METTL14	Methyltransferase 14, N6-adenosine-methyltransferase subunit	1.0000	42
FBXO28	F-box protein 28	1.0000	42
SMC4	Structural maintenance of chromosomes 4	1.0000	42
TES	Testin LIM domain protein	1.0000	42
BLZF1	Basic leucine zipper nuclear factor 1	0.9762	42
RNF168	Ring finger protein 168	0.9762	42
TOPBP1	DNA topoisomerase II binding protein 1	0.9762	42
CCDC82	Coiled-coil domain containing 82	0.9762	42
MINDY3	MINDY lysine 48 deubiquitinase 3	0.9762	42
RNASEL	Ribonuclease L	0.9762	42
IMPA1	Inositol monophosphatase 1	0.9762	42
AP5M1	Adaptor related protein complex 5 subunit mu 1	0.9762	42
SMAP1	Small ArfGAP 1	0.9762	42
PARP4	Poly(ADP-ribose) polymerase family member 4	0.9762	42

Adipocytes	37.2 nTPM
Adipose tissue	45.7 nTPM
Breast	28.7 nTPM

Alveolar cells type 1	30.5 nTPM
Lung	30.5 nTPM

Alveolar cells type 2	29.2 nTPM
Lung	29.2 nTPM

Astrocytes	35.0 nTPM
Brain	35.0 nTPM

B-cells	40.5 nTPM
Adipose tissue	71.2 nTPM
Stomach	49.8 nTPM
Spleen	49.1 nTPM
Salivary gland	43.8 nTPM
Thymus	43.7 nTPM
Lymph node	40.4 nTPM
PBMC	40.0 nTPM
Bone marrow	39.9 nTPM
Kidney	36.4 nTPM
Lung	33.5 nTPM
Skin	30.5 nTPM
Liver	24.2 nTPM
Esophagus	23.6 nTPM

Ciliated cells	21.4 nTPM
Endometrium	29.0 nTPM
Fallopian tube	22.3 nTPM
Lung	19.6 nTPM
Bronchus	14.8 nTPM

Club cells	20.7 nTPM
Lung	26.3 nTPM
Prostate	26.2 nTPM
Bronchus	9.7 nTPM

Dendritic cells	53.5 nTPM
Adipose tissue	67.3 nTPM
PBMC	39.6 nTPM

Endothelial cells	32.5 nTPM
Heart muscle	65.5 nTPM
Vascular	44.1 nTPM
Skeletal muscle	39.5 nTPM
Salivary gland	39.0 nTPM
Breast	38.7 nTPM
Endometrium	37.3 nTPM
Testis	36.9 nTPM
Thymus	35.1 nTPM
Fallopian tube	32.4 nTPM
Prostate	29.9 nTPM
Lung	29.5 nTPM
Tongue	29.0 nTPM
Esophagus	28.6 nTPM
Ovary	27.9 nTPM
Liver	23.9 nTPM
Skin	19.6 nTPM
Placenta	15.9 nTPM
Pancreas	12.9 nTPM

Enteroendocrine cells	20.0 nTPM
Small intestine	20.6 nTPM
Rectum	20.1 nTPM
Colon	19.3 nTPM

Fibroblasts	33.4 nTPM
Heart muscle	71.6 nTPM
Vascular	39.5 nTPM
Fallopian tube	37.8 nTPM
Salivary gland	37.6 nTPM
Stomach	37.5 nTPM
Liver	36.8 nTPM
Skeletal muscle	36.4 nTPM
Lung	36.2 nTPM
Adipose tissue	32.8 nTPM
Esophagus	31.5 nTPM
Thymus	30.3 nTPM
Breast	26.6 nTPM
Prostate	22.4 nTPM
Skin	20.0 nTPM
Pancreas	19.3 nTPM
Placenta	18.0 nTPM

Granulocytes	32.7 nTPM
Fallopian tube	48.4 nTPM
Lung	35.3 nTPM
Tongue	14.6 nTPM

Intestinal goblet cells	26.9 nTPM
Small intestine	32.4 nTPM
Colon	26.1 nTPM
Rectum	22.2 nTPM

Lymphatic endothelial cells	31.2 nTPM
Fallopian tube	46.1 nTPM
Ovary	16.4 nTPM

Macrophages	39.4 nTPM
Adipose tissue	69.2 nTPM
Stomach	51.4 nTPM
Fallopian tube	49.9 nTPM
Skeletal muscle	49.0 nTPM
Salivary gland	44.7 nTPM
Thymus	43.9 nTPM
Spleen	43.1 nTPM
Bone marrow	42.6 nTPM
Vascular	42.3 nTPM
Prostate	41.5 nTPM
Endometrium	40.0 nTPM
Breast	36.9 nTPM
Lung	35.3 nTPM
Tongue	34.9 nTPM
Esophagus	29.5 nTPM
Testis	29.1 nTPM
Skin	25.6 nTPM
Kidney	23.9 nTPM
Pancreas	16.4 nTPM

Basal prostatic cells	25.5 nTPM
Prostate	25.5 nTPM

Basal squamous epithelial cells	18.6 nTPM
Esophagus	18.6 nTPM

Bipolar cells	25.4 nTPM
Eye	25.4 nTPM

Cholangiocytes	17.2 nTPM
Liver	17.2 nTPM

Paneth cells	17.4 nTPM
Small intestine	24.2 nTPM
Rectum	20.6 nTPM
Colon	7.2 nTPM

Plasma cells	45.1 nTPM
Stomach	66.6 nTPM
Salivary gland	59.1 nTPM
Fallopian tube	54.7 nTPM
Spleen	46.9 nTPM
Thymus	43.2 nTPM
Bone marrow	42.3 nTPM
Liver	27.0 nTPM
Esophagus	20.8 nTPM

Schwann cells	30.0 nTPM
Adipose tissue	55.0 nTPM
Vascular	35.0 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	40.8 nTPM
Salivary gland	59.6 nTPM
Tongue	22.1 nTPM

Smooth muscle cells	31.3 nTPM
Vascular	50.9 nTPM
Adipose tissue	39.6 nTPM
Endometrium	39.5 nTPM
Salivary gland	38.9 nTPM
Skeletal muscle	37.1 nTPM
Fallopian tube	35.7 nTPM
Lung	35.3 nTPM
Thymus	31.9 nTPM
Ovary	30.2 nTPM
Breast	29.2 nTPM
Esophagus	26.4 nTPM
Prostate	24.9 nTPM
Tongue	24.2 nTPM
Liver	23.3 nTPM
Placenta	17.4 nTPM
Skin	16.5 nTPM

Suprabasal keratinocytes	14.1 nTPM
Skin	16.9 nTPM
Tongue	11.4 nTPM

T-cells	39.7 nTPM
Adipose tissue	80.9 nTPM
Spleen	51.9 nTPM
Lymph node	51.5 nTPM
Salivary gland	50.3 nTPM
Kidney	48.8 nTPM
Thymus	46.9 nTPM
Fallopian tube	43.9 nTPM
Vascular	43.4 nTPM
Endometrium	42.5 nTPM
Stomach	39.5 nTPM
PBMC	39.1 nTPM
Bone marrow	38.7 nTPM
Skeletal muscle	38.6 nTPM
Tongue	37.0 nTPM
Lung	33.4 nTPM
Breast	30.6 nTPM
Prostate	29.6 nTPM
Liver	26.5 nTPM
Skin	24.9 nTPM
Colon	20.5 nTPM
Esophagus	14.6 nTPM

Undifferentiated cells	16.1 nTPM
Small intestine	17.2 nTPM
Rectum	17.2 nTPM
Colon	13.9 nTPM

Amygdala excitatory	45.1 nTPM
Thalamus	51.3 nTPM
Basal ganglia	49.0 nTPM
Hypothalamus	44.1 nTPM
Cerebral cortex	43.1 nTPM
Amygdala	42.2 nTPM
Hippocampus	40.9 nTPM

Astrocyte	69.1 nTPM
Amygdala	78.3 nTPM
Thalamus	77.2 nTPM
Cerebral cortex	76.8 nTPM
Midbrain	75.4 nTPM
Pons	72.3 nTPM
Basal ganglia	70.4 nTPM
Hippocampus	66.3 nTPM
Hypothalamus	63.6 nTPM
Cerebellum	63.2 nTPM
Spinal cord	59.0 nTPM
Medulla oblongata	57.4 nTPM

Bergmann glia	103.7 nTPM
Cerebellum	104.4 nTPM
Medulla oblongata	104.4 nTPM
Pons	102.1 nTPM

Central nervous system macrophage	114.5 nTPM
Amygdala	131.0 nTPM
Cerebellum	117.2 nTPM
Cerebral cortex	117.0 nTPM
Hypothalamus	116.9 nTPM
Medulla oblongata	114.1 nTPM
Midbrain	113.2 nTPM
Pons	113.0 nTPM
Basal ganglia	112.8 nTPM
Thalamus	111.8 nTPM
Hippocampus	109.3 nTPM
Spinal cord	103.3 nTPM

Cerebellar inhibitory	53.7 nTPM
Cerebellum	60.0 nTPM
Medulla oblongata	54.7 nTPM
Midbrain	53.2 nTPM
Pons	51.0 nTPM
Spinal cord	49.5 nTPM

Cge interneuron	53.5 nTPM
Amygdala	56.8 nTPM
Cerebral cortex	55.1 nTPM
Hypothalamus	53.7 nTPM
Thalamus	53.1 nTPM
Hippocampus	52.5 nTPM
Basal ganglia	51.8 nTPM
Midbrain	51.8 nTPM

Choroid plexus epithelial cell	163.5 nTPM
Basal ganglia	190.4 nTPM
Medulla oblongata	179.2 nTPM
Hippocampus	171.9 nTPM
Thalamus	112.4 nTPM

Committed oligodendrocyte precursor	79.1 nTPM
Cerebral cortex	100.1 nTPM
Cerebellum	93.5 nTPM
Amygdala	90.2 nTPM
Hippocampus	89.5 nTPM
Midbrain	81.5 nTPM
Medulla oblongata	77.5 nTPM
Spinal cord	77.3 nTPM
Basal ganglia	70.1 nTPM
Pons	66.4 nTPM
Hypothalamus	65.5 nTPM
Thalamus	58.8 nTPM

Deep-layer corticothalamic and 6b	47.9 nTPM
Midbrain	53.3 nTPM
Basal ganglia	50.0 nTPM
Cerebral cortex	49.4 nTPM
Hypothalamus	45.6 nTPM
Hippocampus	44.7 nTPM
Amygdala	44.3 nTPM

Deep-layer intratelencephalic	43.0 nTPM
Amygdala	44.8 nTPM
Cerebral cortex	44.6 nTPM
Hypothalamus	43.3 nTPM
Basal ganglia	42.2 nTPM
Hippocampus	40.2 nTPM

Deep-layer near-projecting	50.3 nTPM
Hippocampus	53.3 nTPM
Amygdala	52.8 nTPM
Cerebral cortex	52.0 nTPM
Basal ganglia	48.3 nTPM
Hypothalamus	44.9 nTPM

Eccentric medium spiny neuron	51.6 nTPM
Basal ganglia	53.5 nTPM
Amygdala	52.7 nTPM
Thalamus	51.5 nTPM
Hippocampus	51.0 nTPM
Hypothalamus	51.0 nTPM
Cerebral cortex	49.8 nTPM