Single cell type - RPL39L - The Human Protein Atlas

RPL39L

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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.	RPL39L
Gene descriptionⁱ Full gene name according to HGNC.	Ribosomal protein L39 like
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Ribosomal 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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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.	Spermatocytes - Spermatogenesis (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 (Spermatocytes, Early spermatids, Oocytes, Late spermatids, Spermatogonia)
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.	0.64
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: Cell type enhanced (Spermatocytes, Early spermatids, Oocytes, Late spermatids, Spermatogonia)

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

RPL39L is part of cluster 31 Spermatocytes - Spermatogenesis with confidenceⁱ 1
240 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.
EXD1	Exonuclease 3'-5' domain containing 1	0.9185	31
ANKRD7	Ankyrin repeat domain 7	0.9004	31
GOLGA8F	Golgin A8 family member F	0.8724	31
MGAT4D	MGAT4 family member D	0.8718	31
ADAM18	ADAM metallopeptidase domain 18	0.8709	31
GMCL2	Germ cell-less 2, spermatogenesis associated	0.8701	31
KRBOX1	KRAB box domain containing 1	0.8650	31
HSF5	Heat shock transcription factor 5	0.8624	31
TUBA3E	Tubulin alpha 3e	0.8614	31
SPATA22	Spermatogenesis associated 22	0.8550	31
GLIPR1L2	GLIPR1 like 2	0.8468	31
BOLL	Boule homolog, RNA binding protein	0.8445	31
SPINK2	Serine peptidase inhibitor Kazal type 2	0.8420	31
TUBA3C	Tubulin alpha 3c	0.8361	31
SHCBP1L	SHC binding and spindle associated 1 like	0.8308	31

IMMUNE CELLS

RPL39L is part of cluster 43 Non-specific - Transcription & Translation with confidenceⁱ 0.78
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.
TRIM2	Tripartite motif containing 2	1.0000	43
ADAT2	Adenosine deaminase tRNA specific 2	1.0000	43
H2BC3	H2B clustered histone 3	0.9762	43
RPS26	Ribosomal protein S26	0.9762	43
CCDC198	Coiled-coil domain containing 198	0.9762	43
VSIG1	V-set and immunoglobulin domain containing 1	0.9762	43
SLC16A10	Solute carrier family 16 member 10	0.9762	31
SLC9B1	Solute carrier family 9 member B1	0.9762	43
THOC3	THO complex subunit 3	0.9762	43
ADAM23	ADAM metallopeptidase domain 23	0.9762	43
AGMAT	Agmatinase	0.9762	43
TIMD4	T cell immunoglobulin and mucin domain containing 4	0.9762	43
CD27	CD27 molecule	0.9762	43
ABHD14B	Abhydrolase domain containing 14B	0.9524	43
MTERF4	Mitochondrial transcription termination factor 4	0.9524	43

Adipocytes	2.8 nTPM
Breast	4.8 nTPM
Adipose tissue	0.8 nTPM

Alveolar cells type 1	3.9 nTPM
Lung	3.9 nTPM

Alveolar cells type 2	8.9 nTPM
Lung	8.9 nTPM

Astrocytes	2.2 nTPM
Brain	2.2 nTPM

B-cells	10.3 nTPM
Liver	14.5 nTPM
Skin	13.6 nTPM
Stomach	12.7 nTPM
Lymph node	12.2 nTPM
Esophagus	11.8 nTPM
PBMC	10.8 nTPM
Spleen	10.1 nTPM
Lung	9.4 nTPM
Bone marrow	9.1 nTPM
Salivary gland	8.5 nTPM
Thymus	7.9 nTPM
Adipose tissue	7.8 nTPM
Kidney	5.2 nTPM

Ciliated cells	15.8 nTPM
Fallopian tube	19.8 nTPM
Endometrium	16.7 nTPM
Bronchus	15.2 nTPM
Lung	11.5 nTPM

Club cells	14.4 nTPM
Lung	16.0 nTPM
Bronchus	15.7 nTPM
Prostate	11.5 nTPM

Endothelial cells	6.8 nTPM
Liver	21.4 nTPM
Ovary	18.1 nTPM
Testis	15.0 nTPM
Breast	9.7 nTPM
Placenta	9.1 nTPM
Pancreas	7.8 nTPM
Tongue	7.3 nTPM
Heart muscle	6.3 nTPM
Prostate	5.8 nTPM
Endometrium	4.1 nTPM
Skin	3.4 nTPM
Fallopian tube	2.9 nTPM
Vascular	2.7 nTPM
Thymus	2.4 nTPM
Skeletal muscle	1.8 nTPM
Lung	1.6 nTPM
Salivary gland	1.4 nTPM
Esophagus	0.8 nTPM

Enteroendocrine cells	1.2 nTPM
Colon	3.5 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	12.1 nTPM
Pancreas	43.0 nTPM
Fallopian tube	19.4 nTPM
Breast	18.0 nTPM
Placenta	16.9 nTPM
Skin	14.5 nTPM
Vascular	14.3 nTPM
Adipose tissue	10.2 nTPM
Skeletal muscle	9.4 nTPM
Prostate	9.2 nTPM
Lung	9.0 nTPM
Esophagus	8.8 nTPM
Thymus	7.6 nTPM
Salivary gland	6.2 nTPM
Stomach	2.9 nTPM
Liver	2.4 nTPM
Heart muscle	2.2 nTPM

Granulocytes	12.7 nTPM
Tongue	19.4 nTPM
Lung	12.1 nTPM
Fallopian tube	6.5 nTPM

Intestinal goblet cells	3.7 nTPM
Colon	5.2 nTPM
Rectum	4.1 nTPM
Small intestine	1.9 nTPM

Lymphatic endothelial cells	1.4 nTPM
Fallopian tube	2.9 nTPM
Ovary	0.0 nTPM

Macrophages	9.1 nTPM
Testis	36.0 nTPM
Skin	18.9 nTPM
Esophagus	12.8 nTPM
Kidney	10.6 nTPM
Endometrium	10.5 nTPM
Breast	9.1 nTPM
Pancreas	8.2 nTPM
Tongue	8.2 nTPM
Vascular	7.7 nTPM
Adipose tissue	6.3 nTPM
Prostate	6.2 nTPM
Fallopian tube	6.2 nTPM
Skeletal muscle	5.6 nTPM
Salivary gland	5.5 nTPM
Lung	5.2 nTPM
Stomach	5.1 nTPM
Thymus	4.5 nTPM
Bone marrow	4.1 nTPM
Spleen	2.0 nTPM

Paneth cells	2.0 nTPM
Rectum	6.1 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Basal respiratory cells	30.6 nTPM
Bronchus	30.6 nTPM

Basal squamous epithelial cells	14.0 nTPM
Esophagus	14.0 nTPM

Bipolar cells	2.1 nTPM
Eye	2.1 nTPM

Cholangiocytes	5.7 nTPM
Liver	5.7 nTPM

Plasma cells	32.2 nTPM
Stomach	42.3 nTPM
Liver	39.6 nTPM
Spleen	39.5 nTPM
Thymus	36.7 nTPM
Salivary gland	31.8 nTPM
Fallopian tube	29.9 nTPM
Bone marrow	22.7 nTPM
Esophagus	15.6 nTPM

Schwann cells	4.4 nTPM
Adipose tissue	7.4 nTPM
Vascular	5.7 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	4.8 nTPM
Salivary gland	5.2 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	23.2 nTPM
Ovary	45.5 nTPM
Skin	39.3 nTPM
Breast	36.2 nTPM
Placenta	34.6 nTPM
Esophagus	28.8 nTPM
Fallopian tube	26.1 nTPM
Lung	24.7 nTPM
Vascular	23.7 nTPM
Prostate	20.7 nTPM
Endometrium	20.6 nTPM
Thymus	16.0 nTPM
Salivary gland	14.1 nTPM
Adipose tissue	10.9 nTPM
Skeletal muscle	10.6 nTPM
Tongue	10.5 nTPM
Liver	8.9 nTPM

Suprabasal keratinocytes	13.1 nTPM
Skin	16.9 nTPM
Tongue	9.3 nTPM

T-cells	13.8 nTPM
Kidney	31.9 nTPM
Skin	25.6 nTPM
Esophagus	24.3 nTPM
Liver	21.0 nTPM
Bone marrow	18.3 nTPM
Breast	16.9 nTPM
Skeletal muscle	15.9 nTPM
Lung	14.9 nTPM
Colon	14.6 nTPM
Prostate	13.1 nTPM
Stomach	11.8 nTPM
Spleen	11.1 nTPM
Tongue	10.9 nTPM
Lymph node	9.8 nTPM
PBMC	9.6 nTPM
Endometrium	8.8 nTPM
Fallopian tube	8.2 nTPM
Vascular	8.0 nTPM
Thymus	5.6 nTPM
Salivary gland	4.6 nTPM
Adipose tissue	4.5 nTPM

Undifferentiated cells	15.4 nTPM
Rectum	18.8 nTPM
Colon	15.6 nTPM
Small intestine	11.8 nTPM

Amygdala excitatory	3.3 nTPM
Thalamus	5.0 nTPM
Hypothalamus	3.4 nTPM
Amygdala	3.1 nTPM
Basal ganglia	2.9 nTPM
Cerebral cortex	2.9 nTPM
Hippocampus	2.6 nTPM

Astrocyte	6.4 nTPM
Spinal cord	10.9 nTPM
Hypothalamus	10.5 nTPM
Medulla oblongata	9.4 nTPM
Cerebellum	6.5 nTPM
Pons	5.6 nTPM
Thalamus	5.4 nTPM
Hippocampus	5.2 nTPM
Midbrain	5.1 nTPM
Amygdala	4.5 nTPM
Cerebral cortex	3.8 nTPM
Basal ganglia	3.7 nTPM

Bergmann glia	7.0 nTPM
Pons	12.9 nTPM
Cerebellum	6.1 nTPM
Medulla oblongata	2.1 nTPM

Central nervous system macrophage	2.8 nTPM
Hippocampus	3.5 nTPM
Cerebral cortex	3.3 nTPM
Medulla oblongata	3.3 nTPM
Spinal cord	3.2 nTPM
Pons	3.0 nTPM
Amygdala	2.8 nTPM
Cerebellum	2.7 nTPM
Basal ganglia	2.6 nTPM
Hypothalamus	2.3 nTPM
Thalamus	2.1 nTPM
Midbrain	1.9 nTPM

Cerebellar inhibitory	2.3 nTPM
Pons	3.2 nTPM
Medulla oblongata	2.8 nTPM
Midbrain	2.8 nTPM
Cerebellum	2.7 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	5.0 nTPM
Basal ganglia	6.2 nTPM
Midbrain	6.2 nTPM
Thalamus	5.4 nTPM
Cerebral cortex	4.6 nTPM
Hippocampus	4.5 nTPM
Amygdala	4.3 nTPM
Hypothalamus	4.0 nTPM

Choroid plexus epithelial cell	1.5 nTPM
Thalamus	2.7 nTPM
Medulla oblongata	1.9 nTPM
Basal ganglia	1.3 nTPM
Hippocampus	0.0 nTPM

Committed oligodendrocyte precursor	3.5 nTPM
Spinal cord	7.4 nTPM
Midbrain	6.7 nTPM
Hippocampus	4.7 nTPM
Pons	4.4 nTPM
Cerebral cortex	3.8 nTPM
Cerebellum	3.2 nTPM
Amygdala	2.8 nTPM
Basal ganglia	2.7 nTPM
Thalamus	1.6 nTPM
Hypothalamus	1.4 nTPM
Medulla oblongata	0.0 nTPM

Deep-layer corticothalamic and 6b	4.3 nTPM
Basal ganglia	6.8 nTPM
Amygdala	5.4 nTPM
Hypothalamus	5.1 nTPM
Cerebral cortex	4.0 nTPM
Hippocampus	3.8 nTPM
Midbrain	1.1 nTPM

Deep-layer intratelencephalic	4.3 nTPM
Basal ganglia	5.6 nTPM
Hippocampus	4.5 nTPM
Hypothalamus	4.1 nTPM
Cerebral cortex	4.0 nTPM
Amygdala	3.5 nTPM

Deep-layer near-projecting	4.6 nTPM
Basal ganglia	5.5 nTPM
Hippocampus	4.9 nTPM
Hypothalamus	4.9 nTPM
Amygdala	4.3 nTPM
Cerebral cortex	3.4 nTPM

Eccentric medium spiny neuron	4.2 nTPM
Basal ganglia	4.7 nTPM
Hippocampus	4.6 nTPM
Thalamus	4.3 nTPM
Hypothalamus	4.1 nTPM
Cerebral cortex	3.8 nTPM
Amygdala	3.7 nTPM

Endothelial cell	2.0 nTPM
Medulla oblongata	6.2 nTPM
Thalamus	4.0 nTPM
Hippocampus	2.9 nTPM
Basal ganglia	2.8 nTPM
Cerebral cortex	2.6 nTPM
Hypothalamus	1.2 nTPM
Pons	1.2 nTPM
Midbrain	0.9 nTPM
Amygdala	0.0 nTPM
Cerebellum	0.0 nTPM
Spinal cord	0.0 nTPM