Single cell type - SPDL1 - The Human Protein Atlas

SPDL1

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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.	SPDL1
Gene descriptionⁱ Full gene name according to HGNC.	Spindle apparatus coiled-coil protein 1
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.	8

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, Oocytes, 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.	0.57
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, Oocytes, 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

SPDL1 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.
MTFR2	Mitochondrial fission regulator 2	0.7138	44
SGO2	Shugoshin 2	0.6569	31
NUF2	NUF2 component of NDC80 kinetochore complex	0.6514	52
MIS18A	MIS18 kinetochore protein A	0.6427	52
SASS6	SAS-6 centriolar assembly protein	0.6302	44
TDRD1	Tudor domain containing 1	0.6264	31
EME1	Essential meiotic structure-specific endonuclease 1	0.6192	52
HENMT1	HEN methyltransferase 1	0.6181	31
RNF17	Ring finger protein 17	0.6175	31
CDCA8	Cell division cycle associated 8	0.6124	52
PKMYT1	Protein kinase, membrane associated tyrosine/threonine 1	0.6064	52
YEATS4	YEATS domain containing 4	0.6047	31
SPC25	SPC25 component of NDC80 kinetochore complex	0.6045	52
RBM46	RNA binding motif protein 46	0.5991	31
C12orf40	Chromosome 12 open reading frame 40	0.5775	31

IMMUNE CELLS

SPDL1 is part of cluster 22 Eosinophils - Transcription with confidenceⁱ 0.79
357 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.
ZNF790	Zinc finger protein 790	0.9762	22
ZNF671	Zinc finger protein 671	0.9762	22
ST3GAL1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	0.9524	22
ZNF75A	Zinc finger protein 75a	0.9524	22
CWF19L2	CWF19 like cell cycle control factor 2	0.9524	22
TUT4	Terminal uridylyl transferase 4	0.9524	22
PRKD3	Protein kinase D3	0.9524	22
BBX	BBX high mobility group box domain containing	0.9524	22
ARHGEF7	Rho guanine nucleotide exchange factor 7	0.9286	22
USP48	Ubiquitin specific peptidase 48	0.9286	22
SMARCA4	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	0.9286	22
PCM1	Pericentriolar material 1	0.9286	22
ZNF439	Zinc finger protein 439	0.9286	22
CASTOR1	Cytosolic arginine sensor for mTORC1 subunit 1	0.9286	22
TMEM225B	Transmembrane protein 225B	0.9286	22

Adipocytes	5.4 nTPM
Breast	6.2 nTPM
Adipose tissue	4.5 nTPM

Alveolar cells type 1	5.5 nTPM
Lung	5.5 nTPM

Alveolar cells type 2	6.6 nTPM
Lung	6.6 nTPM

Astrocytes	3.7 nTPM
Brain	3.7 nTPM

B-cells	5.2 nTPM
Skin	11.9 nTPM
Kidney	10.4 nTPM
Salivary gland	8.6 nTPM
Lymph node	6.8 nTPM
Spleen	6.0 nTPM
Thymus	5.8 nTPM
Bone marrow	4.8 nTPM
PBMC	4.6 nTPM
Stomach	3.4 nTPM
Adipose tissue	2.9 nTPM
Lung	2.7 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM

Ciliated cells	5.2 nTPM
Endometrium	6.4 nTPM
Fallopian tube	5.2 nTPM
Lung	4.6 nTPM
Bronchus	4.4 nTPM

Club cells	5.3 nTPM
Lung	5.6 nTPM
Bronchus	5.2 nTPM
Prostate	5.0 nTPM

Endothelial cells	6.8 nTPM
Heart muscle	13.2 nTPM
Placenta	11.9 nTPM
Pancreas	10.3 nTPM
Endometrium	10.1 nTPM
Vascular	9.3 nTPM
Tongue	8.6 nTPM
Thymus	6.8 nTPM
Lung	6.4 nTPM
Testis	6.1 nTPM
Fallopian tube	5.9 nTPM
Salivary gland	5.7 nTPM
Skin	5.2 nTPM
Ovary	5.1 nTPM
Skeletal muscle	4.8 nTPM
Prostate	4.3 nTPM
Esophagus	3.1 nTPM
Breast	2.6 nTPM
Liver	2.5 nTPM

Enteroendocrine cells	2.5 nTPM
Colon	4.0 nTPM
Small intestine	3.4 nTPM
Rectum	0.0 nTPM

Fibroblasts	9.3 nTPM
Pancreas	38.6 nTPM
Heart muscle	17.5 nTPM
Placenta	17.1 nTPM
Vascular	8.6 nTPM
Lung	8.5 nTPM
Liver	8.3 nTPM
Adipose tissue	7.0 nTPM
Salivary gland	6.9 nTPM
Breast	6.1 nTPM
Thymus	5.8 nTPM
Skeletal muscle	5.7 nTPM
Fallopian tube	5.4 nTPM
Skin	4.2 nTPM
Prostate	3.3 nTPM
Esophagus	3.1 nTPM
Stomach	2.9 nTPM

Granulocytes	6.7 nTPM
Tongue	9.7 nTPM
Fallopian tube	6.9 nTPM
Lung	3.5 nTPM

Intestinal goblet cells	4.1 nTPM
Colon	6.9 nTPM
Small intestine	3.1 nTPM
Rectum	2.4 nTPM

Lymphatic endothelial cells	10.4 nTPM
Ovary	10.9 nTPM
Fallopian tube	9.9 nTPM

Macrophages	4.6 nTPM
Tongue	10.8 nTPM
Esophagus	7.7 nTPM
Salivary gland	6.6 nTPM
Pancreas	6.2 nTPM
Vascular	5.7 nTPM
Testis	5.6 nTPM
Endometrium	5.5 nTPM
Prostate	5.3 nTPM
Breast	4.3 nTPM
Bone marrow	4.1 nTPM
Thymus	4.1 nTPM
Fallopian tube	3.9 nTPM
Lung	3.7 nTPM
Skeletal muscle	2.9 nTPM
Adipose tissue	2.9 nTPM
Stomach	2.6 nTPM
Skin	2.2 nTPM
Spleen	2.0 nTPM
Kidney	0.9 nTPM

Paneth cells	4.3 nTPM
Colon	7.2 nTPM
Small intestine	3.5 nTPM
Rectum	2.2 nTPM

Cholangiocytes	3.8 nTPM
Liver	3.8 nTPM

Collecting duct cells	1.9 nTPM
Kidney	1.9 nTPM

Cone photoreceptor cells	1.7 nTPM
Eye	1.7 nTPM

Cytotrophoblasts	14.7 nTPM
Placenta	14.7 nTPM

Plasma cells	15.7 nTPM
Liver	43.1 nTPM
Thymus	28.1 nTPM
Spleen	23.8 nTPM
Bone marrow	15.1 nTPM
Salivary gland	7.6 nTPM
Stomach	4.2 nTPM
Fallopian tube	3.9 nTPM
Esophagus	0.0 nTPM

Schwann cells	3.6 nTPM
Vascular	8.4 nTPM
Adipose tissue	2.3 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	4.4 nTPM
Salivary gland	4.5 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	6.1 nTPM
Endometrium	10.9 nTPM
Placenta	10.8 nTPM
Liver	8.9 nTPM
Tongue	8.4 nTPM
Vascular	7.3 nTPM
Skin	6.0 nTPM
Esophagus	6.0 nTPM
Ovary	5.8 nTPM
Adipose tissue	5.6 nTPM
Fallopian tube	5.6 nTPM
Skeletal muscle	4.8 nTPM
Breast	4.6 nTPM
Thymus	4.2 nTPM
Lung	3.5 nTPM
Salivary gland	3.5 nTPM
Prostate	1.8 nTPM

Suprabasal keratinocytes	29.8 nTPM
Tongue	54.4 nTPM
Skin	5.1 nTPM

T-cells	5.4 nTPM
Salivary gland	11.9 nTPM
Liver	10.9 nTPM
Tongue	7.8 nTPM
Endometrium	7.0 nTPM
Vascular	6.8 nTPM
Prostate	6.6 nTPM
Thymus	6.3 nTPM
PBMC	6.1 nTPM
Spleen	5.6 nTPM
Colon	4.9 nTPM
Lymph node	4.8 nTPM
Bone marrow	4.4 nTPM
Skin	4.2 nTPM
Skeletal muscle	4.2 nTPM
Lung	4.2 nTPM
Fallopian tube	4.2 nTPM
Breast	4.1 nTPM
Adipose tissue	3.4 nTPM
Stomach	2.7 nTPM
Esophagus	2.4 nTPM
Kidney	1.8 nTPM

Undifferentiated cells	13.5 nTPM
Colon	21.7 nTPM
Rectum	10.2 nTPM
Small intestine	8.6 nTPM

Amygdala excitatory	7.9 nTPM
Thalamus	9.5 nTPM
Amygdala	8.3 nTPM
Hippocampus	7.8 nTPM
Hypothalamus	7.6 nTPM
Cerebral cortex	7.5 nTPM
Basal ganglia	6.9 nTPM

Astrocyte	7.6 nTPM
Amygdala	9.7 nTPM
Hippocampus	8.1 nTPM
Pons	8.0 nTPM
Basal ganglia	7.8 nTPM
Hypothalamus	7.8 nTPM
Medulla oblongata	7.7 nTPM
Thalamus	7.6 nTPM
Midbrain	7.5 nTPM
Cerebral cortex	7.4 nTPM
Cerebellum	7.0 nTPM
Spinal cord	5.0 nTPM

Bergmann glia	7.6 nTPM
Medulla oblongata	10.7 nTPM
Cerebellum	7.9 nTPM
Pons	4.3 nTPM

Central nervous system macrophage	7.6 nTPM
Amygdala	10.3 nTPM
Midbrain	8.2 nTPM
Cerebral cortex	8.1 nTPM
Hypothalamus	8.1 nTPM
Thalamus	7.8 nTPM
Basal ganglia	7.7 nTPM
Hippocampus	7.2 nTPM
Pons	7.2 nTPM
Cerebellum	7.1 nTPM
Medulla oblongata	6.7 nTPM
Spinal cord	5.9 nTPM

Cerebellar inhibitory	15.6 nTPM
Spinal cord	33.0 nTPM
Midbrain	13.7 nTPM
Pons	10.5 nTPM
Cerebellum	10.4 nTPM
Medulla oblongata	10.3 nTPM

Cge interneuron	10.5 nTPM
Thalamus	12.3 nTPM
Midbrain	11.6 nTPM
Amygdala	10.7 nTPM
Basal ganglia	10.3 nTPM
Hippocampus	9.8 nTPM
Cerebral cortex	9.6 nTPM
Hypothalamus	9.4 nTPM

Choroid plexus epithelial cell	4.6 nTPM
Basal ganglia	6.5 nTPM
Medulla oblongata	6.5 nTPM
Thalamus	5.5 nTPM
Hippocampus	0.0 nTPM

Committed oligodendrocyte precursor	7.9 nTPM
Spinal cord	11.0 nTPM
Medulla oblongata	10.3 nTPM
Amygdala	9.6 nTPM
Hypothalamus	9.6 nTPM
Thalamus	8.1 nTPM
Cerebral cortex	7.6 nTPM
Basal ganglia	7.1 nTPM
Midbrain	6.7 nTPM
Cerebellum	6.3 nTPM
Hippocampus	6.2 nTPM
Pons	4.4 nTPM

Deep-layer corticothalamic and 6b	6.8 nTPM
Amygdala	9.1 nTPM
Hippocampus	8.0 nTPM
Cerebral cortex	7.9 nTPM
Basal ganglia	7.7 nTPM
Hypothalamus	7.0 nTPM
Midbrain	1.1 nTPM

Deep-layer intratelencephalic	8.6 nTPM
Amygdala	9.5 nTPM
Cerebral cortex	9.1 nTPM
Hippocampus	8.9 nTPM
Basal ganglia	8.8 nTPM
Hypothalamus	6.5 nTPM

Deep-layer near-projecting	9.3 nTPM
Hippocampus	13.7 nTPM
Hypothalamus	9.2 nTPM
Amygdala	8.2 nTPM
Cerebral cortex	7.9 nTPM
Basal ganglia	7.7 nTPM

Eccentric medium spiny neuron	9.6 nTPM
Hippocampus	12.4 nTPM
Amygdala	10.7 nTPM
Hypothalamus	10.2 nTPM
Thalamus	9.1 nTPM
Basal ganglia	7.9 nTPM
Cerebral cortex	7.5 nTPM

Endothelial cell	9.6 nTPM
Basal ganglia	14.9 nTPM
Midbrain	13.2 nTPM
Cerebellum	12.4 nTPM
Spinal cord	12.1 nTPM
Pons	9.4 nTPM
Hippocampus	9.3 nTPM
Medulla oblongata	9.2 nTPM
Hypothalamus	8.7 nTPM
Thalamus	6.2 nTPM
Amygdala	5.6 nTPM
Cerebral cortex	4.5 nTPM