Immune cell - SMARCAL1 - The Human Protein Atlas

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SMARCAL1

SUMMARY

TISSUE

BRAIN

SINGLE CELL

TISSUE CELL

PATHOLOGY

IMMUNE

BLOOD

SUBCELL

CELL LINE

METABOLIC

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.	SMARCAL1
Gene descriptionⁱ Full gene name according to HGNC.	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 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. Read more	Intracellular

IMMUNE CELL SECTION SUMMARY
Immune cell type expression clusterⁱ The RNA data is used to cluster genes according to their expression across immune cells. 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. Read more	Non-specific - Gene expression (mainly)
Immune cell type 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. Read more	Low immune cell specificity
Immune cell type distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in all
Immune cell lineage specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: lineage enriched, group enriched, lineage enhanced, low lineage specificity and not detected. Lineages include B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells. Read more	Low lineage specificity
Immune cell lineage distributionⁱ 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. Read more	Detected in all

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). Read more 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. Read more Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Read more Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SMARCAL1 is part of cluster 27 Non-specific - Gene expression with confidenceⁱ 0.99
649 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on immune 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. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
ZC3H15	Zinc finger CCCH-type containing 15	0.6921	12
SEC63	SEC63 homolog, protein translocation regulator	0.6912	27
DUS3L	Dihydrouridine synthase 3 like	0.6765	27
PDK2	Pyruvate dehydrogenase kinase 2	0.6458	27
TCF12	Transcription factor 12	0.6445	27
CD99L2	CD99 molecule like 2	0.6392	27
ALKBH3	AlkB homolog 3, alpha-ketoglutarate dependent dioxygenase	0.6374	27
CRELD1	Cysteine rich with EGF like domains 1	0.6369	27
PSEN2	Presenilin 2	0.6343	14
MORF4L2	Mortality factor 4 like 2	0.6311	47
MAN1B1	Mannosidase alpha class 1B member 1	0.6289	27
GTF2A1	General transcription factor IIA subunit 1	0.6263	41
HDAC2	Histone deacetylase 2	0.6218	27
RBBP4	RB binding protein 4, chromatin remodeling factor	0.6169	27
RBM10	RNA binding motif protein 10	0.6147	27

Contact

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The Project

The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.