Single cell type - EFCAB11 - 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.	EFCAB11
Gene descriptionⁱ Full gene name according to HGNC.	EF-hand calcium binding domain 11
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
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	5

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. Read more	Spermatids - Unknown function (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. Read more	Group enriched (Early spermatids, Late spermatids, Oligodendrocytes)
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. Read more	Immune cell enhanced (basophil)
Immune cell 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 many
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Low cell line specificity
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in all
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of 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 Group Expression Alphabetical RNA single cell type specificity: Group enriched (Early spermatids, Late spermatids, Oligodendrocytes)

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

EFCAB11 is part of cluster 34 Spermatids - Unknown function with confidenceⁱ 1
366 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type 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
C2orf73	Chromosome 2 open reading frame 73	0.8306	34
NPIPB6	Nuclear pore complex interacting protein family member B6	0.7803	34
C1orf100	Chromosome 1 open reading frame 100	0.7668	34
PP2D1	Protein phosphatase 2C like domain containing 1	0.7628	34
OR4N4	Olfactory receptor family 4 subfamily N member 4	0.7624	34
TRIM42	Tripartite motif containing 42	0.7590	34
BAG5	BAG cochaperone 5	0.7587	34
TTLL2	Tubulin tyrosine ligase like 2	0.7470	34
DNTT	DNA nucleotidylexotransferase	0.7456	34
OR8B2	Olfactory receptor family 8 subfamily B member 2	0.7431	34
PACRGL	Parkin coregulated like	0.7345	34
PLAC8L1	PLAC8 like 1	0.7273	34
HSFY1	Heat shock transcription factor Y-linked 1	0.7268	34
ZNF479	Zinc finger protein 479	0.7252	34
DEFB135	Defensin beta 135	0.7213	34

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	5.8 nTPM
Breast	6.0 nTPM
Adipose tissue	5.7 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	1.1 nTPM
Lung	1.1 nTPM

Astrocytes	30.3 nTPM
Brain	30.3 nTPM

B-cells	6.2 nTPM
Kidney	19.0 nTPM
Liver	8.7 nTPM
Breast	8.1 nTPM
Stomach	5.0 nTPM
Bone marrow	4.9 nTPM
Colon	4.8 nTPM
Lymph node	4.5 nTPM
Adipose tissue	4.0 nTPM
Spleen	3.5 nTPM
PBMC	0.0 nTPM

Dendritic cells	3.0 nTPM
PBMC	4.0 nTPM
Adipose tissue	2.5 nTPM
Breast	2.5 nTPM

Endothelial cells	7.4 nTPM
Liver	20.2 nTPM
Placenta	15.3 nTPM
Heart muscle	9.2 nTPM
Ovary	7.9 nTPM
Testis	6.8 nTPM
Skin	6.6 nTPM
Endometrium	6.6 nTPM
Eye	6.5 nTPM
Breast	6.0 nTPM
Skeletal muscle	5.3 nTPM
Esophagus	4.2 nTPM
Pancreas	3.9 nTPM
Lung	3.1 nTPM
Prostate	2.6 nTPM

Fibroblasts	6.3 nTPM
Placenta	10.2 nTPM
Ovary	9.4 nTPM
Heart muscle	9.0 nTPM
Lung	8.9 nTPM
Adipose tissue	6.9 nTPM
Breast	6.3 nTPM
Esophagus	5.6 nTPM
Skeletal muscle	5.4 nTPM
Skin	5.2 nTPM
Prostate	1.5 nTPM
Stomach	1.5 nTPM

Intestinal goblet cells	6.1 nTPM
Small intestine	10.2 nTPM
Colon	4.3 nTPM
Rectum	3.6 nTPM

Macrophages	5.7 nTPM
Lung	11.4 nTPM
Prostate	9.1 nTPM
Endometrium	8.5 nTPM
Testis	7.5 nTPM
Skeletal muscle	7.5 nTPM
Breast	7.4 nTPM
Ovary	6.1 nTPM
Kidney	5.3 nTPM
Pancreas	5.1 nTPM
Adipose tissue	4.9 nTPM
Esophagus	4.8 nTPM
Bone marrow	3.7 nTPM
Stomach	2.9 nTPM
Spleen	1.0 nTPM
PBMC	0.0 nTPM

Paneth cells	9.7 nTPM
Small intestine	18.8 nTPM
Rectum	7.0 nTPM
Colon	3.3 nTPM

Plasma cells	6.4 nTPM
Spleen	11.1 nTPM
Bone marrow	6.6 nTPM
Esophagus	6.1 nTPM
Stomach	4.2 nTPM
Adipose tissue	3.9 nTPM

Respiratory ciliated cells	47.7 nTPM
Lung	54.0 nTPM
Bronchus	41.5 nTPM

Smooth muscle cells	6.0 nTPM
Bronchus	15.0 nTPM
Pancreas	11.1 nTPM
Ovary	7.7 nTPM
Endometrium	7.3 nTPM
Skeletal muscle	6.4 nTPM
Breast	4.8 nTPM
Adipose tissue	4.5 nTPM
Skin	3.5 nTPM
Prostate	3.2 nTPM
Esophagus	1.5 nTPM
Heart muscle	0.8 nTPM

T-cells	2.5 nTPM
Endometrium	5.9 nTPM
Colon	4.7 nTPM
Ovary	4.5 nTPM
Liver	3.6 nTPM
Skin	3.6 nTPM
Kidney	3.4 nTPM
Lung	3.0 nTPM
Skeletal muscle	2.8 nTPM
Bone marrow	2.3 nTPM
Spleen	2.3 nTPM
Breast	2.1 nTPM
Lymph node	1.5 nTPM
Adipose tissue	1.3 nTPM
Stomach	1.2 nTPM
PBMC	1.0 nTPM
Prostate	0.0 nTPM
Esophagus	0.0 nTPM

Basal respiratory cells	14.2 nTPM
Bronchus	14.2 nTPM

Basal squamous epithelial cells	2.2 nTPM
Esophagus	2.2 nTPM

Cholangiocytes	11.5 nTPM
Liver	11.5 nTPM

Collecting duct cells	18.4 nTPM
Kidney	18.4 nTPM

Undifferentiated cells	12.2 nTPM
Small intestine	24.7 nTPM
Rectum	6.5 nTPM
Colon	5.4 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC