Single cell type - NECAP1 - 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.	NECAP1
Gene descriptionⁱ Full gene name according to HGNC.	NECAP endocytosis associated 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes
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.	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. Read more	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. Read more	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. Read more	Low immune cell specificity
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 all
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: Low cell type specificity

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

NECAP1 is part of cluster 52 Non-specific - Transcription with confidenceⁱ 1
611 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
RAB39B	RAB39B, member RAS oncogene family	0.5850	63
CREBZF	CREB/ATF bZIP transcription factor	0.5389	52
RBM6	RNA binding motif protein 6	0.4576	52
PUS7L	Pseudouridine synthase 7 like	0.4565	52
TTC14	Tetratricopeptide repeat domain 14	0.4558	52
KMT2E	Lysine methyltransferase 2E (inactive)	0.4549	24
MFSD8	Major facilitator superfamily domain containing 8	0.4535	52
TMEM259	Transmembrane protein 259	0.4357	52
USP11	Ubiquitin specific peptidase 11	0.4314	56
SF1	Splicing factor 1	0.4295	57
ZFYVE27	Zinc finger FYVE-type containing 27	0.4277	9
TSC22D3	TSC22 domain family member 3	0.4216	24
ZRANB2	Zinc finger RANBP2-type containing 2	0.4211	52
CA5B	Carbonic anhydrase 5B	0.4195	24
PPM1B	Protein phosphatase, Mg2+/Mn2+ dependent 1B	0.4183	46

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	18.9 nTPM
Adipose tissue	24.7 nTPM
Breast	13.3 nTPM

Alveolar cells type 1	38.5 nTPM
Lung	38.5 nTPM

Alveolar cells type 2	24.0 nTPM
Lung	24.0 nTPM

Astrocytes	11.4 nTPM
Brain	11.4 nTPM

B-cells	36.1 nTPM
Adipose tissue	70.1 nTPM
Kidney	47.6 nTPM
Stomach	41.3 nTPM
Colon	39.9 nTPM
Lymph node	33.7 nTPM
Spleen	33.6 nTPM
Bone marrow	28.6 nTPM
Breast	25.5 nTPM
PBMC	22.8 nTPM
Liver	18.1 nTPM

Dendritic cells	32.9 nTPM
Adipose tissue	67.6 nTPM
Breast	27.0 nTPM
PBMC	4.0 nTPM

Endothelial cells	18.1 nTPM
Skin	33.0 nTPM
Prostate	25.5 nTPM
Skeletal muscle	21.1 nTPM
Ovary	21.1 nTPM
Lung	18.7 nTPM
Heart muscle	18.1 nTPM
Endometrium	17.8 nTPM
Testis	17.7 nTPM
Esophagus	16.5 nTPM
Pancreas	15.5 nTPM
Liver	13.7 nTPM
Placenta	13.1 nTPM
Breast	13.1 nTPM
Eye	8.9 nTPM

Fibroblasts	17.9 nTPM
Adipose tissue	31.2 nTPM
Skin	23.9 nTPM
Prostate	21.5 nTPM
Breast	18.0 nTPM
Skeletal muscle	17.5 nTPM
Placenta	17.2 nTPM
Stomach	16.3 nTPM
Ovary	14.3 nTPM
Esophagus	13.9 nTPM
Heart muscle	12.3 nTPM
Lung	11.1 nTPM

Intestinal goblet cells	16.1 nTPM
Colon	19.3 nTPM
Rectum	15.7 nTPM
Small intestine	13.3 nTPM

Macrophages	22.4 nTPM
Adipose tissue	38.9 nTPM
Stomach	35.1 nTPM
Kidney	32.5 nTPM
Endometrium	29.4 nTPM
Spleen	27.0 nTPM
Lung	22.7 nTPM
Ovary	21.8 nTPM
Breast	21.3 nTPM
Bone marrow	21.2 nTPM
Skeletal muscle	20.0 nTPM
Prostate	19.5 nTPM
Testis	18.6 nTPM
Esophagus	17.3 nTPM
Pancreas	10.2 nTPM
PBMC	0.0 nTPM

Paneth cells	16.0 nTPM
Small intestine	18.8 nTPM
Rectum	16.2 nTPM
Colon	13.2 nTPM

Plasma cells	33.7 nTPM
Adipose tissue	53.5 nTPM
Stomach	50.1 nTPM
Spleen	28.0 nTPM
Bone marrow	24.7 nTPM
Esophagus	12.3 nTPM

Respiratory ciliated cells	13.1 nTPM
Lung	13.1 nTPM
Bronchus	13.0 nTPM

Smooth muscle cells	21.3 nTPM
Bronchus	38.1 nTPM
Heart muscle	31.3 nTPM
Skin	25.8 nTPM
Adipose tissue	25.1 nTPM
Endometrium	19.8 nTPM
Prostate	19.6 nTPM
Skeletal muscle	17.6 nTPM
Ovary	17.3 nTPM
Pancreas	16.5 nTPM
Breast	14.1 nTPM
Esophagus	9.3 nTPM

T-cells	35.6 nTPM
Skin	61.7 nTPM
Adipose tissue	56.4 nTPM
Endometrium	54.6 nTPM
Ovary	53.4 nTPM
Prostate	37.9 nTPM
Stomach	37.3 nTPM
Lymph node	31.4 nTPM
Breast	31.0 nTPM
Colon	30.4 nTPM
Kidney	30.2 nTPM
Liver	29.9 nTPM
Spleen	29.8 nTPM
Bone marrow	28.7 nTPM
Lung	25.8 nTPM
PBMC	25.0 nTPM
Skeletal muscle	22.9 nTPM
Esophagus	19.7 nTPM

Basal prostatic cells	22.0 nTPM
Prostate	22.0 nTPM

Basal squamous epithelial cells	25.6 nTPM
Esophagus	25.6 nTPM

Cholangiocytes	7.2 nTPM
Liver	7.2 nTPM

Cone photoreceptor cells	27.1 nTPM
Eye	27.1 nTPM

Undifferentiated cells	14.1 nTPM
Colon	15.7 nTPM
Rectum	13.8 nTPM
Small intestine	12.7 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