Single cell type - CLIP1 - 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.	CLIP1
Gene descriptionⁱ Full gene name according to HGNC.	CAP-Gly domain containing linker protein 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes Plasma 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. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	11

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	Syncytiotrophoblasts - Pregnancy hormone signaling (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	Cell type enhanced (Syncytiotrophoblasts)
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: Cell type enhanced (Syncytiotrophoblasts)

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

CLIP1 is part of cluster 18 Syncytiotrophoblasts - Pregnancy hormone signaling with confidenceⁱ 1
186 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
KRT23	Keratin 23	0.5933	22
TACC2	Transforming acidic coiled-coil containing protein 2	0.5878	18
BTG3	BTG anti-proliferation factor 3	0.5180	18
PTPN21	Protein tyrosine phosphatase non-receptor type 21	0.5085	18
RDH13	Retinol dehydrogenase 13	0.5052	18
HSPB8	Heat shock protein family B (small) member 8	0.4955	18
PPFIA1	PTPRF interacting protein alpha 1	0.4863	29
SLK	STE20 like kinase	0.4778	22
SLC38A9	Solute carrier family 38 member 9	0.4760	18
KIAA0040	KIAA0040	0.4685	18
KRTAP19-5	Keratin associated protein 19-5	0.4586	18
IGSF5	Immunoglobulin superfamily member 5	0.4573	18
HECTD1	HECT domain E3 ubiquitin protein ligase 1	0.4436	22
KISS1	KiSS-1 metastasis suppressor	0.4413	18
PSG8	Pregnancy specific beta-1-glycoprotein 8	0.4412	18

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	50.2 nTPM
Adipose tissue	64.9 nTPM
Breast	35.5 nTPM

Alveolar cells type 1	134.6 nTPM
Lung	134.6 nTPM

Alveolar cells type 2	129.9 nTPM
Lung	129.9 nTPM

Astrocytes	116.2 nTPM
Brain	116.2 nTPM

B-cells	32.4 nTPM
Adipose tissue	53.1 nTPM
Colon	51.1 nTPM
PBMC	37.1 nTPM
Bone marrow	32.7 nTPM
Breast	30.7 nTPM
Stomach	30.4 nTPM
Spleen	29.4 nTPM
Lymph node	27.6 nTPM
Liver	26.5 nTPM
Kidney	4.8 nTPM

Dendritic cells	34.5 nTPM
Adipose tissue	44.5 nTPM
PBMC	31.8 nTPM
Breast	27.0 nTPM

Endothelial cells	57.3 nTPM
Lung	118.5 nTPM
Prostate	101.0 nTPM
Heart muscle	73.8 nTPM
Skeletal muscle	67.3 nTPM
Testis	65.8 nTPM
Eye	53.4 nTPM
Liver	51.3 nTPM
Pancreas	42.5 nTPM
Skin	41.5 nTPM
Endometrium	41.2 nTPM
Esophagus	40.3 nTPM
Ovary	40.1 nTPM
Breast	34.0 nTPM
Placenta	31.3 nTPM

Fibroblasts	69.1 nTPM
Lung	160.8 nTPM
Prostate	99.8 nTPM
Heart muscle	96.6 nTPM
Skeletal muscle	96.3 nTPM
Adipose tissue	68.8 nTPM
Skin	57.4 nTPM
Stomach	56.4 nTPM
Esophagus	38.2 nTPM
Placenta	35.6 nTPM
Breast	27.9 nTPM
Ovary	22.5 nTPM

Intestinal goblet cells	22.3 nTPM
Small intestine	23.8 nTPM
Rectum	23.0 nTPM
Colon	20.1 nTPM

Macrophages	57.0 nTPM
Lung	118.0 nTPM
Skeletal muscle	82.0 nTPM
Adipose tissue	74.6 nTPM
Stomach	64.5 nTPM
Pancreas	61.2 nTPM
Testis	56.9 nTPM
Ovary	56.9 nTPM
Spleen	56.0 nTPM
Prostate	55.1 nTPM
Endometrium	49.2 nTPM
Kidney	42.4 nTPM
Bone marrow	41.2 nTPM
Esophagus	39.3 nTPM
Breast	31.0 nTPM
PBMC	27.3 nTPM

Paneth cells	28.5 nTPM
Colon	36.2 nTPM
Small intestine	26.3 nTPM
Rectum	23.1 nTPM

Plasma cells	33.0 nTPM
Adipose tissue	47.7 nTPM
Stomach	42.1 nTPM
Bone marrow	33.0 nTPM
Spleen	29.9 nTPM
Esophagus	12.3 nTPM

Respiratory ciliated cells	146.5 nTPM
Bronchus	150.1 nTPM
Lung	142.8 nTPM

Smooth muscle cells	68.4 nTPM
Heart muscle	127.4 nTPM
Prostate	120.0 nTPM
Bronchus	92.1 nTPM
Skeletal muscle	77.3 nTPM
Ovary	73.0 nTPM
Endometrium	49.0 nTPM
Esophagus	46.5 nTPM
Pancreas	45.0 nTPM
Adipose tissue	42.5 nTPM
Skin	41.5 nTPM
Breast	38.2 nTPM

T-cells	48.5 nTPM
Skeletal muscle	76.9 nTPM
Adipose tissue	65.2 nTPM
PBMC	59.1 nTPM
Stomach	58.9 nTPM
Lung	57.7 nTPM
Colon	57.5 nTPM
Endometrium	50.2 nTPM
Esophagus	45.9 nTPM
Bone marrow	45.3 nTPM
Lymph node	44.8 nTPM
Spleen	43.6 nTPM
Kidney	41.8 nTPM
Ovary	40.0 nTPM
Prostate	37.9 nTPM
Liver	35.9 nTPM
Breast	34.2 nTPM
Skin	29.9 nTPM

Basal keratinocytes	67.2 nTPM
Skin	67.2 nTPM

Basal prostatic cells	162.6 nTPM
Prostate	162.6 nTPM

Basal squamous epithelial cells	23.9 nTPM
Esophagus	23.9 nTPM

Cholangiocytes	50.1 nTPM
Liver	50.1 nTPM

Undifferentiated cells	23.0 nTPM
Colon	23.9 nTPM
Small intestine	23.6 nTPM
Rectum	21.3 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