Single cell type - KLHDC3 - 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.	KLHDC3
Gene descriptionⁱ Full gene name according to HGNC.	Kelch domain containing 3
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.	3

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 - 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. Read more	Group enriched (Late spermatids, Early spermatids)
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: Group enriched (Late spermatids, Early spermatids)

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

KLHDC3 is part of cluster 31 Spermatids - Spermatogenesis with confidenceⁱ 1
413 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
ACTL7A	Actin like 7A	0.7969	31
PDYN	Prodynorphin	0.7955	31
GAPDHS	Glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	0.7928	31
TEX22	Testis expressed 22	0.7871	31
TMCO5A	Transmembrane and coiled-coil domains 5A	0.7861	31
LIN28A	Lin-28 homolog A	0.7841	31
LEMD1	LEM domain containing 1	0.7776	31
LRRC27	Leucine rich repeat containing 27	0.7695	31
SPEM1	Spermatid maturation 1	0.7647	31
STX8	Syntaxin 8	0.7636	31
ACTRT2	Actin related protein T2	0.7580	31
PGK2	Phosphoglycerate kinase 2	0.7565	31
C16orf90	Chromosome 16 open reading frame 90	0.7484	25
TBC1D21	TBC1 domain family member 21	0.7481	31
PRM2	Protamine 2	0.7443	31

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	21.3 nTPM
Breast	27.1 nTPM
Adipose tissue	15.6 nTPM

Alveolar cells type 1	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	17.0 nTPM
Lung	17.0 nTPM

Astrocytes	10.4 nTPM
Brain	10.4 nTPM

B-cells	26.7 nTPM
Liver	45.0 nTPM
PBMC	44.2 nTPM
Colon	38.3 nTPM
Kidney	28.5 nTPM
Bone marrow	26.2 nTPM
Breast	25.5 nTPM
Spleen	21.5 nTPM
Stomach	16.8 nTPM
Lymph node	13.9 nTPM
Adipose tissue	7.0 nTPM

Dendritic cells	32.7 nTPM
Breast	37.5 nTPM
Adipose tissue	32.7 nTPM
PBMC	27.9 nTPM

Endothelial cells	30.4 nTPM
Placenta	73.3 nTPM
Pancreas	54.0 nTPM
Liver	44.0 nTPM
Ovary	39.2 nTPM
Testis	38.0 nTPM
Breast	30.6 nTPM
Prostate	28.2 nTPM
Endometrium	24.4 nTPM
Skin	19.2 nTPM
Skeletal muscle	17.6 nTPM
Esophagus	17.5 nTPM
Eye	17.0 nTPM
Heart muscle	15.9 nTPM
Lung	6.2 nTPM

Fibroblasts	36.2 nTPM
Placenta	84.2 nTPM
Breast	50.1 nTPM
Ovary	47.2 nTPM
Adipose tissue	43.8 nTPM
Skin	34.8 nTPM
Skeletal muscle	32.5 nTPM
Esophagus	31.2 nTPM
Prostate	28.0 nTPM
Heart muscle	22.8 nTPM
Stomach	13.4 nTPM
Lung	10.1 nTPM

Intestinal goblet cells	43.7 nTPM
Small intestine	56.8 nTPM
Rectum	44.4 nTPM
Colon	30.0 nTPM

Macrophages	31.8 nTPM
Pancreas	61.2 nTPM
Ovary	59.2 nTPM
PBMC	54.6 nTPM
Testis	47.0 nTPM
Breast	33.1 nTPM
Kidney	30.3 nTPM
Prostate	27.5 nTPM
Skeletal muscle	26.9 nTPM
Bone marrow	22.5 nTPM
Esophagus	22.0 nTPM
Spleen	20.7 nTPM
Adipose tissue	19.6 nTPM
Endometrium	19.1 nTPM
Stomach	17.6 nTPM
Lung	15.4 nTPM

Paneth cells	44.3 nTPM
Small intestine	71.4 nTPM
Rectum	48.2 nTPM
Colon	13.2 nTPM

Plasma cells	31.7 nTPM
Bone marrow	49.4 nTPM
Spleen	47.8 nTPM
Adipose tissue	34.9 nTPM
Stomach	20.5 nTPM
Esophagus	6.1 nTPM

Respiratory ciliated cells	16.9 nTPM
Bronchus	28.0 nTPM
Lung	5.8 nTPM

Smooth muscle cells	32.2 nTPM
Pancreas	60.3 nTPM
Ovary	57.0 nTPM
Prostate	37.5 nTPM
Breast	36.1 nTPM
Heart muscle	28.1 nTPM
Skin	27.2 nTPM
Esophagus	26.4 nTPM
Endometrium	24.6 nTPM
Skeletal muscle	24.3 nTPM
Adipose tissue	20.8 nTPM
Bronchus	12.2 nTPM

T-cells	28.3 nTPM
Liver	52.4 nTPM
PBMC	51.4 nTPM
Kidney	50.0 nTPM
Ovary	40.0 nTPM
Colon	32.8 nTPM
Skin	29.0 nTPM
Bone marrow	26.9 nTPM
Breast	24.6 nTPM
Prostate	23.6 nTPM
Adipose tissue	21.7 nTPM
Esophagus	19.7 nTPM
Stomach	19.6 nTPM
Lymph node	18.9 nTPM
Skeletal muscle	18.5 nTPM
Lung	18.2 nTPM
Spleen	17.8 nTPM
Endometrium	16.7 nTPM

Basal keratinocytes	18.7 nTPM
Skin	18.7 nTPM

Basal prostatic cells	32.9 nTPM
Prostate	32.9 nTPM

Basal respiratory cells	33.5 nTPM
Bronchus	33.5 nTPM

Basal squamous epithelial cells	14.8 nTPM
Esophagus	14.8 nTPM

Undifferentiated cells	53.7 nTPM
Small intestine	69.7 nTPM
Rectum	49.6 nTPM
Colon	41.6 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