Single cell type - TTC39A - 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.	TTC39A
Gene descriptionⁱ Full gene name according to HGNC.	Tetratricopeptide repeat domain 39A
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,Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	17

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 (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	Immune cell enriched (plasmacytoid DC)
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 single
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	Cell line enhanced (HDLM-2, MCF7, SK-BR-3, T-47d)
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 many
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

TTC39A 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
FAM71D	Family with sequence similarity 71 member D	0.7290	34
FAM71E1	Family with sequence similarity 71 member E1	0.7261	34
FAM71F1	Family with sequence similarity 71 member F1	0.7241	34
C10orf82	Chromosome 10 open reading frame 82	0.7232	34
FAM205C	Family with sequence similarity 205 member C	0.7230	34
CBY3	Chibby family member 3	0.7182	34
TXNDC8	Thioredoxin domain containing 8	0.7178	34
MS4A5	Membrane spanning 4-domains A5	0.7101	34
FBXO39	F-box protein 39	0.7084	34
CCDC179	Coiled-coil domain containing 179	0.7083	34
TEX35	Testis expressed 35	0.7072	34
HMGB4	High mobility group box 4	0.7037	34
C8orf74	Chromosome 8 open reading frame 74	0.6925	34
IGHV3OR16-10	Immunoglobulin heavy variable 3/OR16-10 (non-functional)	0.6909	34
FHL5	Four and a half LIM domains 5	0.6908	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	0.4 nTPM
Breast	0.5 nTPM
Adipose tissue	0.3 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	25.2 nTPM
Lung	25.2 nTPM

Astrocytes	1.3 nTPM
Brain	1.3 nTPM

B-cells	1.1 nTPM
Kidney	4.8 nTPM
Colon	3.2 nTPM
Breast	2.6 nTPM
Stomach	0.5 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Dendritic cells	15.3 nTPM
PBMC	43.8 nTPM
Breast	1.1 nTPM
Adipose tissue	0.9 nTPM

Endothelial cells	1.9 nTPM
Endometrium	5.9 nTPM
Placenta	5.1 nTPM
Pancreas	3.9 nTPM
Prostate	2.7 nTPM
Testis	2.4 nTPM
Breast	1.8 nTPM
Heart muscle	1.7 nTPM
Eye	0.8 nTPM
Skeletal muscle	0.8 nTPM
Skin	0.7 nTPM
Esophagus	0.6 nTPM
Ovary	0.2 nTPM
Liver	0.0 nTPM
Lung	0.0 nTPM

Fibroblasts	0.9 nTPM
Lung	2.2 nTPM
Heart muscle	1.8 nTPM
Skeletal muscle	1.4 nTPM
Breast	1.4 nTPM
Prostate	1.2 nTPM
Skin	0.8 nTPM
Placenta	0.7 nTPM
Ovary	0.3 nTPM
Adipose tissue	0.3 nTPM
Esophagus	0.2 nTPM
Stomach	0.0 nTPM

Intestinal goblet cells	56.0 nTPM
Colon	74.3 nTPM
Rectum	53.1 nTPM
Small intestine	40.5 nTPM

Macrophages	0.9 nTPM
Endometrium	5.1 nTPM
Testis	2.3 nTPM
Breast	1.8 nTPM
Kidney	1.5 nTPM
Skeletal muscle	1.4 nTPM
Ovary	0.8 nTPM
Lung	0.3 nTPM
Adipose tissue	0.2 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	13.7 nTPM
Rectum	27.5 nTPM
Colon	9.9 nTPM
Small intestine	3.7 nTPM

Plasma cells	0.4 nTPM
Adipose tissue	1.3 nTPM
Stomach	0.5 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Respiratory ciliated cells	9.3 nTPM
Lung	11.7 nTPM
Bronchus	7.0 nTPM

Smooth muscle cells	1.3 nTPM
Endometrium	2.3 nTPM
Prostate	2.2 nTPM
Pancreas	1.9 nTPM
Bronchus	1.9 nTPM
Breast	1.4 nTPM
Heart muscle	1.2 nTPM
Skeletal muscle	1.2 nTPM
Skin	1.1 nTPM
Ovary	0.5 nTPM
Adipose tissue	0.4 nTPM
Esophagus	0.0 nTPM

T-cells	1.7 nTPM
Lung	7.6 nTPM
Prostate	4.7 nTPM
Kidney	4.2 nTPM
Skeletal muscle	3.3 nTPM
Ovary	2.2 nTPM
Colon	1.9 nTPM
Endometrium	1.7 nTPM
Skin	1.4 nTPM
Breast	1.3 nTPM
Adipose tissue	0.4 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Basal prostatic cells	5.3 nTPM
Prostate	5.3 nTPM

Cholangiocytes	5.7 nTPM
Liver	5.7 nTPM

Collecting duct cells	9.2 nTPM
Kidney	9.2 nTPM

Endometrial stromal cells	3.0 nTPM
Endometrium	3.0 nTPM

Undifferentiated cells	20.7 nTPM
Rectum	35.1 nTPM
Colon	23.1 nTPM
Small intestine	4.1 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