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Aliases for TMEM39A Gene

Aliases for TMEM39A Gene

  • Transmembrane Protein 39A 2 3 5

External Ids for TMEM39A Gene

Previous GeneCards Identifiers for TMEM39A Gene

  • GC03M120632
  • GC03M119148
  • GC03M116525

Summaries for TMEM39A Gene

GeneCards Summary for TMEM39A Gene

TMEM39A (Transmembrane Protein 39A) is a Protein Coding gene. An important paralog of this gene is TMEM39B.

Additional gene information for TMEM39A Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TMEM39A Gene

Genomics for TMEM39A Gene

GeneHancer (GH) Regulatory Elements for TMEM39A Gene

Promoters and enhancers for TMEM39A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03I119462 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.4 +5.4 5392 2.8 HDGF PKNOX1 FOXA2 SMAD1 ZFP64 ARID4B SIN3A DMAP1 IRF4 YY1 TMEM39A POGLUT1 TIMMDC1 GC03P119428
GH03I119468 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 561.7 -0.3 -295 2.2 HDGF FOXA2 SMAD1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF766 POGLUT1 TMEM39A RPS26P21 B4GALT4 CD80 FSTL1 TIMMDC1 ENSG00000272662
GH03I120090 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 12.3 -625.1 -625108 7.1 HDGF PKNOX1 CLOCK ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 POLR2B GSK3B ENSG00000242622 POGLUT1 TMEM39A GC03M119752
GH03I120347 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.9 -880.6 -880597 3.4 CLOCK MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B LOC100130701 LRRC58 GPR156 TMEM39A MAATS1 LOC442087
GH03I119497 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.3 -30.4 -30393 3.7 PKNOX1 SMAD1 ZFP64 ARID4B SIN3A DMAP1 IRF4 YY1 POLR2B ZNF766 TIMMDC1 ENSG00000272662 GC03P119501 PIR33513 POGLUT1 CD80 TMEM39A ADPRH POPDC2 MAATS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TMEM39A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TMEM39A gene promoter:

Genomic Locations for TMEM39A Gene

Genomic Locations for TMEM39A Gene
39,871 bases
Minus strand

Genomic View for TMEM39A Gene

Genes around TMEM39A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TMEM39A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TMEM39A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TMEM39A Gene

Proteins for TMEM39A Gene

  • Protein details for TMEM39A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Transmembrane protein 39A
    Protein Accession:
    Secondary Accessions:
    • D3DN80
    • Q53FN4
    • Q53GI1
    • Q6PKB5

    Protein attributes for TMEM39A Gene

    488 amino acids
    Molecular mass:
    55667 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for TMEM39A Gene


neXtProt entry for TMEM39A Gene

Post-translational modifications for TMEM39A Gene

  • Ubiquitination at isoforms=358
  • Glycosylation at isoforms=231 and isoforms=239
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TMEM39A Gene

Domains & Families for TMEM39A Gene

Gene Families for TMEM39A Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for TMEM39A Gene


Suggested Antigen Peptide Sequences for TMEM39A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the TMEM39 family.
  • Belongs to the TMEM39 family.
genes like me logo Genes that share domains with TMEM39A: view

Function for TMEM39A Gene

Phenotypes From GWAS Catalog for TMEM39A Gene

genes like me logo Genes that share phenotypes with TMEM39A: view

Animal Model Products

  • Taconic Biosciences Mouse Models for TMEM39A

miRNA for TMEM39A Gene

miRTarBase miRNAs that target TMEM39A

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TMEM39A Gene

Localization for TMEM39A Gene

Subcellular locations from UniProtKB/Swiss-Prot for TMEM39A Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TMEM39A gene
Compartment Confidence
plasma membrane 3
nucleus 3
mitochondrion 1
peroxisome 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TMEM39A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with TMEM39A: view

Pathways & Interactions for TMEM39A Gene

SuperPathways for TMEM39A Gene

No Data Available

Interacting Proteins for TMEM39A Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
Selected Interacting proteins: ENSP00000326063 Q9NV64-TM39A_HUMAN for TMEM39A Gene via STRING IID

Gene Ontology (GO) - Biological Process for TMEM39A Gene


No data available for Pathways by source and SIGNOR curated interactions for TMEM39A Gene

Drugs & Compounds for TMEM39A Gene

No Compound Related Data Available

Transcripts for TMEM39A Gene

Unigene Clusters for TMEM39A Gene

Transmembrane protein 39A:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TMEM39A Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c ^ 10a · 10b ^ 11 ^ 12a · 12b
SP1: -
SP2: - -
SP3: -
SP4: - - - -
SP5: - -
SP6: -
SP7: -
SP8: - - - - - - -
SP9: - -

Relevant External Links for TMEM39A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for TMEM39A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TMEM39A Gene

Protein differential expression in normal tissues from HIPED for TMEM39A Gene

This gene is overexpressed in Lung (48.9) and Placenta (20.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TMEM39A Gene

Protein tissue co-expression partners for TMEM39A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TMEM39A Gene:


SOURCE GeneReport for Unigene cluster for TMEM39A Gene:


Evidence on tissue expression from TISSUES for TMEM39A Gene

  • Intestine(4.2)
  • Kidney(4.2)
  • Stomach(4.2)
  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with TMEM39A: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TMEM39A Gene

Orthologs for TMEM39A Gene

This gene was present in the common ancestor of animals.

Orthologs for TMEM39A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia TMEM39A 33 34
  • 99.8 (n)
(Monodelphis domestica)
Mammalia TMEM39A 34
  • 95 (a)
(Canis familiaris)
Mammalia TMEM39A 33 34
  • 94.81 (n)
(Bos Taurus)
Mammalia TMEM39A 33 34
  • 93.78 (n)
(Mus musculus)
Mammalia Tmem39a 33 16 34
  • 90.12 (n)
(Rattus norvegicus)
Mammalia Tmem39a 33
  • 89.24 (n)
(Gallus gallus)
Aves TMEM39A 33 34
  • 80.85 (n)
(Anolis carolinensis)
Reptilia TMEM39A 34
  • 90 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia tmem39a 33
  • 76.2 (n)
Str.10539 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.11343 33
(Danio rerio)
Actinopterygii tmem39a 33 34
  • 66.53 (n)
wufb92e03 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011817 33
  • 44.16 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG13016 33 34
  • 44 (n)
(Caenorhabditis elegans)
Secernentea D1007.5 33 34
  • 43.71 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 36 (a)
Species where no ortholog for TMEM39A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TMEM39A Gene

Gene Tree for TMEM39A (if available)
Gene Tree for TMEM39A (if available)

Paralogs for TMEM39A Gene

Paralogs for TMEM39A Gene

(1) SIMAP similar genes for TMEM39A Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with TMEM39A: view

Variants for TMEM39A Gene

Sequence variations from dbSNP and Humsavar for TMEM39A Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
VAR_036095 A breast cancer sample p.Ser247Leu
rs1000000439 -- 119,434,141(-) G/A genic_downstream_transcript_variant, intron_variant
rs1000101276 -- 119,455,343(-) AT/ intron_variant
rs1000109190 -- 119,461,908(-) A/T intron_variant
rs1000165201 -- 119,458,635(-) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TMEM39A Gene

Variant ID Type Subtype PubMed ID
esv2725823 CNV deletion 23290073
esv3597558 CNV loss 21293372
nsv829694 CNV gain 17160897
nsv829695 CNV loss 17160897

Variation tolerance for TMEM39A Gene

Residual Variation Intolerance Score: 16% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.52; 71.93% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TMEM39A Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TMEM39A Gene

Disorders for TMEM39A Gene

Additional Disease Information for TMEM39A

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for TMEM39A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TMEM39A Gene

Publications for TMEM39A Gene

  1. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M … Yamada Y (American journal of hypertension 2010) 3 44 58
  2. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PMID: 20198315) Yoshida T … Yamada Y (International journal of molecular medicine 2010) 3 44 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 58
  5. Association of novel polymorphisms in TMEM39A gene with systemic lupus erythematosus in a Chinese Han population. (PMID: 28427360) Cai X … Jiang Y (BMC medical genetics 2017) 3 58

Products for TMEM39A Gene

Sources for TMEM39A Gene

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