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Aliases for TMEM59 Gene

Aliases for TMEM59 Gene

  • Transmembrane Protein 59 2 3 3 5
  • Liver Membrane-Bound Protein 3 4
  • C1orf8 3 4
  • Chromosome 1 Open Reading Frame 8 2
  • Dendritic Cell Factor 1 3
  • HSPC001 3
  • PRO195 3
  • UNQ169 3
  • DCF1 3

External Ids for TMEM59 Gene

Previous HGNC Symbols for TMEM59 Gene

  • C1orf8

Previous GeneCards Identifiers for TMEM59 Gene

  • GC01M054210
  • GC01M054269
  • GC01M054497
  • GC01M052613

Summaries for TMEM59 Gene

Entrez Gene Summary for TMEM59 Gene

  • This gene encodes a protein shown to regulate autophagy in response to bacterial infection. This protein may also regulate the retention of amyloid precursor protein (APP) in the Golgi apparatus through its control of APP glycosylation. Overexpression of this protein has been found to promote apoptosis in a glioma cell line. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]

GeneCards Summary for TMEM59 Gene

TMEM59 (Transmembrane Protein 59) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include serine-type endopeptidase inhibitor activity and endopeptidase activity. An important paralog of this gene is TMEM59L.

UniProtKB/Swiss-Prot for TMEM59 Gene

  • Acts as a regulator of autophagy in response to S.aureus infection by promoting activation of LC3 (MAP1LC3A, MAP1LC3B or MAP1LC3C). Acts by interacting with ATG16L1, leading to promote a functional complex between LC3 and ATG16L1 and promoting LC3 lipidation and subsequent activation of autophagy (PubMed:27273576, PubMed:23376921). Modulates the O-glycosylation and complex N-glycosylation steps occurring during the Golgi maturation of several proteins such as APP, BACE1, SEAP or PRNP (PubMed:20427278). Inhibits APP transport to the cell surface and further shedding (PubMed:20427278).

Gene Wiki entry for TMEM59 Gene

Additional gene information for TMEM59 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TMEM59 Gene

Genomics for TMEM59 Gene

GeneHancer (GH) Regulatory Elements for TMEM59 Gene

Promoters and enhancers for TMEM59 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J054051 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +0.4 350 3.7 DMAP1 YY1 SLC30A9 E2F8 ZNF416 ZNF143 ZNF548 SP3 NFYC SSRP1 TCEANC2 TMEM59 MIR4781 MAGOH NDC1 ENSG00000228838 HSPB11 SSBP3-AS1 LRRC42 PARS2
GH01J054403 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.8 -353.4 -353408 7.5 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZBTB7B YY1 SSBP3 PIR46432 ENSG00000225632 SSBP3-AS1 TCEANC2 TMEM59 ENSG00000230728 GC01M054384
GH01J054271 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 15.1 -223.0 -223037 10.6 HDGF FOXA2 PKNOX1 ARNT FEZF1 ZNF2 YY1 CBX5 ZNF213 E2F8 SSBP3-AS1 SSBP3 TMEM59 CYB5RL NDC1 ENSG00000256407 TCEANC2 ENSG00000237453 TTC22 ENSG00000225632
GH01J053835 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 9.7 +216.4 216372 4.1 MLX DMAP1 YBX1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 MEF2D NDC1 MAGOH SSBP3-AS1 HSPB11 LRRC42 ECHDC2 ENSG00000256407 CYB5RL C1orf123 ENSG00000279049
GH01J054309 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 10.2 -259.0 -259029 5.9 SIN3A RAD21 RARA GLIS2 ARID2 ZNF143 ZFP91 THAP11 EGR2 ZNF654 ENSG00000225632 SSBP3 SSBP3-AS1 CDCP2 TCEANC2 TMEM59 TTC22 ENSG00000237453 GC01M054384
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TMEM59 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TMEM59 gene promoter:
  • Cdc5
  • FOXL1
  • Evi-1
  • LCR-F1
  • NF-kappaB1
  • Spz1
  • HNF-3beta
  • IRF-7A
  • STAT3

Genomic Locations for TMEM59 Gene

Genomic Locations for TMEM59 Gene
chr1:54,026,681-54,053,504
(GRCh38/hg38)
Size:
26,824 bases
Orientation:
Minus strand
chr1:54,497,347-54,519,177
(GRCh37/hg19)
Size:
21,831 bases
Orientation:
Minus strand

Genomic View for TMEM59 Gene

Genes around TMEM59 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TMEM59 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TMEM59 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TMEM59 Gene

Proteins for TMEM59 Gene

  • Protein details for TMEM59 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BXS4-TMM59_HUMAN
    Recommended name:
    Transmembrane protein 59
    Protein Accession:
    Q9BXS4
    Secondary Accessions:
    • B3KQL7
    • O75393
    • Q4VBP9
    • Q5T705
    • Q96KX7

    Protein attributes for TMEM59 Gene

    Size:
    323 amino acids
    Molecular mass:
    36223 Da
    Quaternary structure:
    • Interacts with ATG16L1 (via WD repeats).
    SequenceCaution:
    • Sequence=AAC39890.1; Type=Frameshift; Positions=6; Evidence={ECO:0000305}; Sequence=AAH03106.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

neXtProt entry for TMEM59 Gene

Post-translational modifications for TMEM59 Gene

No data available for DME Specific Peptides for TMEM59 Gene

Domains & Families for TMEM59 Gene

Gene Families for TMEM59 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Predicted secreted proteins

Protein Domains for TMEM59 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for TMEM59 Gene

Graphical View of Domain Structure for InterPro Entry

Q9BXS4

UniProtKB/Swiss-Prot:

TMM59_HUMAN :
  • The ATG16L1-binding motif mediates interaction with ATG16L1 and promotes autophagy.
  • Belongs to the TMEM59 family.
Domain:
  • The ATG16L1-binding motif mediates interaction with ATG16L1 and promotes autophagy.
Family:
  • Belongs to the TMEM59 family.
genes like me logo Genes that share domains with TMEM59: view

Function for TMEM59 Gene

Molecular function for TMEM59 Gene

UniProtKB/Swiss-Prot Function:
Acts as a regulator of autophagy in response to S.aureus infection by promoting activation of LC3 (MAP1LC3A, MAP1LC3B or MAP1LC3C). Acts by interacting with ATG16L1, leading to promote a functional complex between LC3 and ATG16L1 and promoting LC3 lipidation and subsequent activation of autophagy (PubMed:27273576, PubMed:23376921). Modulates the O-glycosylation and complex N-glycosylation steps occurring during the Golgi maturation of several proteins such as APP, BACE1, SEAP or PRNP (PubMed:20427278). Inhibits APP transport to the cell surface and further shedding (PubMed:20427278).

Phenotypes From GWAS Catalog for TMEM59 Gene

Gene Ontology (GO) - Molecular Function for TMEM59 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004175 endopeptidase activity IEA --
GO:0005515 protein binding IPI 23376921
genes like me logo Genes that share ontologies with TMEM59: view
genes like me logo Genes that share phenotypes with TMEM59: view

Animal Model Products

  • Taconic Biosciences Mouse Models for TMEM59

miRNA for TMEM59 Gene

miRTarBase miRNAs that target TMEM59

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TMEM59 Gene

Localization for TMEM59 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TMEM59 Gene

Late endosome membrane; Single-pass type I membrane protein. Lysosome membrane; Single-pass type I membrane protein. Cell membrane; Single-pass type I membrane protein. Golgi apparatus membrane; Single-pass type I membrane protein. Note=Mainly localizes to late endosomes/lysosomes. Probably first exported to the cell surface and then actively endocytosed to transiently localize in early endosomes on its way to the late endosomal/lysosomal compartment where it becomes quickly degraded. {ECO:0000269 PubMed:23376921}.

Subcellular locations from

COMPARTMENTS
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 TMEM59 gene
Compartment Confidence
extracellular 5
lysosome 5
golgi apparatus 5
endosome 5
plasma membrane 4

Gene Ontology (GO) - Cellular Components for TMEM59 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000137 Golgi cis cisterna IDA 20427278
GO:0000138 Golgi trans cisterna IDA 20427278
GO:0000139 Golgi membrane IEA --
GO:0005764 lysosome IEA,IDA 23376921
GO:0005765 lysosomal membrane IEA --
genes like me logo Genes that share ontologies with TMEM59: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TMEM59 Gene

Pathways & Interactions for TMEM59 Gene

SuperPathways for TMEM59 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TMEM59 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0006914 autophagy IEA --
GO:0010508 positive regulation of autophagy IMP 23376921
GO:0010955 negative regulation of protein processing IDA 20427278
GO:0090285 negative regulation of protein glycosylation in Golgi IDA 20427278
genes like me logo Genes that share ontologies with TMEM59: view

No data available for Pathways by source and SIGNOR curated interactions for TMEM59 Gene

Drugs & Compounds for TMEM59 Gene

No Compound Related Data Available

Transcripts for TMEM59 Gene

Unigene Clusters for TMEM59 Gene

Transmembrane protein 59:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TMEM59 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c · 2d · 2e ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b · 8c · 8d ^ 9a · 9b ^ 10a · 10b · 10c ·
SP1: - -
SP2: - - - - - - -
SP3: - - - - - - -
SP4: - -
SP5: - - -
SP6:
SP7: - - - - - - - -
SP8: - - - - - - - -
SP9: - - - -
SP10: - - - -
SP11: -
SP12: -
SP13: - - - - - -
SP14: - - -
SP15: -
SP16: - - - -
SP17: - - -

ExUns: 10d · 10e · 10f
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:

Relevant External Links for TMEM59 Gene

GeneLoc Exon Structure for
TMEM59
ECgene alternative splicing isoforms for
TMEM59

Expression for TMEM59 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TMEM59 Gene

Protein differential expression in normal tissues from HIPED for TMEM59 Gene

This gene is overexpressed in Bone (44.2) and Placenta (17.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TMEM59 Gene



Protein tissue co-expression partners for TMEM59 Gene

NURSA nuclear receptor signaling pathways regulating expression of TMEM59 Gene:

TMEM59

SOURCE GeneReport for Unigene cluster for TMEM59 Gene:

Hs.523262

Evidence on tissue expression from TISSUES for TMEM59 Gene

  • Nervous system(5)
  • Lung(4.8)
  • Blood(4.4)
  • Pancreas(3.9)
  • Intestine(3.4)
  • Kidney(3.2)
  • Eye(3.1)
  • Adrenal gland(2.6)
  • Spleen(2.6)
  • Liver(2.5)
  • Lymph node(2.5)
  • Stomach(2.4)
  • Skin(2.2)
  • Thyroid gland(2.2)
  • Gall bladder(2.1)
  • Heart(2)
  • Muscle(2)
genes like me logo Genes that share expression patterns with TMEM59: 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 TMEM59 Gene

Orthologs for TMEM59 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TMEM59 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TMEM59 34 33
  • 99.9 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TMEM59 34 33
  • 94.32 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TMEM59 34 33
  • 93.91 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Tmem59 16 34 33
  • 89.47 (n)
rat
(Rattus norvegicus)
Mammalia RGD1310313 33
  • 87.1 (n)
oppossum
(Monodelphis domestica)
Mammalia TMEM59 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves TMEM59 34 33
  • 79.27 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TMEM59 34
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tmem59 33
  • 65.98 (n)
Str.6280 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.29361 33
zebrafish
(Danio rerio)
Actinopterygii tmem59 34 33
  • 63.58 (n)
OneToOne
Dr.5932 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3043 34
  • 18 (a)
OneToMany
Species where no ortholog for TMEM59 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for TMEM59 Gene

ENSEMBL:
Gene Tree for TMEM59 (if available)
TreeFam:
Gene Tree for TMEM59 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TMEM59: view image

Paralogs for TMEM59 Gene

Paralogs for TMEM59 Gene

(1) SIMAP similar genes for TMEM59 Gene using alignment to 7 proteins:

  • TMM59_HUMAN
  • D3DQ48_HUMAN
  • Q5T6Z8_HUMAN
  • Q5T703_HUMAN
  • Q5T704_HUMAN
  • Q5T706_HUMAN
  • Q6P5R1_HUMAN
genes like me logo Genes that share paralogs with TMEM59: view

Variants for TMEM59 Gene

Sequence variations from dbSNP and Humsavar for TMEM59 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000024454 -- 54,046,921(-) A/G intron_variant
rs1000122576 -- 54,032,287(-) C/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1000235823 -- 54,051,805(-) T/C intron_variant
rs1000259021 -- 54,045,401(-) A/G downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant
rs1000364078 -- 54,045,239(-) T/A/C downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TMEM59 Gene

Variant ID Type Subtype PubMed ID
nsv477511 CNV novel sequence insertion 20440878
nsv475372 CNV novel sequence insertion 20440878
nsv1011262 CNV gain 25217958
nsv1003904 CNV gain 25217958

Variation tolerance for TMEM59 Gene

Residual Variation Intolerance Score: 40.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.76; 33.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TMEM59 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TMEM59

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TMEM59 Gene

Disorders for TMEM59 Gene

Additional Disease Information for TMEM59

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for TMEM59 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TMEM59 Gene

Publications for TMEM59 Gene

  1. TMEM59 defines a novel ATG16L1-binding motif that promotes local activation of LC3. (PMID: 23376921) Boada-Romero E … Pimentel-Muiños FX (The EMBO journal 2013) 2 3 4 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. The novel membrane protein TMEM59 modulates complex glycosylation, cell surface expression, and secretion of the amyloid precursor protein. (PMID: 20427278) Ullrich S … Lichtenthaler SF (The Journal of biological chemistry 2010) 3 4 58
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  5. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. (PMID: 16303743) Otsuki T … Isogai T (DNA research : an international journal for rapid publication of reports on genes and genomes 2005) 3 4 58

Products for TMEM59 Gene

Sources for TMEM59 Gene

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