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Aliases for TBC1D25 Gene

Aliases for TBC1D25 Gene

  • TBC1 Domain Family Member 25 2 3 5
  • Ornithine Aminotransferase-Like 1 2 3
  • OATL1 3 4
  • TBC1 Domain Family, Member 25 2
  • 5SN3 SnoRNA 3
  • MG81 3

External Ids for TBC1D25 Gene

Previous HGNC Symbols for TBC1D25 Gene

  • OATL1

Previous GeneCards Identifiers for TBC1D25 Gene

  • GC0XP048283
  • GC0XP048397
  • GC0XP046061

Summaries for TBC1D25 Gene

Entrez Gene Summary for TBC1D25 Gene

  • This gene encodes a protein with a TBC domain and functions as a Rab GTPase activating protein. The encoded protein is involved in the fusion of autophagosomes with endosomes and lysosomes. This gene was previously known as ornithine aminotransferase-like 1, but has no similarity to ornithine aminotransferase. [provided by RefSeq, Jan 2017]

GeneCards Summary for TBC1D25 Gene

TBC1D25 (TBC1 Domain Family Member 25) is a Protein Coding gene. Diseases associated with TBC1D25 include Synovium Cancer and Aland Island Eye Disease. Among its related pathways are Vesicle-mediated transport and TBC/RABGAPs. Gene Ontology (GO) annotations related to this gene include GTPase activator activity. An important paralog of this gene is TBC1D17.

UniProtKB/Swiss-Prot for TBC1D25 Gene

  • Acts as a GTPase-activating protein specific for RAB33B. Involved in the regulation of autophagosome maturation, the process in which autophagosomes fuse with endosomes and lysosomes.

Additional gene information for TBC1D25 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TBC1D25 Gene

Genomics for TBC1D25 Gene

GeneHancer (GH) Regulatory Elements for TBC1D25 Gene

Promoters and enhancers for TBC1D25 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
GH0XI048538 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 569.6 +0.5 452 3.3 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B TBC1D25 ENSG00000204620 RBM3 PORCN LOC101927635 FTSJ1 RN7SL262P ZNF630 ENSG00000228343 ZNF182
GH0XI048933 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 7.1 +399.0 399043 9.7 HDGF FOXA2 SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 YBX1 IRF4 ENSG00000279155 PQBP1 WAS OTUD5 SLC35A2 TIMM17B PIM2 TBC1D25 ENSG00000204620 ENSG00000228343
GH0XI048916 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 3.8 +380.3 380308 5.6 HNRNPUL1 PKNOX1 FOXA2 SMAD1 ARID4B SIN3A ZNF2 ZBTB7B POLR2B ZNF213 PIM2 ENSG00000204620 FTSJ1 ENSG00000270012 RBM3 PQBP1 CCDC22 ZNF182 PLP2 OTUD5
GH0XI048472 Enhancer 0.6 ENCODE 5.3 -65.9 -65883 1.6 MEIS2 CTCF PKNOX1 CEBPB CEBPG ZNF384 REST RAD21 ZNF341 SMC3 GC0XM048470 FTSJ1 TBC1D25 SLC38A5
GH0XI048710 Enhancer 1.1 FANTOM5 ENCODE 1.5 +174.1 174076 6 FOXA2 ZNF48 RARA YY1 ATF7 CREM RXRA REST RFX3 ZBTB33 PQBP1 OTUD5 PIM2 GRIPAP1 TBC1D25 GC0XM048725 RNU6-1056P SUV39H1 ENSG00000232828
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TBC1D25 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TBC1D25 gene promoter:

Genomic Locations for TBC1D25 Gene

Genomic Locations for TBC1D25 Gene
chrX:48,539,457-48,562,609
(GRCh38/hg38)
Size:
23,153 bases
Orientation:
Plus strand
chrX:48,397,845-48,420,997
(GRCh37/hg19)

Genomic View for TBC1D25 Gene

Genes around TBC1D25 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TBC1D25 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TBC1D25 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TBC1D25 Gene

Proteins for TBC1D25 Gene

  • Protein details for TBC1D25 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q3MII6-TBC25_HUMAN
    Recommended name:
    TBC1 domain family member 25
    Protein Accession:
    Q3MII6
    Secondary Accessions:
    • Q08AN9
    • Q3MII4
    • Q8TAR9

    Protein attributes for TBC1D25 Gene

    Size:
    688 amino acids
    Molecular mass:
    76327 Da
    Quaternary structure:
    • Interacts (via N-terminus) with MAP1LC3B, GABARAP and GABARAPL2.

    Alternative splice isoforms for TBC1D25 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBC1D25 Gene

Post-translational modifications for TBC1D25 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TBC1D25 Gene

No data available for DME Specific Peptides for TBC1D25 Gene

Domains & Families for TBC1D25 Gene

Gene Families for TBC1D25 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for TBC1D25 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with TBC1D25: view

No data available for UniProtKB/Swiss-Prot for TBC1D25 Gene

Function for TBC1D25 Gene

Molecular function for TBC1D25 Gene

UniProtKB/Swiss-Prot Function:
Acts as a GTPase-activating protein specific for RAB33B. Involved in the regulation of autophagosome maturation, the process in which autophagosomes fuse with endosomes and lysosomes.

Gene Ontology (GO) - Molecular Function for TBC1D25 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IDA 21383079
GO:0005515 protein binding IPI 21383079
GO:0017137 Rab GTPase binding IBA --
genes like me logo Genes that share ontologies with TBC1D25: view
genes like me logo Genes that share phenotypes with TBC1D25: view

Animal Model Products

  • Taconic Biosciences Mouse Models for TBC1D25

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TBC1D25 Gene

Localization for TBC1D25 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBC1D25 Gene

Cytoplasm. Cytoplasmic vesicle, autophagosome. Note=It is dispersed in the cytoplasm under nutrient-rich conditions. Localizes at autophagosomes under cell starving conditions.

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 TBC1D25 gene
Compartment Confidence
nucleus 2
cytosol 2
mitochondrion 1
lysosome 1

Gene Ontology (GO) - Cellular Components for TBC1D25 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005776 autophagosome TAS --
GO:0012505 endomembrane system IBA --
GO:0031410 cytoplasmic vesicle IEA --
genes like me logo Genes that share ontologies with TBC1D25: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TBC1D25 Gene

Pathways & Interactions for TBC1D25 Gene

genes like me logo Genes that share pathways with TBC1D25: view

Pathways by source for TBC1D25 Gene

3 Reactome pathways for TBC1D25 Gene

SIGNOR curated interactions for TBC1D25 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for TBC1D25 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IBA --
GO:0006914 autophagy IEA --
GO:0031338 regulation of vesicle fusion IBA --
GO:0090630 activation of GTPase activity IBA --
GO:1901096 regulation of autophagosome maturation IMP 21383079
genes like me logo Genes that share ontologies with TBC1D25: view

Drugs & Compounds for TBC1D25 Gene

No Compound Related Data Available

Transcripts for TBC1D25 Gene

Unigene Clusters for TBC1D25 Gene

TBC1 domain family, member 25:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TBC1D25 Gene

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

Relevant External Links for TBC1D25 Gene

GeneLoc Exon Structure for
TBC1D25
ECgene alternative splicing isoforms for
TBC1D25

Expression for TBC1D25 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TBC1D25 Gene

Protein differential expression in normal tissues from HIPED for TBC1D25 Gene

This gene is overexpressed in CD8 Tcells (34.8), Ovary (13.6), Testis (6.8), NK cells (6.6), and Blymphocyte (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for TBC1D25 Gene



Protein tissue co-expression partners for TBC1D25 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TBC1D25 Gene:

TBC1D25

SOURCE GeneReport for Unigene cluster for TBC1D25 Gene:

Hs.694353

Evidence on tissue expression from TISSUES for TBC1D25 Gene

  • Nervous system(4.7)
  • Pancreas(4.2)
  • Liver(4.1)
  • Lung(2.4)
genes like me logo Genes that share expression patterns with TBC1D25: 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 TBC1D25 Gene

Orthologs for TBC1D25 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for TBC1D25 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TBC1D25 33
  • 98.35 (n)
dog
(Canis familiaris)
Mammalia TBC1D25 33 34
  • 89.91 (n)
cow
(Bos Taurus)
Mammalia TBC1D25 33 34
  • 88.16 (n)
mouse
(Mus musculus)
Mammalia Tbc1d25 33 16 34
  • 87.16 (n)
rat
(Rattus norvegicus)
Mammalia Tbc1d25 33
  • 86.63 (n)
oppossum
(Monodelphis domestica)
Mammalia TBC1D25 34
  • 68 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TBC1D25 34
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves TBC1D25 34
  • 54 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TBC1D25 34
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100495342 33
  • 67.54 (n)
zebrafish
(Danio rerio)
Actinopterygii tbc1d25 33 34
  • 70.79 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG8155 34
  • 26 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GYP7 34
  • 15 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 48 (a)
OneToOne
Species where no ortholog for TBC1D25 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • 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 TBC1D25 Gene

ENSEMBL:
Gene Tree for TBC1D25 (if available)
TreeFam:
Gene Tree for TBC1D25 (if available)

Paralogs for TBC1D25 Gene

Paralogs for TBC1D25 Gene

(3) SIMAP similar genes for TBC1D25 Gene using alignment to 4 proteins:

Pseudogenes.org Pseudogenes for TBC1D25 Gene

genes like me logo Genes that share paralogs with TBC1D25: view

Variants for TBC1D25 Gene

Sequence variations from dbSNP and Humsavar for TBC1D25 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs782184431 benign, Abnormality of neuronal migration 48,560,053(+) T/G coding_sequence_variant, missense_variant
rs1000001287 -- 48,541,796(+) G/A intron_variant
rs1000143427 -- 48,562,407(+) A/G 3_prime_UTR_variant
rs1000433336 -- 48,561,917(+) G/A 3_prime_UTR_variant
rs1000483857 -- 48,553,955(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TBC1D25 Gene

Variant ID Type Subtype PubMed ID
esv32909 CNV gain+loss 17666407
nsv528292 CNV gain 19592680

Variation tolerance for TBC1D25 Gene

Residual Variation Intolerance Score: 9.02% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.11; 22.47% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TBC1D25 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBC1D25

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TBC1D25 Gene

Disorders for TBC1D25 Gene

MalaCards: The human disease database

(2) MalaCards diseases for TBC1D25 Gene - From: DISEASES

Disorder Aliases PubMed IDs
synovium cancer
  • malignant tumor of synovium
aland island eye disease
  • aied
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TBC1D25

genes like me logo Genes that share disorders with TBC1D25: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TBC1D25 Gene

Publications for TBC1D25 Gene

  1. OATL1, a novel autophagosome-resident Rab33B-GAP, regulates autophagosomal maturation. (PMID: 21383079) Itoh T … Fukuda M (The Journal of cell biology 2011) 2 3 4 58
  2. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  3. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. (PMID: 27173435) Boldt K … UK10K Rare Diseases Group (Nature communications 2016) 3 58
  4. Differing susceptibility to autophagic degradation of two LC3-binding proteins: SQSTM1/p62 and TBC1D25/OATL1. (PMID: 26902585) Hirano S … Fukuda M (Autophagy 2016) 3 58
  5. A systematic High-Content Screening microscopy approach reveals key roles for Rab33b, OATL1 and Myo6 in nanoparticle trafficking in HeLa cells. (PMID: 27374232) Panarella A … Simpson JC (Scientific reports 2016) 3 58

Products for TBC1D25 Gene

Sources for TBC1D25 Gene

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