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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 TBC/RABGAPs and Vesicle-mediated transport. 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.

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

Regulatory Elements for TBC1D25 Gene

Enhancers for TBC1D25 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XG048538 1.1 ENCODE 19.6 +0.5 452 3.3 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 FOS TBC1D25 ENSG00000204620 RBM3 LOC101927635 PORCN FTSJ1 ENSG00000228343 EBP GC0XP048563
GH0XG048933 2 FANTOM5 Ensembl ENCODE dbSUPER 7.1 +399.0 399044 9.7 HDGF FOXA2 PKNOX1 ARNT AGO1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1 PQBP1 WAS OTUD5 SLC35A2 TIMM17B PIM2 TBC1D25 ENSG00000204620 ENSG00000228343 FOXP3
GH0XG048916 1.7 FANTOM5 ENCODE dbSUPER 3.8 +380.3 380309 5.6 HNRNPUL1 FOXA2 PKNOX1 AGO1 WRNIP1 ARID4B SIN3A ZNF2 ZBTB7B ZNF143 ENSG00000204620 PQBP1 PIM2 OTUD5 WAS ENSG00000228343 TBC1D25 GRIPAP1 PPP1R3F ENSG00000279155
GH0XG048472 0.7 ENCODE 5.3 -65.9 -65883 1.6 CTCF PKNOX1 CEBPB CEBPG ZNF384 REST RAD21 ZNF341 SMC3 ZNF24 FTSJ1 TBC1D25 GC0XM048470 SLC38A5
GH0XG048710 1.5 FANTOM5 ENCODE 1.5 +174.1 174077 6.0 HDGF FOXA2 PKNOX1 CREB3L1 ARNT ARID4B SIN3A DMAP1 FEZF1 ZNF2 ENSG00000204620 ZNF182 ZNF630 ZNF81 ENSG00000270012 PRAF2 SYP PQBP1 OTUD5 PIM2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TBC1D25 on UCSC Golden Path with GeneCards custom track

Promoters for TBC1D25 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000246484 243 1401 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 FOS

Genomic Location for TBC1D25 Gene

Chromosome:
X
Start:
48,539,457 bp from pter
End:
48,562,609 bp from pter
Size:
23,153 bases
Orientation:
Plus strand

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

No data available for Gene Families and 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

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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

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:0061024 membrane organization TAS --
GO:0090630 activation of GTPase activity IBA --
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:

CRISPR Products

Inhibitory RNA Products

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

Primer Products

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 34
  • 98.35 (n)
dog
(Canis familiaris)
Mammalia TBC1D25 34 35
  • 89.91 (n)
cow
(Bos Taurus)
Mammalia TBC1D25 34 35
  • 88.16 (n)
mouse
(Mus musculus)
Mammalia Tbc1d25 34 16 35
  • 87.16 (n)
rat
(Rattus norvegicus)
Mammalia Tbc1d25 34
  • 86.63 (n)
oppossum
(Monodelphis domestica)
Mammalia TBC1D25 35
  • 68 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TBC1D25 35
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves TBC1D25 35
  • 54 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TBC1D25 35
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100495342 34
  • 67.54 (n)
zebrafish
(Danio rerio)
Actinopterygii tbc1d25 34 35
  • 70.79 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG8155 35
  • 26 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GYP7 35
  • 15 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 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 Sequence Context AA Info Type
rs782184431 Benign 48,560,053(+) GAAGC(G/T)GTTGC reference, missense
rs1000001287 -- 48,541,796(+) GATAC(A/G)CATTT intron-variant
rs1000143427 -- 48,562,407(+) TGACT(A/G)TTCCT utr-variant-3-prime
rs1000433336 -- 48,561,917(+) TTTCA(A/G)CAGTA utr-variant-3-prime
rs1000483857 -- 48,553,955(+) GTAGG(C/T)GGATC 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)

Relevant External Links 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

(3) MalaCards diseases for TBC1D25 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
synovium cancer
  • malignant tumor of synovium
aland island eye disease
  • forsius-eriksson syndrome
renal cell carcinoma, papillary
  • renal cell carcinoma
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for TBC1D25

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. (J. Cell Biol. 2011) 2 3 4 64
  2. 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 J.C. (Sci Rep 2016) 3 64
  3. Differing susceptibility to autophagic degradation of two LC3-binding proteins: SQSTM1/p62 and TBC1D25/OATL1. (PMID: 26902585) Hirano S. … Fukuda M. (Autophagy 2016) 3 64
  4. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. (PMID: 24275569) Bian Y. … Zou H. (J. Proteomics 2014) 4 64
  5. Toward a comprehensive characterization of a human cancer cell phosphoproteome. (PMID: 23186163) Zhou H. … Mohammed S. (J. Proteome Res. 2013) 4 64

Products for TBC1D25 Gene

Sources for TBC1D25 Gene

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