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] See more...

Aliases for TBC1D25 Gene

Aliases for TBC1D25 Gene

  • TBC1 Domain Family Member 25 2 3 4 5
  • Ornithine Aminotransferase-Like 1 2 3
  • OATL1 3 4
  • TBC1 Domain Family, Member 25 2
  • 5SN3 SnoRNA 3
  • TBC1D25 5
  • 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 Oligospermia and Spindle Cell Synovial Sarcoma. 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 TBC1D16.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for TBC1D25 Gene

Genomics for TBC1D25 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TBC1D25 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TBC1D25 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TBC1D25

Top Transcription factor binding sites by QIAGEN in the TBC1D25 gene promoter:
  • AML1a
  • C/EBPalpha
  • CREB
  • deltaCREB
  • FOXI1
  • GATA-6
  • HFH-3
  • Pax-4a
  • PPAR-alpha

Genomic Locations for TBC1D25 Gene

Latest Assembly
chrX:48,539,714-48,562,609
(GRCh38/hg38)
Size:
22,896 bases
Orientation:
Plus strand

Previous Assembly
chrX:48,398,102-48,420,997
(GRCh37/hg19 by Entrez Gene)
Size:
22,896 bases
Orientation:
Plus strand

chrX:48,397,845-48,420,997
(GRCh37/hg19 by Ensembl)
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

Gene Families for TBC1D25 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for TBC1D25 Gene

InterPro:
Blocks:
  • RabGAP/TBC domain
ProtoNet:

Suggested Antigen Peptide Sequences for TBC1D25 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ59474, highly similar to Homo sapiens ornithine aminotransferase-like 1 (OATL1), transcript variant 2, mRNA (B4DE92_HUMAN)
  • cDNA FLJ54629, highly similar to Homo sapiens ornithine aminotransferase-like 1 (OATL1), transcript variant 2, mRNA (B4DF03_HUMAN)
  • TBC1 domain family, member 25 (B9A6M7_HUMAN)
  • MG81 protein (Q14830_HUMAN)
  • TBC1 domain family member 25 (TBC25_HUMAN)
genes like me logo Genes that share domains with TBC1D25: view

No data available for Graphical View of Domain Structure 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 IBA,IDA 21383079
GO:0005515 protein binding IPI 21383079
GO:0031267 small 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 Models for research

  • Taconic Biosciences Mouse Models for TBC1D25

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBC1D25

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
lysosome 2
cytoskeleton 1
mitochondrion 1
endosome 1
golgi apparatus 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: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

PathCards logo

SuperPathways 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 21873635
GO:0006914 autophagy IEA --
GO:0090630 activation of GTPase activity IBA 21873635
GO:1901096 regulation of autophagosome maturation IBA,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

mRNA/cDNA for TBC1D25 Gene

6 REFSEQ mRNAs :
31 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBC1D25

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

Expression for TBC1D25 Gene

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



Protein tissue co-expression partners for TBC1D25 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TBC1D25

SOURCE GeneReport for Unigene cluster for TBC1D25 Gene:

Hs.694353

Evidence on tissue expression from TISSUES for TBC1D25 Gene

  • Nervous system(4.8)
  • Pancreas(4.2)
  • Liver(4.1)
  • Lung(2.4)
genes like me logo Genes that share expression patterns with TBC1D25: view

Primer products for research

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 30
  • 98.35 (n)
Dog
(Canis familiaris)
Mammalia TBC1D25 30 31
  • 89.91 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TBC1D25 30 31
  • 88.16 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Tbc1d25 30 17 31
  • 87.16 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Tbc1d25 30
  • 86.63 (n)
Oppossum
(Monodelphis domestica)
Mammalia TBC1D25 31
  • 68 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TBC1D25 31
  • 68 (a)
OneToOne
Chicken
(Gallus gallus)
Aves TBC1D25 31
  • 54 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TBC1D25 31
  • 66 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100495342 30
  • 67.54 (n)
Zebrafish
(Danio rerio)
Actinopterygii tbc1d25 30 31
  • 70.79 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG8155 31
  • 26 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GYP7 31
  • 15 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 48 (a)
OneToOne
Species where no ortholog for TBC1D25 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for TBC1D25: view image

Paralogs for TBC1D25 Gene

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

  • TBC25_HUMAN
  • B4DE92_HUMAN
  • B9A6M7_HUMAN
  • C9JMI8_HUMAN

Pseudogenes.org Pseudogenes for TBC1D25 Gene

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

Variants for TBC1D25 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TBC1D25 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
rs1602125411 Likely Pathogenic: Oligospermia 48,563,517(+) C/T
NM_002536.4(TBC1D25):c.4609C>T
rs782184431 Benign: Abnormality of neuronal migration 48,560,053(+) T/G
NM_002536.4(TBC1D25):c.1145T>G (p.Leu382Arg)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
rs2293948 - p.Asn277Ser

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TBC1D25 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

SNP Genotyping and Copy Number Assays for research

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

Disorders for TBC1D25 Gene

MalaCards: The human disease database

(7) MalaCards diseases for TBC1D25 Gene - From: CVR, COP, and GCD

Disorder Aliases PubMed IDs
oligospermia
spindle cell synovial sarcoma
  • synovial sarcoma with spindle cell components
synovium cancer
  • malignant tumor of synovium
aland island eye disease
  • aied
sarcoma, synovial
  • synovial sarcoma
- 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
  2. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  3. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. (PMID: 30021884) Fasci D … Heck AJR (Molecular & cellular proteomics : MCP 2018) 3
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3
  5. Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism. (PMID: 28986522) Antoniali G … Tell G (Nature communications 2017) 3

Products for TBC1D25 Gene

Sources for TBC1D25 Gene