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    TBC1D25 TBC1 domain family member 25 [ Homo sapiens (human) ]

    Gene ID: 4943, updated on 5-Mar-2024

    Summary

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    Official Symbol
    TBC1D25provided by HGNC
    Official Full Name
    TBC1 domain family member 25provided by HGNC
    Primary source
    HGNC:HGNC:8092
    See related
    Ensembl:ENSG00000068354 MIM:311240; AllianceGenome:HGNC:8092
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MG81; OATL1
    Summary
    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]
    Expression
    Ubiquitous expression in testis (RPKM 5.6), brain (RPKM 5.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TBC1D25 in Genome Data Viewer
    Location:
    Xp11.23
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (48539714..48562609)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (47948728..47971622)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (48398102..48420997)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20814 Neighboring gene porcupine O-acyltransferase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20815 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20817 Neighboring gene EBP cholestenol delta-isomerase Neighboring gene CRISPRi-validated cis-regulatory element chrX.929 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:48397756-48398256 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:48398257-48398757 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:48426332-48426532 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 4 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:48436957-48437166 Neighboring gene RNA binding motif protein 3 Neighboring gene MRPL32 pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. RabGAP TBC1D25 is involved in human osteoclast activity. Roy M, et al. Eur J Cell Biol, 2021 Apr. PMID 33353759
    2. Differential expression of human 5S snoRNA genes. Chang LS, et al. Biochem Biophys Res Commun, 2002 Nov 29. PMID 12437969
    3. The isolation of cDNAs from OATL1 at Xp 11.2 using a 480-kb YAC. Geraghty MT, et al. Genomics, 1993 May. PMID 8314581
    4. Adenovirus-mediated expression of both antisense ornithine decarboxylase and S-adenosylmethionine decarboxylase inhibits lung cancer cell growth. Tian H, et al. Acta Biochim Biophys Sin (Shanghai), 2007 Jun. PMID 17558447
    5. A systematic High-Content Screening microscopy approach reveals key roles for Rab33b, OATL1 and Myo6 in nanoparticle trafficking in HeLa cells. Panarella A, et al. Sci Rep, 2016 Jul 4. PMID 27374232, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RabGAP TBC1D25 is involved in human osteoclast activity.
      Title: RabGAP TBC1D25 is involved in human osteoclast activity.
    2. Rab33b, OATL1 and Myo6 have roles in nanoparticle trafficking in HeLa cells
      Title: A systematic High-Content Screening microscopy approach reveals key roles for Rab33b, OATL1 and Myo6 in nanoparticle trafficking in HeLa cells.
    3. Our study showed that adenovirus-mediated antisense ODC and expression inhibits tumor cell growth through blocking the polyamine synthesis pathway.
      Title: Adenovirus-mediated expression of both antisense ornithine decarboxylase and S-adenosylmethionine decarboxylase inhibits lung cancer cell growth.
    4. Studies indicate that each of the 4 genes was associated with at least one main outcome: anxiety (SAT1, SMS), mood disorders (SAT1, SMOX), and suicide attempts (SAT1, OATL1).
      Title: Association of polyaminergic loci with anxiety, mood disorders, and attempted suicide.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC126866, MGC126868, MGC149731, MGC149732

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTPase activator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in activation of GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of autophagosome maturation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in autophagosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in autophagosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in autophagosome TAS
    Traceable Author Statement
    more info
    		  
    located_in cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    TBC1 domain family member 25
    Names
    5SN3 snoRNA
    ornithine aminotransferase-like 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_052856.1 RefSeqGene

      Range
      5028..27923
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001348262.2 → NP_001335191.1  TBC1 domain family member 25 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC115618, AF196969, BC101817, BE279778, BU630180, HY154299
      UniProtKB/TrEMBL
      B9A6M7
      Conserved Domains (1) summary
      smart00164
      Location:241 → 470
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    2. NM_001348263.2 → NP_001335192.1  TBC1 domain family member 25 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses two alternate in-frame splice junctions compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AC115618, AF196969
      UniProtKB/TrEMBL
      B4DF03, B9A6M7
      Conserved Domains (1) summary
      smart00164
      Location:229 → 458
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    3. NM_001348264.2 → NP_001335193.1  TBC1 domain family member 25 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice junction compared to variant 1. The resulting isoform (d) has a shorter and distinct N-terminus compared to isoform a. Variants 4 and 5 both encode the same isoform (d).
      Source sequence(s)
      AC115618, AF196969
      UniProtKB/TrEMBL
      B4DGU3
      Conserved Domains (1) summary
      smart00164
      Location:167 → 396
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    4. NM_001348265.2 → NP_001335194.1  TBC1 domain family member 25 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses two alternate splice junctions compared to variant 1. The resulting isoform (d) has a shorter and distinct N-terminus compared to isoform a. Variants 4 and 5 both encode the same isoform (d).
      Source sequence(s)
      AC115618, AF196969
      UniProtKB/TrEMBL
      B4DGU3
      Conserved Domains (1) summary
      smart00164
      Location:167 → 396
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    5. NM_002536.4 → NP_002527.1  TBC1 domain family member 25 isoform c

      See identical proteins and their annotated locations for NP_002527.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AC115618, AF196969, BC101817, BU630180, HY154299
      Consensus CDS
      CCDS35242.1
      UniProtKB/Swiss-Prot
      Q08AN9, Q3MII4, Q3MII6, Q8TAR9
      UniProtKB/TrEMBL
      B9A6M7
      Related
      ENSP00000365962.4, ENST00000376771.9
      Conserved Domains (1) summary
      smart00164
      Location:225 → 454
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    RNA

    1. NR_145494.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC115618, AF196969, AK298884, BU630180

    2. NR_145495.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC115618, AF196969

    3. NR_145496.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC115618, AF196969, BU630180, DA031057

    4. NR_145497.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC115618, AF196969, BU630180, DC309515, HY154299

    5. NR_145498.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC115618, AF196969

    6. NR_145499.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC115618, AF196969

    7. NR_145500.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC115618, AF196969

    8. NR_145501.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC115618, AF196969, BU630180, DA688823, HY154299

    9. NR_145502.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC115618, AF196969, BC143395, BU630180, HY154299

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      48539714..48562609
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      47948728..47971622
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001006113.1: Suppressed sequence

      Description
      NM_001006113.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3MII6.2 GenPept UniProtKB/Swiss-Prot:Q3MII6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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