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

    Gene ID: 4943, updated on 28-Oct-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TBC1D25 in Genome Data Viewer
    Location:
    Xp11.23
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (48539714..48562609)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (47948728..47971622)
    RS_2024_09 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

    Expression

    • Project title: HPA RNA-seq normal tissues 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001348262.2NP_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:241470
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    2. NM_001348263.2NP_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:229458
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    3. NM_001348264.2NP_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:167396
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    4. NM_001348265.2NP_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:167396
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    5. NM_002536.4NP_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:225454
      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_2024_08

    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.