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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
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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

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