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    Tbc1d23 TBC1 domain family, member 23 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 304019, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Tbc1d23provided by RGD
    Official Full Name
    TBC1 domain family, member 23provided by RGD
    Primary source
    RGD:1307925
    See related
    EnsemblRapid:ENSRNOG00000001642 AllianceGenome:RGD:1307925
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1307925
    Summary
    Predicted to be involved in several processes, including embryonic brain development; nervous system development; and vesicle tethering to Golgi. Predicted to act upstream of or within positive regulation of interleukin-6 production; regulation of inflammatory response; and regulation of tumor necrosis factor production. Predicted to be located in Golgi apparatus and cytoplasmic vesicle. Predicted to be part of WASH complex. Predicted to be active in trans-Golgi network. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 11. Orthologous to human TBC1D23 (TBC1 domain family member 23). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Lung (RPKM 168.7), Spleen (RPKM 155.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Tbc1d23 in Genome Data Viewer
    Location:
    11q12
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (56772476..56830625)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (43303355..43361507)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (45401396..45459841)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene ribosomal protein S13, pseudogene 3 Neighboring gene ribosomal protein SA, pseudogene 2 Neighboring gene transfer RNA alanine (anticodon AGC) 25 Neighboring gene ribosome biogenesis protein NSA2 homolog pseudogene Neighboring gene nitrilase family, member 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Homozygous Truncating Variants in TBC1D23 Cause Pontocerebellar Hypoplasia and Alter Cortical Development. Ivanova EL, et al. Am J Hum Genet, 2017 Sep 7. PMID 28823707, Free PMC Article
    2. Homozygous Mutations in TBC1D23 Lead to a Non-degenerative Form of Pontocerebellar Hypoplasia. Marin-Valencia I, et al. Am J Hum Genet, 2017 Sep 7. PMID 28823706, Free PMC Article
    3. Spatiotemporal inhibition of innate immunity signaling by the Tbc1d23 RAB-GAP. De Arras L, et al. J Immunol, 2012 Mar 15. PMID 22312129, Free PMC Article
    4. The WDR11 complex facilitates the tethering of AP-1-derived vesicles. Navarro Negredo P, et al. Nat Commun, 2018 Feb 9. PMID 29426865, Free PMC Article
    5. TBC1D23 is a bridging factor for endosomal vesicle capture by golgins at the trans-Golgi. Shin JJH, et al. Nat Cell Biol, 2017 Dec. PMID 29084197, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in brain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in embryonic brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in embryonic brain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in neuron projection development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of interleukin-6 production ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of tumor necrosis factor production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, endosome to Golgi ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in vesicle tethering to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle tethering to Golgi ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in vesicle-mediated transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of WASH complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasmic vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    TBC1 domain family member 23

    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.

    mRNA and Protein(s)

    1. NM_001371895.1 → NP_001358824.1  TBC1 domain family member 23 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      BG673671, JAXUCZ010000011
      UniProtKB/TrEMBL
      A0A8I5YBN9, D4AAH9
      Related
      ENSRNOP00000002240.6, ENSRNOT00000002240.9
      Conserved Domains (2) summary
      pfam00566
      Location:48 → 246
      RabGAP-TBC; Rab-GTPase-TBC domain
      pfam00581
      Location:334 → 381
      Rhodanese; Rhodanese-like domain

    2. NM_001371896.1 → NP_001358825.1  TBC1 domain family member 23 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      BG673671, JAXUCZ010000011
      UniProtKB/TrEMBL
      A0A8I5YBN9, A0A8I6AAK0, A6IQM8
      Related
      ENSRNOP00000089797.1, ENSRNOT00000102661.2
      Conserved Domains (2) summary
      pfam00566
      Location:48 → 246
      RabGAP-TBC; Rab-GTPase-TBC domain
      pfam00581
      Location:334 → 381
      Rhodanese; Rhodanese-like domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086029.1 Reference GRCr8

      Range
      56772476..56830625
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039088379.2 → XP_038944307.1  TBC1 domain family member 23 isoform X1

      UniProtKB/TrEMBL
      A0A8I5YBN9
      Conserved Domains (3) summary
      cl02495
      Location:4 → 94
      RabGAP-TBC; Rab-GTPase-TBC domain
      pfam00581
      Location:182 → 229
      Rhodanese; Rhodanese-like domain
      cd20788
      Location:427 → 541
      TBC1D23_C-like; C-terminal domain of TBC1 domain family member 23, and similar proteins

    2. XM_039088380.2 → XP_038944308.1  TBC1 domain family member 23 isoform X2

      UniProtKB/TrEMBL
      A6IQM9
      Conserved Domains (2) summary
      pfam00581
      Location:101 → 148
      Rhodanese; Rhodanese-like domain
      cd20788
      Location:346 → 460
      TBC1D23_C-like; C-terminal domain of TBC1 domain family member 23, and similar proteins

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001107099.1: Suppressed sequence

      Description
      NM_001107099.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from human: TBC1D23 (GeneID:55773).
    Nucleotide Protein Strain
    Heading Accession and Version

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