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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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