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Tbc1d23 TBC1 domain family, member 23 [ Mus musculus (house mouse) ]

Gene ID: 67581, updated on 2-Nov-2024

Summary

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Official Symbol
Tbc1d23provided by MGI
Official Full Name
TBC1 domain family, member 23provided by MGI
Primary source
MGI:MGI:1914831
See related
Ensembl:ENSMUSG00000022749 AllianceGenome:MGI:1914831
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
4930451A13Rik; D030022P07Rik
Summary
Involved in embryonic brain development; neuron projection development; and vesicle-mediated transport. Acts upstream of or within positive regulation of interleukin-6 production; regulation of inflammatory response; and regulation of tumor necrosis factor production. Part of WASH complex. Is expressed in pallium. 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
Ubiquitous expression in CNS E18 (RPKM 9.9), limb E14.5 (RPKM 9.6) and 27 other tissues See more
Orthologs
human all
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Genomic context

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See Tbc1d23 in Genome Data Viewer
Location:
16 C1.1; 16 34.22 cM
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (56989225..57051891, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (57168862..57231528, complement)

Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene translocase of outer mitochondrial membrane 70A Neighboring gene STARR-seq mESC enhancer starr_41078 Neighboring gene STARR-positive B cell enhancer ABC_E8637 Neighboring gene predicted gene, 16892 Neighboring gene nitrilase family, member 2 Neighboring gene STARR-positive B cell enhancer ABC_E11617 Neighboring gene STARR-positive B cell enhancer mm9_chr16:57231379-57231680 Neighboring gene STARR-seq mESC enhancer starr_41080 Neighboring gene STARR-seq mESC enhancer starr_41081 Neighboring gene STARR-seq mESC enhancer starr_41082 Neighboring gene STARR-seq mESC enhancer starr_41083 Neighboring gene transmembrane protein 30C Neighboring gene predicted gene, 26800 Neighboring gene RIKEN cDNA 4921517D16 gene Neighboring gene cms small ribosomal subunit 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

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. 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
  3. 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
  4. Identification of FMRP target mRNAs in the developmental brain: FMRP might coordinate Ras/MAPK, Wnt/β-catenin, and mTOR signaling during corticogenesis. Casingal CR, et al. Mol Brain, 2020 Dec 16. PMID 33323119, Free PMC Article
  5. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Homozygous Truncating Variants in TBC1D23 gene are associated with Pontocerebellar Hypoplasia and Alter Cortical Development.
    Title: Homozygous Truncating Variants in TBC1D23 Cause Pontocerebellar Hypoplasia and Alter Cortical Development.
  2. we now show that Tbc1d23 is a general inhibitor of innate immunity signaling, strongly inhibiting multiple TLR and dectin-signaling pathways
    Title: Spatiotemporal inhibition of innate immunity signaling by the Tbc1d23 RAB-GAP.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 
  • Gene trapped (1) 
  • Targeted (1) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in brain development ISO
Inferred from Sequence Orthology
more info
  
involved_in brain development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in embryonic brain development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in embryonic brain development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in neuron projection development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within positive regulation of interleukin-6 production IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of inflammatory response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of tumor necrosis factor production IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retrograde transport, endosome to Golgi IEA
Inferred from Electronic Annotation
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 tethering to Golgi ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus ISO
Inferred from Sequence Orthology
more info
  
part_of WASH complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of WASH complex ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasmic vesicle ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasmic vesicle ISS
Inferred from Sequence or Structural Similarity
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
  
located_in trans-Golgi network ISS
Inferred from Sequence or Structural Similarity
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_001358433.1 → NP_001345362.1  TBC1 domain family member 23 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC154625
    Consensus CDS
    CCDS88947.1
    UniProtKB/TrEMBL
    A0A2I3BRD1
    Related
    ENSMUSP00000154535.2, ENSMUST00000226586.2
    Conserved Domains (2) summary
    pfam00566
    Location:48 → 246
    RabGAP-TBC; Rab-GTPase-TBC domain
    pfam00581
    Location:334 → 384
    Rhodanese; Rhodanese-like domain

  2. NM_001358434.1 → NP_001345363.1  TBC1 domain family member 23 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC154625
    Conserved Domains (2) summary
    pfam00581
    Location:101 → 151
    Rhodanese; Rhodanese-like domain
    cd20788
    Location:346 → 460
    TBC1D23_C-like; C-terminal domain of TBC1 domain family member 23, and similar proteins

  3. NM_026254.2 → NP_080530.2  TBC1 domain family member 23 isoform 2

    See identical proteins and their annotated locations for NP_080530.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    BC031706
    Consensus CDS
    CCDS28228.1
    UniProtKB/Swiss-Prot
    Q3TAW9, Q8K0F1, Q8VE48
    Related
    ENSMUSP00000023431.7, ENSMUST00000023431.8
    Conserved Domains (2) summary
    pfam00566
    Location:79 → 246
    RabGAP-TBC; Rab-GTPase-TBC domain
    cl00125
    Location:328 → 439
    RHOD; Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins ...

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000082.7 Reference GRCm39 C57BL/6J

    Range
    56989225..57051891 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036160099.1 → XP_036015992.1  TBC1 domain family member 23 isoform X5

    Conserved Domains (2) summary
    pfam00581
    Location:101 → 151
    Rhodanese; Rhodanese-like domain
    cd20788
    Location:331 → 445
    TBC1D23_C-like; C-terminal domain of TBC1 domain family member 23, and similar proteins

  2. XM_030249251.1 → XP_030105111.1  TBC1 domain family member 23 isoform X2

    Conserved Domains (2) summary
    pfam00581
    Location:182 → 229
    Rhodanese; Rhodanese-like domain
    cl02495
    Location:4 → 94
    RabGAP-TBC; Rab-GTPase-TBC domain

  3. XM_036160100.1 → XP_036015993.1  TBC1 domain family member 23 isoform X5

    Conserved Domains (2) summary
    pfam00581
    Location:101 → 151
    Rhodanese; Rhodanese-like domain
    cd20788
    Location:331 → 445
    TBC1D23_C-like; C-terminal domain of TBC1 domain family member 23, and similar proteins

  4. XM_030249252.2 → XP_030105112.1  TBC1 domain family member 23 isoform X4

    Conserved Domains (2) summary
    pfam00581
    Location:97 → 147
    Rhodanese; Rhodanese-like domain
    cd20788
    Location:342 → 456
    TBC1D23_C-like; C-terminal domain of TBC1 domain family member 23, and similar proteins

  5. XM_030249253.2 → XP_030105113.1  TBC1 domain family member 23 isoform X4

    Conserved Domains (2) summary
    pfam00581
    Location:97 → 147
    Rhodanese; Rhodanese-like domain
    cd20788
    Location:342 → 456
    TBC1D23_C-like; C-terminal domain of TBC1 domain family member 23, and similar proteins

  6. XM_006522485.3 → XP_006522548.1  TBC1 domain family member 23 isoform X1

    Conserved Domains (2) summary
    pfam00581
    Location:182 → 229
    Rhodanese; Rhodanese-like domain
    cl02495
    Location:4 → 94
    RabGAP-TBC; Rab-GTPase-TBC domain

  7. XM_036160098.1 → XP_036015991.1  TBC1 domain family member 23 isoform X4

    Conserved Domains (2) summary
    pfam00581
    Location:97 → 147
    Rhodanese; Rhodanese-like domain
    cd20788
    Location:342 → 456
    TBC1D23_C-like; C-terminal domain of TBC1 domain family member 23, and similar proteins

  8. XM_030249250.2 → XP_030105110.1  TBC1 domain family member 23 isoform X1

    Conserved Domains (2) summary
    pfam00581
    Location:182 → 229
    Rhodanese; Rhodanese-like domain
    cl02495
    Location:4 → 94
    RabGAP-TBC; Rab-GTPase-TBC domain

  9. XM_036160097.1 → XP_036015990.1  TBC1 domain family member 23 isoform X3

    Conserved Domains (2) summary
    pfam00581
    Location:101 → 151
    Rhodanese; Rhodanese-like domain
    cd20788
    Location:346 → 460
    TBC1D23_C-like; C-terminal domain of TBC1 domain family member 23, and similar proteins
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8K0F1.1 GenPept UniProtKB/Swiss-Prot:Q8K0F1

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