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TBC1D23 Gene

protein-coding   GIFtS: 46
GCID: GC03P099979

TBC1 Domain Family, Member 23

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
TBC1 Domain Family, Member 231 2
NS4ATP12 3
HCV Non-Structural Protein 4A-Transactivated Protein 12 3
HCV Nonstructural Protein 4A-Transactivated Protein 12
TBC1 Domain Family Member 232

External Ids:    HGNC: 256221   Entrez Gene: 557732   Ensembl: ENSG000000360547   UniProtKB: Q9NUY83   

Export aliases for TBC1D23 gene to outside databases

Previous GC identifers: GC03P101463 GC03P097347


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TBC1D23 Gene:
TBC1D23 (TBC1 domain family, member 23) is a protein-coding gene. Diseases associated with TBC1D23 include pneumocystosis, and malaria. GO annotations related to this gene include Rab GTPase activator activity.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000003.12  NC_018914.2  NT_005612.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the TBC1D23 gene promoter:
         ISGF-3   ATF-2   IRF-1   Meis-1b   FAC1   c-Myb   Cart-1   c-Jun   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTBC1D23 promoter sequence
   Search Chromatin IP Primers for TBC1D23

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TBC1D23


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3q12.2   Ensembl cytogenetic band:  3q12.1   HGNC cytogenetic band: 3q12.2

TBC1D23 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TBC1D23 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P099979:  view genomic region     (about GC identifiers)

Start:
99,979,686 bp from pter      End:
100,044,095 bp from pter
Size:
64,410 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: TBC23_HUMAN, Q9NUY8 (See protein sequence)
Recommended Name: TBC1 domain family member 23  
Size: 699 amino acids; 78322 Da
Sequence caution: Sequence=AAH10221.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=AAH20955.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAA91881.1;
Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: Q8TCN8 Q8WUB7 Q96D90 Q9NV75
Alternative splicing: 2 isoforms:  Q9NUY8-1   Q9NUY8-2   

Explore the universe of human proteins at neXtProt for TBC1D23: NX_Q9NUY8

Explore proteomics data for TBC1D23 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys495
  • Modification sites at PhosphoSitePlus

  • See TBC1D23 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001186127.1  NP_060779.2  

    ENSEMBL proteins: 
     ENSP00000417487   ENSP00000340693   ENSP00000377700   ENSP00000418714   ENSP00000418059  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR001763 Rhodanese-like_dom
     IPR000195 Rab-GTPase-TBC_dom

    Graphical View of Domain Structure for InterPro Entry Q9NUY8

    ProtoNet protein and cluster: Q9NUY8

    1 Blocks protein domain: IPB001763 Rhodanese-like

    UniProtKB/Swiss-Prot: TBC23_HUMAN, Q9NUY8
    Similarity: Contains 1 Rab-GAP TBC domain
    Similarity: Contains 1 rhodanese domain


    TBC1D23 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005097Rab GTPase activator activity IEA--
         
    TBC1D23 for ontologies           About GeneDecksing


    Phenotypes:
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Tbc1d23):
     homeostasis/metabolism  immune system 

    TBC1D23 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for TBC1D23
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for TBC1D23
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    miRNA
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    4 qRT-PCR Assays for microRNAs that regulate TBC1D23:
    hsa-miR-374b hsa-miR-802 hsa-miR-4276 hsa-miR-374a
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat TBC1D23

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    GenScript: all cDNA clones in your preferred vector (see all 2): TBC1D23 (NM_018309)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for TBC1D23
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TBC1D23

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TBC1D23


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    golgi apparatus2
    endoplasmic reticulum1
    extracellular1
    mitochondrion1
    nucleus1
    plasma membrane1

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TBC1D23
    Interactions:

        Search GeneGlobe Interaction Network for TBC1D23

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    Selected Interacting proteins for TBC1D23 (Q9NUY83 ENSP000003406934) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    KBTBD7Q8WVZ93I2D: score=1 
    PRKAB2O437413I2D: score=1 
    STK11Q158313I2D: score=1 
    UBCENSP000003448184STRING: ENSP00000344818
    C12orf45ENSP000002807494STRING: ENSP00000280749
    About this table

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0032313regulation of Rab GTPase activity ----
    GO:0032680regulation of tumor necrosis factor production IEA--
    GO:0032755positive regulation of interleukin-6 production IEA--
    GO:0050727regulation of inflammatory response IEA--

    TBC1D23 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for TBC1D23 (TBC23)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for TBC1D23 gene (2 alternative transcripts): 
    NM_001199198.2  NM_018309.4  

    Unigene Cluster for TBC1D23:

    TBC1 domain family, member 23
    Hs.477003  [show with all ESTs]
    Unigene Representative Sequence: NM_001199198
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000485687 ENST00000344949(uc003dts.3) ENST00000394144(uc003dtt.3)
    ENST00000486274 ENST00000471098 ENST00000475134 ENST00000484231 ENST00000496167
    ENST00000471273(uc003dtu.3)
    miRNA
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    4 qRT-PCR Assays for microRNAs that regulate TBC1D23:
    hsa-miR-374b hsa-miR-802 hsa-miR-4276 hsa-miR-374a
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector (see all 2): TBC1D23 (NM_018309)
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      QuantiTect SYBR Green Assays in human, mouse, rat TBC1D23
      QuantiFast Probe-based Assays in human, mouse, rat TBC1D23

    Additional mRNA sequence: 

    AB449910.1 AK001750.1 AK001908.1 AK092926.1 AL713684.1 AY740521.1 BC010221.1 BC020955.1 
    BX648032.1 

    14 DOTS entries:

    DT.446666  DT.100814822  DT.100814824  DT.95319818  DT.95270780  DT.120900654  DT.120900690  DT.100733077 
    DT.120900684  DT.40197174  DT.95270787  DT.95358374  DT.120900678  DT.40108879 

    Selected AceView cDNA sequences (see all 177):

    AA446792 AL713684 BU183391 BC010221 BF223650 AW192122 BU162166 AA846312 
    AI565492 AI378361 AW206365 AU133432 AI635361 AK001750 BU634334 BM712058 
    AI290887 BF059314 CF552493 BM977274 AI248888 BM820374 AI040209 BF223711 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for TBC1D23 (see all 10)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b · 7c · 7d ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^
    SP1:                    -     -     -           -                       -                                                                                       
    SP2:                    -     -     -           -                       -                                                                                       
    SP3:                                                                                                                                                  -         
    SP4:                    -     -     -                                   -                                                                                       
    SP5:                    -     -     -     -     -                       -                                                                                       

    ExUns: 16a · 16b ^ 17 ^ 18a · 18b ^ 19 ^ 20a · 20b
    SP1:                    -                           
    SP2:              -     -                           
    SP3:                                                
    SP4:                                                
    SP5:                                                


    ECgene alternative splicing isoforms for TBC1D23

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    TBC1D23 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGACATTTTT
    TBC1D23 Expression
    About this image


    TBC1D23 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Ovary (Reproductive System)
             Oviduct
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    TBC1D23 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TBC1D23 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.477003
        Custom PCR Arrays for TBC1D23
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TBC1D23

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for TBC1D23 gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tbc1d231 , 5 TBC1 domain family, member 231, 5 88.6(n)1
    94.44(a)1
      16 (34.22 cM)5
    675811  NM_026254.21  NP_080530.21 
     571688665 
    chicken
    (Gallus gallus)
    Aves TBC1D231 TBC1 domain family, member 23 82.03(n)
    89.96(a)
      418383  NM_001030784.1  NP_001025955.1 
    lizard
    (Anolis carolinensis)
    Reptilia TBC1D236
    TBC1 domain family, member 23
    85(a)
    1 ↔ 1
    3(174224153-174263274)
    African clawed frog
    (Xenopus laevis)
    Amphibia 480140362   -- 79.54(n)    48014036 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc637562 hypothetical protein MGC63756 75.56(n)   393459  BC055235.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG45521 CG4552 50.25(n)
    46.55(a)
      33289  NM_134725.2  NP_608569.1 
    worm
    (Caenorhabditis elegans)
    Secernentea tbc-11 tbc-1 47.29(n)
    34.04(a)
      181592  NM_078084.5  NP_510485.2 


    ENSEMBL Gene Tree for TBC1D23 (if available)
    TreeFam Gene Tree for TBC1D23 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for TBC1D23 (see all 1289)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1398214791,2
    --99977837(+) AGATTC/GTGTCT 2 -- us2k10--------
    rs345572081,2
    C--99977867(+) AAAAA-/A/AA  
            
    TCCGC
    2 -- us2k12NA 4
    rs1145037251,2
    F--99977870(+) AAATCC/TGCTAG 2 -- us2k12Minor allele frequency- T:0.03WA NA 238
    rs98646531,2
    C,F,H--99977873(+) TCCGCC/TAGAAG 2 -- us2k116Minor allele frequency- T:0.01NS EA NA WA CSA 1056
    rs1454232141,2
    --99977913(+) TCTTGC/TCCCCA 2 -- us2k10--------
    rs16148611,2
    C,H--99978149(-) GACTTC/ATATGT 2 -- us2k14Minor allele frequency- A:0.00NS EA 416
    rs1487960921,2
    --99978194(+) CTGTTC/TAAAAA 2 -- us2k10--------
    rs780340941,2
    --99978285(+) AATCAC/TAATTG 2 -- us2k10--------
    rs773391291,2
    F--99978543(+) GAGATC/ACGGGC 2 -- us2k11Minor allele frequency- A:0.06WA 118
    rs173356141,2
    C,F,H--99978562(+) TGGGTG/CCAGTA 2 -- us2k128Minor allele frequency- C:0.20NA NS EA WA 2904

    HapMap Linkage Disequilibrium report for TBC1D23 (99979686 - 100044095 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for TBC1D23: --
    Human Gene Mutation Database (HGMD): TBC1D23
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing TBC1D23
    DNA2.0 Custom Variant and Variant Library Synthesis for TBC1D23

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    2 diseases for TBC1D23:    
    About MalaCards
    pneumocystosis    malaria


    TBC1D23 for disorders           About GeneDecksing


    Export disorders for TBC1D23 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for TBC1D23 gene, integrated from 10 sources (see all 19):
    (articles sorted by number of sources associating them with TBC1D23)
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    1. Spatiotemporal inhibition of innate immunity signaling by the Tbc1d23 RAB-GAP. (PubMed id 22312129)1, 3 De Arras L....Alper S. (J. Immunol. 2012)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error. (PubMed id 24144296)1 Cheng C.Y....Baird P.N. (Am. J. Hum. Genet. 2013)
    4. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    5. Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. (PubMed id 22589738)1 Fox C.S....Borecki I.B. (PLoS Genet. 2012)
    6. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    7. Toward an understanding of the protein interaction network of the human liver. (PubMed id 21988832)1 Wang J....Yang X. (Mol. Syst. Biol. 2011)
    8. A data set of human endogenous protein ubiquitination sites. (PubMed id 20972266)1 Shi Y....Qin J. (amp 2011)
    9. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    10. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (Sci. Signal. 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 55773 HGNC: 25622 AceView: FLJ11046 Ensembl:ENSG00000036054 euGenes: HUgn55773
    ECgene: TBC1D23 H-InvDB: TBC1D23

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for TBC1D23 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for TBC1D23 gene:
    Search GeneIP for patents involving TBC1D23

    GeneCards and IP:
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