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TBC1D28 Gene

protein-coding   GIFtS: 38
GCID: GC17M018538

TBC1 Domain Family, Member 28

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(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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
TBC1 Domain Family, Member 281 2
TBC1 Domain Family Member 282

External Ids:    HGNC: 268581   Entrez Gene: 2542722   Ensembl: ENSG000001893757   UniProtKB: Q2M2D73   
ORGUL members:         

Export aliases for TBC1D28 gene to outside databases

Previous GC identifers: GC17M018480 GC17M018482 GC17M018146


(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 TBC1D28 Gene:
TBC1D28 (TBC1 domain family, member 28) is a protein-coding gene. GO annotations related to this gene include Rab GTPase activator activity. An important paralog of this gene is TBC1D3H.


(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 at NCBI GenBank:
NC_000017.10  NT_010718.17  NC_018928.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the TBC1D28 gene promoter:
         Nkx3-1   Spz1   Pax-6   Nkx3-1 v1   CUTL1   AP-2gamma   c-Ets-1   HFH-1   Pax-4a   RSRFC4   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for TBC1D28

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TBC1D28


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

Entrez Gene cytogenetic band: 17p11.2   Ensembl cytogenetic band:  17p11.2   HGNC cytogenetic band: 17p11.2

TBC1D28 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TBC1D28 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M018538:  view genomic region     (about GC identifiers)

Start:
18,538,319 bp from pter      End:
18,565,263 bp from pter
Size:
26,945 bases      Orientation:
minus 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: TBC28_HUMAN, Q2M2D7 (See protein sequence)
Recommended Name: TBC1 domain family member 28  
Size: 210 amino acids; 24072 Da
Caution: The Rab-GAP TBC domain is short and lacks the C-terminal part. It is therefore unclear whether the
protein has GTPase-activating activity
Secondary accessions: Q2M2E1

Explore the universe of human proteins at neXtProt for TBC1D28: NX_Q2M2D7

Explore proteomics data for TBC1D28 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See TBC1D28 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001034486.2  
    ENSEMBL proteins: 
     ENSP00000339973   ENSP00000458676   ENSP00000461503   ENSP00000461684   ENSP00000460935  
     ENSP00000385821  

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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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    1 InterPro protein domain:
     IPR000195 Rab-GTPase-TBC_dom

    Graphical View of Domain Structure for InterPro Entry Q2M2D7

    ProtoNet protein and cluster: Q2M2D7

    UniProtKB/Swiss-Prot: TBC28_HUMAN, Q2M2D7
    Similarity: Contains 1 Rab-GAP TBC domain


    Find genes that share domains with TBC1D28           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, 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--
         
    Find genes that share ontologies with TBC1D28           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for TBC1D28

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    (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
    extracellular1
    mitochondrion1

    (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 TBC1D28
    Interactions:

        Search GeneGlobe Interaction Network for TBC1D28

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0032313regulation of Rab GTPase activity ----

    Find genes that share ontologies with TBC1D28           About GenesLikeMe



    (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 TBC1D28 (TBC28)



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for TBC1D28 gene: 
    NM_001039397.2  

    Unigene Cluster for TBC1D28:

    TBC1 domain family, member 28
    Hs.434123  [show with all ESTs]
    Unigene Representative Sequence: AK097563
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000345096 ENST00000570881 ENST00000575220 ENST00000572213 ENST00000573652
    ENST00000575211 ENST00000575570 ENST00000575970 ENST00000579178 ENST00000405044(uc002gud.2)

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      QuantiFast Probe-based Assays in human, mouse, rat TBC1D28

    Additional mRNA sequence: 

    AK097563.1 AK292544.1 AL137747.1 BC112012.1 BC112016.1 

    3 DOTS entries:

    DT.40298868  DT.102838138  DT.121002760 

    9 AceView cDNA sequences:

    AA933929 AK097563 BX097621 AI205891 CD676640 AL137747 AI149683 BI561256 
    AW119095 

    GeneLoc Exon Structure


    (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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    TBC1D28 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATCTCTTGGC
    TBC1D28 Expression
    About this image

    TBC1D28 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TBC1D28 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.434123
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    In Situ
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    (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 TBC1D28 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    dog
    (Canis familiaris)
    Mammalia --
    --
    (see all 9)
    Uncharacterized protein
    (see all 9)
    2(a)
    18(a)
    (see all 9)
    many ↔ many
    many ↔ many
    (see all 9)
    30(40210136-40212674)
    38(23900814-23911859)
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    18(a)
    1 → many
    5(15411217-15475247)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    21(a)
    1 → many
    1(74862925-74883710)
    zebrafish
    (Danio rerio)
    Actinopterygii TBC1D3G6
    TBC1 domain family, member 3G
    6(a)
    1 → many
    25(16824916-16909191) ENSDARG00000086840
    fruit fly
    (Drosophila melanogaster)
    Insecta RN-tre6
    tre oncogene-related protein
    10(a)
    1 → many
    2R(9872320-9878215)
    worm
    (Caenorhabditis elegans)
    Secernentea tbc-176
    Protein TBC-17, isoform d (tbc-17) mRNA, complete ...
    5(a)
    1 → many
    II(12694412-12725483) WBGene00012894


    ENSEMBL Gene Tree for TBC1D28 (if available)
    TreeFam Gene Tree for TBC1D28 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TBC1D28 gene
    TBC1D3H2  TBC1D3F2  TBC1D32  TBC1D262  ENSG000002487512  TBC1D3C2  GRTP12  TBC1D10C2  
    TBC1D10A2  TBC1D3G2  TBC1D10B2  USP6NL2  TBC1D3B2  
    8 SIMAP similar genes for TBC1D28 using alignment to 5 protein entries:     TBC28_HUMAN (see all proteins):
    TBC1D26    TBC1D3H    tre    TBC1D3C    TBC1D3F    TBC1D3
    TBC1D3B    TBC1D3G

    Find genes that share paralogs with TBC1D28           About GenesLikeMe



    (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 TBC1D28 (see all 219)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1817362501,2
    --18538363(+) GTCCGC/GGGGAG 1 -- ds50010--------
    rs3771906281,2
    C--18538470(+) GCCCCA/GTCTGT 1 -- ds50010--------
    rs31046061,2
    C--18538754(+) AACCCA/CACACC 1 -- ds50012Minor allele frequency- C:0.00NA 4
    rs37520141,2
    C--18539004(+) CTTTCA/CGAGGC 1 -- ut310--------
    rs1466986491,2
    C--18539302(+) CCTGCC/TGAACA 1 -- ut310--------
    rs65026621,2
    C,H--18539304(+) TGCCGG/AACATA 1 -- ut315Minor allele frequency- A:0.00NA 10
    rs1855572531,2
    --18539405(+) AGGAAC/GAGCCA 1 -- ut310--------
    rs1899479261,2
    --18539605(+) GGGACC/TCTGCC 1 -- ut310--------
    rs1808542991,2
    --18539640(+) CCAGGA/TGGGGA 1 -- ut310--------
    rs2017493331,2
    --18539937(+) TTTTG-/TTTTTT 1 -- int10--------

    HapMap Linkage Disequilibrium report for TBC1D28 (18538319 - 18565263 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for TBC1D28:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv29176CNV Gain19812545
    nsv827913CNV Gain20364138
    nsv907782CNV Gain21882294
    nsv9504CNV Gain+Loss18304495
    nsv499818OTHER Inversion21111241

    Site Specific Mutation Identification with PCR Assays
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    (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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      --

    (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 TBC1D28 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with TBC1D28)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 254272 HGNC: 26858 AceView: FLJ40244 Ensembl:ENSG00000189375 euGenes: HUgn254272
    ECgene: TBC1D28 H-InvDB: TBC1D28

    (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 TBC1D28 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 TBC1D28 gene:
    Search GeneIP for patents involving TBC1D28

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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