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    TBC1D7-LOC100130357 TBC1D7-LOC100130357 readthrough [ Homo sapiens (human) ]

    Gene ID: 107080638, updated on 14-Mar-2024

    Summary

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    Gene symbol
    TBC1D7-LOC100130357
    Gene description
    TBC1D7-LOC100130357 readthrough
    See related
    Ensembl:ENSG00000145979
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This locus represents naturally occurring readthrough transcription between the neighboring TBC1D7 (TBC1 domain family member 7) gene and downstream uncharacterized LOC100130357 on chromosome 6. Readthrough transcripts may encode the same protein as TBC1 domain family member 7 or may be candidates for nonsense-mediated mRNA decay (NMD). [provided by RefSeq, Jan 2016]
    Expression
    Ubiquitous expression in heart (RPKM 3.6), bone marrow (RPKM 3.1) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    Location:
    6p24.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (13266536..13328537, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (13139813..13201777, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (13266768..13328769, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene phosphatase and actin regulator 1 Neighboring gene MPRA-validated peak5664 silencer Neighboring gene uncharacterized LOC105374933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16925 Neighboring gene Sharpr-MPRA regulatory region 805 Neighboring gene RNA, U1 small nuclear 11, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:13257894-13258394 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:13258395-13258895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24021 Neighboring gene uncharacterized LOC100130357 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:13273523-13274722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24023 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:13307473-13308672 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:13328608-13329114 Neighboring gene uncharacterized LOC124901261 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16927 Neighboring gene uncharacterized LOC105374936 Neighboring gene TBC1 domain family member 7

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Disruption of TBC1D7, a subunit of the TSC1-TSC2 protein complex, in intellectual disability and megalencephaly. Capo-Chichi JM, et al. J Med Genet, 2013 Nov. PMID 23687350
    2. TBC1D7 mutations are associated with intellectual disability, macrocrania, patellar dislocation, and celiac disease. Alfaiz AA, et al. Hum Mutat, 2014 Apr. PMID 24515783
    3. Identification of TBC7 having TBC domain as a novel binding protein to TSC1-TSC2 complex. Nakashima A, et al. Biochem Biophys Res Commun, 2007 Sep 14. PMID 17658474
    4. TBC1D7 is a third subunit of the TSC1-TSC2 complex upstream of mTORC1. Dibble CC, et al. Mol Cell, 2012 Aug 24. PMID 22795129, Free PMC Article
    5. Rab GTPase-activating proteins in autophagy: regulation of endocytic and autophagy pathways by direct binding to human ATG8 modifiers. Popovic D, et al. Mol Cell Biol, 2012 May. PMID 22354992, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    Genotypes

    Pathways from PubChem

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    General gene information

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    Homology

    Clone Names

    • FLJ32666, FLJ60615

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTPase activator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in activation of GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in activation of GTPase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cellular response to starvation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of TOR signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of TOR signaling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of TOR signaling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of TORC1 signaling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of GTPase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of protein ubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to growth factor IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of TSC1-TSC2 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of TSC1-TSC2 complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    TBC1 domain family member 7

    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_001318809.2 → NP_001305738.1  TBC1 domain family member 7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer readthrough transcript and encodes a protein.
      Source sequence(s)
      AK057228, AL008729, AL589984
      UniProtKB/Swiss-Prot
      E7EV96, Q2TU37, Q53F44, Q5SZL7, Q86VM8, Q96MB8, Q9P0N9
      UniProtKB/TrEMBL
      Q5SZL4
      Related
      ENSP00000475727.1, ENST00000606214.5
      Conserved Domains (1) summary
      cl02495
      Location:147 → 251
      RabGAP-TBC; Rab-GTPase-TBC domain

    RNA

    1. NR_134872.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks four 3' exons and contains three alternate 3' exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK296391, AL008729, AL589984
      Related
      ENST00000421203.6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      13266536..13328537 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      13139813..13201777 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P0N9.1 GenPept UniProtKB/Swiss-Prot:Q9P0N9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.