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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.