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    TBC1D9B TBC1 domain family member 9B [ Homo sapiens (human) ]

    Gene ID: 23061, updated on 28-Oct-2024

    Summary

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    Official Symbol
    TBC1D9Bprovided by HGNC
    Official Full Name
    TBC1 domain family member 9Bprovided by HGNC
    Primary source
    HGNC:HGNC:29097
    See related
    Ensembl:ENSG00000197226 MIM:618039; AllianceGenome:HGNC:29097
    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
    Also known as
    GRAMD9B
    Summary
    Predicted to enable GTPase activator activity. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in fat (RPKM 32.0), thyroid (RPKM 25.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TBC1D9B in Genome Data Viewer
    Location:
    5q35.3
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (179862071..179907897, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (180417215..180462876, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (179289071..179334897, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr5:179278643-179278802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23765 Neighboring gene RN7SK pseudogene 150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23766 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16752 Neighboring gene MRN complex interacting protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:179294147-179294673 Neighboring gene MRNIP divergent transcript Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:179302124-179303323 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:179320466-179320966 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:179320967-179321467 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:179329571-179330070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:179333851-179334628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:179344075-179344992 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:179352751-179353251 Neighboring gene ring finger protein 130 Neighboring gene dnaJ homolog subfamily B member 6-like Neighboring gene ribosomal protein S15a pseudogene 18

    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 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. Interaction of TBC1D9B with Mammalian ATG8 Homologues Regulates Autophagic Flux. Liao Y, et al. Sci Rep, 2018 Sep 10. PMID 30202024, Free PMC Article
    2. 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
    3. Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity. Ishibashi K, et al. Genes Cells, 2009 Jan. PMID 19077034
    4. Functional dissection of Rab GTPases involved in primary cilium formation. Yoshimura S, et al. J Cell Biol, 2007 Jul 30. PMID 17646400, Free PMC Article
    5. Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. Ishikawa K, et al. DNA Res, 1998 Jun 30. PMID 9734811

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ41880, KIAA0676, MGC157757

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    NOT involved_in regulation of cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    TBC1 domain family member 9B
    Names
    TBC1 domain family, member 9B (with GRAM domain)

    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_015043.4 → NP_055858.2  TBC1 domain family member 9B isoform b

      See identical proteins and their annotated locations for NP_055858.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame coding exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AC008393, AC010285
      Consensus CDS
      CCDS4450.1
      UniProtKB/TrEMBL
      A1L3A9
      Related
      ENSP00000347375.3, ENST00000355235.8
      Conserved Domains (4) summary
      smart00164
      Location:505 → 715
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      cd13354
      Location:299 → 394
      PH-GRAM2_TCB1D9_TCB1D9B; TBC1 domain family members 9 and 9B (TBC1D9 and TBC1D9B) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 2
      cd13351
      Location:153 → 251
      PH-GRAM1_TCB1D9_TCB1D9B; TBC1 domain family members 9 and 9B (TBC1D9 and TBC1D9B) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 1
      cl08302
      Location:855 → 906
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    2. NM_198868.3 → NP_942568.2  TBC1 domain family member 9B isoform a

      See identical proteins and their annotated locations for NP_942568.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AC008393, AC010285
      Consensus CDS
      CCDS43408.1
      UniProtKB/Swiss-Prot
      D3DWQ5, D3DWQ6, O75163, Q53EY0, Q66K14, Q6MZI2, Q96H49
      UniProtKB/TrEMBL
      B9A6K8
      Related
      ENSP00000349291.3, ENST00000356834.7
      Conserved Domains (4) summary
      smart00164
      Location:505 → 715
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      cd13354
      Location:299 → 394
      PH-GRAM2_TCB1D9_TCB1D9B; TBC1 domain family members 9 and 9B (TBC1D9 and TBC1D9B) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 2
      cd13351
      Location:153 → 251
      PH-GRAM1_TCB1D9_TCB1D9B; TBC1 domain family members 9 and 9B (TBC1D9 and TBC1D9B) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 1
      cl08302
      Location:855 → 906
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      179862071..179907897 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_016107298.1 Reference GRCh38.p14 PATCHES

      Range
      627631..670372 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      180417215..180462876 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q66K14.3 GenPept UniProtKB/Swiss-Prot:Q66K14

    Gene LinkOut

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

    Other Literature Sources
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    Research Materials
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