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    TBC1D13 TBC1 domain family member 13 [ Homo sapiens (human) ]

    Gene ID: 54662, updated on 27-Nov-2024

    Summary

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    Official Symbol
    TBC1D13provided by HGNC
    Official Full Name
    TBC1 domain family member 13provided by HGNC
    Primary source
    HGNC:HGNC:25571
    See related
    Ensembl:ENSG00000107021 MIM:616218; AllianceGenome:HGNC:25571
    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
    Predicted to enable GTPase activator activity. Predicted to be involved in intracellular protein transport. Predicted to be located in cytosol and membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 17.4), ovary (RPKM 10.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TBC1D13 in Genome Data Viewer
    Location:
    9q34.11
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (128787253..128810430)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (140992029..141015220)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (131549532..131572709)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene zyg-11 related cell cycle regulator Neighboring gene uncharacterized LOC124902282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20351 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131534571-131535297 Neighboring gene CRISPRi-validated cis-regulatory element chr9.3033 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20352 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:131574071-131574244 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20353 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131581177-131581742 Neighboring gene KYAT1-SPOUT1 readthrough Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131590537-131591467 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29093 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:131592801-131593024 Neighboring gene SPOUT domain containing methyltransferase 1 Neighboring gene endonuclease G Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131600611-131601111 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:131607420-131607646 Neighboring gene kynurenine aminotransferase 1 Neighboring gene Sharpr-MPRA regulatory region 9337 Neighboring gene Sharpr-MPRA regulatory region 7409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20355 Neighboring gene leucine rich repeat containing 8 VRAC subunit A

    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. TBC1D13 is a RAB35 specific GAP that plays an important role in GLUT4 trafficking in adipocytes. Davey JR, et al. Traffic, 2012 Oct. PMID 22762500, Free PMC Article
    2. 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
    3. 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
    4. An atlas of genetic influences on human blood metabolites. Shin SY, et al. Nat Genet, 2014 Jun. PMID 24816252, Free PMC Article
    5. Sequential genome-wide CRISPR-Cas9 screens identify genes regulating cell-surface expression of tetraspanins. Yang J, et al. Cell Rep, 2023 Feb 28. PMID 36724073

    See all (13) 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

    EBI GWAS Catalog

    Description
    An atlas of genetic influences on human blood metabolites.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10743

    Gene Ontology Provided by GOA

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

    General protein information

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    Preferred Names
    TBC1 domain family member 13
    Names
    epididymis secretory sperm binding protein

    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_001286772.2 → NP_001273701.1  TBC1 domain family member 13 isoform b

      See identical proteins and their annotated locations for NP_001273701.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two alternate exons that result in the loss of an in-frame segment in the 3' coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AL441992
      Consensus CDS
      CCDS69677.1
      Related
      ENSP00000223865.8, ENST00000223865.8
      Conserved Domains (1) summary
      smart00164
      Location:32 → 242
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    2. NM_018201.5 → NP_060671.3  TBC1 domain family member 13 isoform a

      See identical proteins and their annotated locations for NP_060671.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AL441992
      Consensus CDS
      CCDS6911.1
      UniProtKB/Swiss-Prot
      A7E2E7, B3KW04, B9EGJ8, Q5T270, Q5T271, Q9NVG8
      UniProtKB/TrEMBL
      A0A024R8C8, Q59F95
      Related
      ENSP00000361731.5, ENST00000372648.10
      Conserved Domains (1) summary
      smart00164
      Location:32 → 367
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      128787253..128810430
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423479.1 → XP_047279435.1  TBC1 domain family member 13 isoform X1

    2. XM_005252060.3 → XP_005252117.1  TBC1 domain family member 13 isoform X2

      See identical proteins and their annotated locations for XP_005252117.1

      UniProtKB/TrEMBL
      B4DHM6, Q59F95
      Conserved Domains (1) summary
      smart00164
      Location:28 → 291
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      140992029..141015220
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363130.1 → XP_054219105.1  TBC1 domain family member 13 isoform X1

    2. XM_054363131.1 → XP_054219106.1  TBC1 domain family member 13 isoform X2

      UniProtKB/TrEMBL
      B4DHM6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NVG8.3 GenPept UniProtKB/Swiss-Prot:Q9NVG8

    Gene LinkOut

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