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

Gene ID: 54662, updated on 2-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
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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 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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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)

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

  • 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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