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    Ttc39b tetratricopeptide repeat domain 39B [ Mus musculus (house mouse) ]

    Gene ID: 69863, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Ttc39bprovided by MGI
    Official Full Name
    tetratricopeptide repeat domain 39Bprovided by MGI
    Primary source
    MGI:MGI:1917113
    See related
    Ensembl:ENSMUSG00000038172 AllianceGenome:MGI:1917113
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    1810054D07Rik; 9130422G05Rik
    Summary
    Involved in several processes, including cholesterol homeostasis; negative regulation of cholesterol storage; and regulation of cholesterol efflux. Is expressed in cerebral cortex marginal layer; dentate gyrus subgranular zone; and olfactory epithelium. Orthologous to human TTC39B (tetratricopeptide repeat domain 39B). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in cerebellum adult (RPKM 4.8), cortex adult (RPKM 3.8) and 27 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ttc39b in Genome Data Viewer
    Location:
    4 C3; 4 39.41 cM
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (83138537..83242488, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (83220300..83324309, complement)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 46887 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene STARR-seq mESC enhancer starr_10629 Neighboring gene STARR-seq mESC enhancer starr_10632 Neighboring gene predicted gene, 42307 Neighboring gene predicted gene, 23412 Neighboring gene STARR-positive B cell enhancer mm9_chr4:82969964-82970265 Neighboring gene STARR-seq mESC enhancer starr_10639 Neighboring gene predicted gene, 42306 Neighboring gene predicted gene 11413 Neighboring gene predicted gene 11184

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. TTC39B deficiency stabilizes LXR reducing both atherosclerosis and steatohepatitis. Hsieh J, et al. Nature, 2016 Jul 14. PMID 27383786, Free PMC Article
    2. Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates. Miller JA, et al. Development, 2013 Nov. PMID 24154525, Free PMC Article
    3. Mouse screen reveals multiple new genes underlying mouse and human hearing loss. Ingham NJ, et al. PLoS Biol, 2019 Apr. PMID 30973865, Free PMC Article
    4. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article
    5. BioID screening of biotinylation sites using the avidin-like protein Tamavidin 2-REV identifies global interactors of stimulator of interferon genes (STING). Motani K, et al. J Biol Chem, 2020 Aug 7. PMID 32554809, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (3) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in cholesterol homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cholesterol homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cholesterol storage IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of cholesterol storage IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cholesterol efflux IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cholesterol efflux IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cholesterol metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cholesterol metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  

    General protein information

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    Preferred Names
    tetratricopeptide repeat protein 39B
    Names
    TPR repeat protein 39B

    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_027238.2 → NP_081514.1  tetratricopeptide repeat protein 39B

      See identical proteins and their annotated locations for NP_081514.1

      Status: VALIDATED

      Source sequence(s)
      AK031930, AK037208, AK043383, AK134680, BB289912, BU515835, BX571885, CK780404
      Consensus CDS
      CCDS18297.1
      UniProtKB/Swiss-Prot
      B2RX73, Q3V168, Q8BX40, Q8BYY4, Q9D8N8
      Related
      ENSMUSP00000099887.4, ENSMUST00000102823.10
      Conserved Domains (2) summary
      pfam10300
      Location:76 → 533
      DUF3808; Protein of unknown function (DUF3808)
      pfam13424
      Location:527 → 593
      TPR_12; Tetratricopeptide repeat

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000070.7 Reference GRCm39 C57BL/6J

      Range
      83138537..83242488 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006538241.5 → XP_006538304.1  tetratricopeptide repeat protein 39B isoform X4

      Conserved Domains (2) summary
      pfam13424
      Location:339 → 403
      TPR_12; Tetratricopeptide repeat
      pfam10300
      Location:13 → 343
      DUF3808; Protein of unknown function (DUF3808)

    2. XM_030253766.2 → XP_030109626.1  tetratricopeptide repeat protein 39B isoform X4

      Conserved Domains (2) summary
      pfam13424
      Location:339 → 403
      TPR_12; Tetratricopeptide repeat
      pfam10300
      Location:13 → 343
      DUF3808; Protein of unknown function (DUF3808)

    3. XM_011250101.4 → XP_011248403.3  tetratricopeptide repeat protein 39B isoform X1

      Conserved Domains (2) summary
      pfam13424
      Location:522 → 586
      TPR_12; Tetratricopeptide repeat
      pfam10300
      Location:69 → 526
      DUF3808; Protein of unknown function (DUF3808)

    4. XM_006538239.4 → XP_006538302.1  tetratricopeptide repeat protein 39B isoform X2

      Conserved Domains (2) summary
      pfam13424
      Location:499 → 563
      TPR_12; Tetratricopeptide repeat
      pfam10300
      Location:46 → 503
      DUF3808; Protein of unknown function (DUF3808)

    5. XM_036164405.1 → XP_036020298.1  tetratricopeptide repeat protein 39B isoform X3

      Conserved Domains (1) summary
      pfam10300
      Location:69 → 425
      DUF3808; Protein of unknown function (DUF3808)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_025782.2: Suppressed sequence

      Description
      NM_025782.2: This RefSeq was permanently suppressed because it is primarily UTR sequence.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BYY4.1 GenPept UniProtKB/Swiss-Prot:Q8BYY4

    Gene LinkOut

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

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