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    Ttc39b tetratricopeptide repeat domain 39B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 298186, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Ttc39bprovided by RGD
    Official Full Name
    tetratricopeptide repeat domain 39Bprovided by RGD
    Primary source
    RGD:1305797
    See related
    EnsemblRapid:ENSRNOG00000042603 AllianceGenome:RGD:1305797
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1305797
    Summary
    Predicted to be involved in several processes, including cholesterol homeostasis; negative regulation of cholesterol storage; and regulation of cholesterol efflux. Orthologous to human TTC39B (tetratricopeptide repeat domain 39B). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 109.1), Liver (RPKM 102.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ttc39b in Genome Data Viewer
    Location:
    5q31
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (102649259..102754092, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (97603329..97708103, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (101304982..101405689, complement)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102552278 Neighboring gene uncharacterized LOC134479004 Neighboring gene ribosomal protein S12, pseudogene Neighboring gene ribosomal protein S29, pseudogene 11

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    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. (-)-Epigallocatechin-3-Gallate Ameliorates Atherosclerosis and Modulates Hepatic Lipid Metabolic Gene Expression in Apolipoprotein E Knockout Mice: Involvement of TTC39B. Wang W, et al. Front Pharmacol, 2018. PMID 29593532, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in cholesterol homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cholesterol homeostasis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cholesterol homeostasis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cholesterol homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cholesterol storage ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of cholesterol storage ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cholesterol efflux IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cholesterol efflux IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cholesterol efflux ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cholesterol efflux ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cholesterol metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cholesterol metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cholesterol metabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cholesterol metabolic process ISS
    Inferred from Sequence or Structural Similarity
    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_001106665.1 → NP_001100135.1  tetratricopeptide repeat protein 39B

      See identical proteins and their annotated locations for NP_001100135.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473978
      UniProtKB/Swiss-Prot
      D3ZC96
      UniProtKB/TrEMBL
      A0A8I5ZU64
      Related
      ENSRNOP00000055409.3, ENSRNOT00000058611.4
      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_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      102649259..102754092 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039109510.2 → XP_038965438.1  tetratricopeptide repeat protein 39B isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZU64
      Conserved Domains (2) summary
      pfam13424
      Location:495 → 559
      TPR_12; Tetratricopeptide repeat
      pfam10300
      Location:42 → 499
      DUF3808; Protein of unknown function (DUF3808)

    2. XM_006238350.5 → XP_006238412.1  tetratricopeptide repeat protein 39B isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZU64, A0A8I6A1P9
      Related
      ENSRNOP00000086184.1, ENSRNOT00000105460.2
      Conserved Domains (2) summary
      pfam10300
      Location:91 → 548
      DUF3808; Protein of unknown function (DUF3808)
      pfam13424
      Location:542 → 608
      TPR_12; Tetratricopeptide repeat
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    D3ZC96.1 GenPept UniProtKB/Swiss-Prot:D3ZC96

    Gene LinkOut

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

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