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    Rnf39 ring finger protein 39 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 171387, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Rnf39provided by RGD
    Official Full Name
    ring finger protein 39provided by RGD
    Primary source
    RGD:628854
    See related
    AllianceGenome:RGD:628854
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Lirf; Hzfw1
    Summary
    Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in innate immune response. Predicted to be active in cytoplasm. Orthologous to human RNF39 (ring finger protein 39). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 51.3), Liver (RPKM 37.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Rnf39 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (1610027..1615516, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (1604794..1610283, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (2098375..2103864, complement)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene RT1 class I, locus M6, gene 2 Neighboring gene ZNRD1 antisense RNA 1 Neighboring gene RNA polymerase I subunit H Neighboring gene protein phosphatase 1, regulatory (inhibitor) subunit 11 Neighboring gene uncharacterized LOC102554813 Neighboring gene tripartite motif-containing 31

    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. LIRF, a gene induced during hippocampal long-term potentiation as an immediate-early gene, encodes a novel RING finger protein. Matsuo R, et al. Biochem Biophys Res Commun, 2001 Nov 30. PMID 11716498
    2. Identification and cataloging of genes induced by long-lasting long-term potentiation in awake rats. Matsuo R, et al. J Neurochem, 2000 Jun. PMID 10820183
    3. Identification of key genes and pathways associated with cholangiocarcinoma development based on weighted gene correlation network analysis. Liu J, et al. PeerJ, 2019. PMID 31687280, Free PMC Article
    4. The genomic sequence and comparative analysis of the rat major histocompatibility complex. Hurt P, et al. Genome Res, 2004 Apr. PMID 15060004, Free PMC Article
    5. 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

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in innate immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of neuronal synaptic plasticity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    RING finger protein 39
    Names
    LTP-induced RING finger 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_134374.2 → NP_599201.1  RING finger protein 39

      See identical proteins and their annotated locations for NP_599201.1

      Status: VALIDATED

      Source sequence(s)
      BX883051
      UniProtKB/Swiss-Prot
      Q920M2
      UniProtKB/TrEMBL
      A0A8I6ASY8, A6KR81
      Conserved Domains (4) summary
      TIGR00599
      Location:14 → 205
      rad18; DNA repair protein rad18
      cd00162
      Location:20 → 66
      RING_Ubox; RING-HC finger (C3HC4-type) [structural motif]
      cl02614
      Location:161 → 347
      SPRY; SPRY domain
      cl17238
      Location:18 → 66
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    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_086038.1 Reference GRCr8

      Range
      1610027..1615516 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q920M2.1 GenPept UniProtKB/Swiss-Prot:Q920M2

    Gene LinkOut

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

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