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    Rnf138 ring finger protein 138 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 94196, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Rnf138provided by RGD
    Official Full Name
    ring finger protein 138provided by RGD
    Primary source
    RGD:621485
    See related
    EnsemblRapid:ENSRNOG00000015645 AllianceGenome:RGD:621485
    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
    Rsd4; Trif
    Summary
    Predicted to enable protein kinase binding activity; single-stranded DNA binding activity; and ubiquitin protein ligase activity. Predicted to be involved in DNA double-strand break processing involved in repair via single-strand annealing; double-strand break repair via homologous recombination; and protein ubiquitination. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Is active in glutamatergic synapse; postsynapse; and presynapse. Orthologous to human RNF138 (ring finger protein 138). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Testes (RPKM 257.8), Thymus (RPKM 86.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Rnf138 in Genome Data Viewer
    Location:
    18p12
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 18 NC_086036.1 (12558430..12590849)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 18 NC_051353.1 (12291557..12315931)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 18 NC_005117.4 (15146925..15167361, complement)

    Chromosome 18 - NC_086036.1Genomic Context describing neighboring genes Neighboring gene elongation factor 2-like Neighboring gene eukaryotic translation elongation factor 2, pseudogene 4 Neighboring gene ring finger protein 125 Neighboring gene meprin A subunit beta Neighboring gene GRB2 associated regulator of MAPK1 subtype 1 Neighboring gene uncharacterized LOC120098265

    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 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. Ethanol extracts from Ilex pubescens promotes cerebral ischemic tolerance via modulation of TLR4-MyD88/TRIF signaling pathway in rats. Fang X, et al. J Ethnopharmacol, 2020 Jun 28. PMID 32084554
    2. The RNF138 E3 ligase displaces Ku to promote DNA end resection and regulate DNA repair pathway choice. Ismail IH, et al. Nat Cell Biol, 2015 Nov. PMID 26502055
    3. Ubiquitin Ligase RNF138 Promotes Episodic Ataxia Type 2-Associated Aberrant Degradation of Human Ca(v)2.1 (P/Q-Type) Calcium Channels. Fu SJ, et al. J Neurosci, 2017 Mar 1. PMID 28167673, Free PMC Article
    4. Systematic E2 screening reveals a UBE2D-RNF138-CtIP axis promoting DNA repair. Schmidt CK, et al. Nat Cell Biol, 2015 Nov. PMID 26502057, Free PMC Article
    5. NARF, an nemo-like kinase (NLK)-associated ring finger protein regulates the ubiquitylation and degradation of T cell factor/lymphoid enhancer factor (TCF/LEF). Yamada M, et al. J Biol Chem, 2006 Jul 28. PMID 16714285

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Ethanol extracts from Ilex pubescens promotes cerebral ischemic tolerance via modulation of TLR4-MyD88/TRIF signaling pathway in rats.
      Title: Ethanol extracts from Ilex pubescens promotes cerebral ischemic tolerance via modulation of TLR4-MyD88/TRIF signaling pathway in rats.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC72355

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables single-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables single-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables single-stranded DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin protein ligase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA double-strand break processing involved in repair via single-strand annealing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA double-strand break processing involved in repair via single-strand annealing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA double-strand break processing involved in repair via single-strand annealing ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to leukemia inhibitory factor IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cellular response to leukemia inhibitory factor ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair via homologous recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in double-strand break repair via homologous recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair via homologous recombination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein ubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein ubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in postsynapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in presynapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in site of double-strand break IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in site of double-strand break ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase RNF138
    Names
    RING-type E3 ubiquitin transferase RNF138
    RSD-4
    ring finger protein 138, E3 ubiquitin protein ligase
    NP_446040.1
    XP_038953128.1
    XP_038953129.1

    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_053588.3 → NP_446040.1  E3 ubiquitin-protein ligase RNF138

      See identical proteins and their annotated locations for NP_446040.1

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000018
      UniProtKB/Swiss-Prot
      Q99PD2
      UniProtKB/TrEMBL
      A6J2H0, A6J2H1
      Related
      ENSRNOP00000021061.8, ENSRNOT00000021061.8
      Conserved Domains (3) summary
      cd00162
      Location:18 → 57
      RING_Ubox; RING-HC finger (C3HC4-type) [structural motif]
      pfam18574
      Location:80 → 112
      zf_C2HC_14; C2HC Zing finger domain
      cl17238
      Location:14 → 59
      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_086036.1 Reference GRCr8

      Range
      12558430..12590849
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039097200.2 → XP_038953128.1  E3 ubiquitin-protein ligase RNF138 isoform X1

      UniProtKB/TrEMBL
      A0A8I6ABB7, A6J2G9
      Related
      ENSRNOP00000091039.2, ENSRNOT00000100953.2
      Conserved Domains (3) summary
      cd16544
      Location:14 → 59
      RING-HC_RNF138; RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins
      pfam05605
      Location:156 → 215
      zf-Di19; Drought induced 19 protein (Di19), zinc-binding
      pfam18574
      Location:80 → 112
      zf_C2HC_14; C2HC Zing finger domain

    2. XM_039097201.2 → XP_038953129.1  E3 ubiquitin-protein ligase RNF138 isoform X2

      UniProtKB/Swiss-Prot
      Q99PD2
      UniProtKB/TrEMBL
      A6J2H0, A6J2H1
      Related
      ENSRNOP00000084639.1, ENSRNOT00000102423.2
      Conserved Domains (3) summary
      cd00162
      Location:18 → 57
      RING_Ubox; RING-HC finger (C3HC4-type) [structural motif]
      pfam18574
      Location:80 → 112
      zf_C2HC_14; C2HC Zing finger domain
      cl17238
      Location:14 → 59
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99PD2.1 GenPept UniProtKB/Swiss-Prot:Q99PD2

    Gene LinkOut

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