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    Rlim ring finger protein, LIM domain interacting [ Mus musculus (house mouse) ]

    Gene ID: 19820, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Rlimprovided by MGI
    Official Full Name
    ring finger protein, LIM domain interactingprovided by MGI
    Primary source
    MGI:MGI:1342291
    See related
    Ensembl:ENSMUSG00000056537 AllianceGenome:MGI:1342291
    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
    Ha1r; Rlim1; Rnf12
    Summary
    Enables ubiquitin protein ligase activity. Involved in protein ubiquitination; random inactivation of X chromosome; and ubiquitin-dependent protein catabolic process. Acts upstream of or within negative regulation of DNA-binding transcription factor activity and negative regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including central nervous system; extraembryonic component; limb; male reproductive system; and urinary system. Human ortholog(s) of this gene implicated in Tonne-Kalscheuer syndrome. Orthologous to human RLIM (ring finger protein, LIM domain interacting). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in placenta adult (RPKM 25.8), CNS E11.5 (RPKM 7.6) and 20 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Rlim in Genome Data Viewer
    Location:
    X 46.42 cM; X D
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (103000770..103024886, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (103957163..103981296, complement)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene ribosomal protein S2 pseudogene Neighboring gene STARR-seq mESC enhancer starr_47700 Neighboring gene STARR-seq mESC enhancer starr_47701 Neighboring gene STARR-seq mESC enhancer starr_47703 Neighboring gene predicted gene, 23378 Neighboring gene STARR-seq mESC enhancer starr_47704 Neighboring gene predicted gene, 22266

    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
    • 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. Molecular cloning of a novel retinoic acid-responsive gene, HA1R-62, which is also up-regulated in Hoxa-1-overexpressing cells. Shen J, et al. Cell Growth Differ, 2000 Jan. PMID 10672899
    2. The X-inactivation trans-activator Rnf12 is negatively regulated by pluripotency factors in embryonic stem cells. Navarro P, et al. Hum Genet, 2011 Aug. PMID 21544581, Free PMC Article
    3. Rlim-Dependent and -Independent Pathways for X Chromosome Inactivation in Female ESCs. Wang F, et al. Cell Rep, 2017 Dec 26. PMID 29281819, Free PMC Article
    4. Paternal RLIM/Rnf12 is a survival factor for milk-producing alveolar cells. Jiao B, et al. Cell, 2012 Apr 27. PMID 22541433, Free PMC Article
    5. RNF12 activates Xist and is essential for X chromosome inactivation. Barakat TS, et al. PLoS Genet, 2011 Jan 27. PMID 21298085, Free PMC Article

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Roles of the Rlim-Rex1 axis during X chromosome inactivation in mice.
      Title: Roles of the Rlim-Rex1 axis during X chromosome inactivation in mice.
    2. An RNF12-USP26 amplification loop drives germ cell specification and is disrupted by disease-associated mutations.
      Title: An RNF12-USP26 amplification loop drives germ cell specification and is disrupted by disease-associated mutations.
    3. These data uncover a key function for RNF12 E3 ubiquitin ligase activity in stem cell and neural development.
      Title: RNF12 X-Linked Intellectual Disability Mutations Disrupt E3 Ligase Activity and Neural Differentiation.
    4. RNF12 targets pluripotency protein REX1 for degradation to initiate random X chromosome inactivation in embryonic stem cells.
      Title: REX1 is the critical target of RNF12 in imprinted X chromosome inactivation in mice.
    5. the existence of Rlim-dependent and Rlim-independent pathways for random X chromosome inactivation in differentiating female embryonic stem cells.
      Title: Rlim-Dependent and -Independent Pathways for X Chromosome Inactivation in Female ESCs.
    6. These findings show that control of Lhx2 function by Ldb1 and Rnf12 underpins the coordinated differentiation of neurons and Muller glia in postnatal retina.
      Title: Ldb1- and Rnf12-dependent regulation of Lhx2 controls the relative balance between neurogenesis and gliogenesis in the retina.
    7. These results reveal crucial roles of Rlim for the maintenance of high Xist RNA levels, Xist clouds and X-silencing in female embryos at blastocyst stages, while initial Xist expression appears Rlim-independent.
      Title: Regulation of X-linked gene expression during early mouse development by Rlim.
    8. In late preimplantation, Oct4 served as a chromatin opener to create transcriptional permissive states at Xm-Xist/Tsix genomic loci. In parthenogenetic embryos, Rnf12 overdose caused Xm-Xist derepression via Xm-Tsix repression; physiological Rnf12 levels were essential for Xm-Xist silencing maintenance in fertilized embryos.
      Title: Maintenance of Xist Imprinting Depends on Chromatin Condensation State and Rnf12 Dosage in Mice.
    9. high RNF12 levels may contribute to the specific activation of maternal Xist in XpDeltaXist female ROSI embryos, but upregulation of additional Xp derived factors and/or the specific epigenetic constitution of the round spermatid-derived Xp are expected to be more critical
      Title: Round Spermatid Injection Rescues Female Lethality of a Paternally Inherited Xist Deletion in Mouse.
    10. results provide evidence that RLIM is dispensable for rXCI, indicating that in mice an RLIM-independent mechanism activates Xist in the embryo proper
      Title: RLIM is dispensable for X-chromosome inactivation in the mouse embryonic epiblast.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (5) 
    • Gene trapped (1) 
    • Targeted (2)  1 citation

    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin-protein transferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within negative regulation of DNA-binding transcription factor activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein ubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in random inactivation of X chromosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in random inactivation of X chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within random inactivation of X chromosome IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within random inactivation of X chromosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in random inactivation of X chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase RLIM
    Names
    Hoxa1 regulated
    LIM domain-interacting RING finger protein
    RING finger LIM domain-binding protein
    RING-type E3 ubiquitin transferase RLIM
    ring finger protein 12
    NP_001345134.1
    NP_001412889.1
    NP_001412890.1
    NP_001412891.1
    NP_001412892.1
    NP_001412893.1
    NP_001412894.1
    NP_001412895.1
    NP_035406.3
    XP_006527981.1
    XP_006527983.1
    XP_006527984.1

    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_001358205.2 → NP_001345134.1  E3 ubiquitin-protein ligase RLIM

      Status: VALIDATED

      Source sequence(s)
      AL805911
      Consensus CDS
      CCDS30331.1
      UniProtKB/Swiss-Prot
      Q8CE02, Q91X19, Q9CYY2, Q9WTV7
      Related
      ENSMUSP00000070662.5, ENSMUST00000070705.6
      Conserved Domains (1) summary
      cl17238
      Location:544 → 588
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    2. NM_001425960.1 → NP_001412889.1  E3 ubiquitin-protein ligase RLIM

      Status: VALIDATED

      Source sequence(s)
      AL805911
      UniProtKB/Swiss-Prot
      Q8CE02, Q91X19, Q9CYY2, Q9WTV7

    3. NM_001425961.1 → NP_001412890.1  E3 ubiquitin-protein ligase RLIM

      Status: VALIDATED

      Source sequence(s)
      AL805911
      UniProtKB/Swiss-Prot
      Q8CE02, Q91X19, Q9CYY2, Q9WTV7

    4. NM_001425962.1 → NP_001412891.1  E3 ubiquitin-protein ligase RLIM

      Status: VALIDATED

      Source sequence(s)
      AL805911
      UniProtKB/Swiss-Prot
      Q8CE02, Q91X19, Q9CYY2, Q9WTV7

    5. NM_001425963.1 → NP_001412892.1  E3 ubiquitin-protein ligase RLIM

      Status: VALIDATED

      Source sequence(s)
      AL805911
      UniProtKB/Swiss-Prot
      Q8CE02, Q91X19, Q9CYY2, Q9WTV7

    6. NM_001425964.1 → NP_001412893.1  E3 ubiquitin-protein ligase RLIM

      Status: VALIDATED

      Source sequence(s)
      AL805911
      UniProtKB/Swiss-Prot
      Q8CE02, Q91X19, Q9CYY2, Q9WTV7

    7. NM_001425965.1 → NP_001412894.1  E3 ubiquitin-protein ligase RLIM

      Status: VALIDATED

      Source sequence(s)
      AL805911
      UniProtKB/Swiss-Prot
      Q8CE02, Q91X19, Q9CYY2, Q9WTV7

    8. NM_001425966.1 → NP_001412895.1  E3 ubiquitin-protein ligase RLIM

      Status: VALIDATED

      Source sequence(s)
      AL805911
      UniProtKB/Swiss-Prot
      Q8CE02, Q91X19, Q9CYY2, Q9WTV7

    9. NM_011276.5 → NP_035406.3  E3 ubiquitin-protein ligase RLIM

      See identical proteins and their annotated locations for NP_035406.3

      Status: VALIDATED

      Source sequence(s)
      AL805911
      Consensus CDS
      CCDS30331.1
      UniProtKB/Swiss-Prot
      Q8CE02, Q91X19, Q9CYY2, Q9WTV7
      Related
      ENSMUSP00000112820.2, ENSMUST00000121153.8
      Conserved Domains (1) summary
      cl17238
      Location:544 → 588
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    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_000086.8 Reference GRCm39 C57BL/6J

      Range
      103000770..103024886 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006527918.5 → XP_006527981.1  E3 ubiquitin-protein ligase RLIM isoform X1

      See identical proteins and their annotated locations for XP_006527981.1

      UniProtKB/Swiss-Prot
      Q8CE02, Q91X19, Q9CYY2, Q9WTV7
      Conserved Domains (1) summary
      cl17238
      Location:544 → 588
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    2. XM_006527921.5 → XP_006527984.1  E3 ubiquitin-protein ligase RLIM isoform X1

      See identical proteins and their annotated locations for XP_006527984.1

      UniProtKB/Swiss-Prot
      Q8CE02, Q91X19, Q9CYY2, Q9WTV7
      Conserved Domains (1) summary
      cl17238
      Location:544 → 588
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    3. XM_006527920.4 → XP_006527983.1  E3 ubiquitin-protein ligase RLIM isoform X1

      See identical proteins and their annotated locations for XP_006527983.1

      UniProtKB/Swiss-Prot
      Q8CE02, Q91X19, Q9CYY2, Q9WTV7
      Conserved Domains (1) summary
      cl17238
      Location:544 → 588
      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
    Q9WTV7.2 GenPept UniProtKB/Swiss-Prot:Q9WTV7

    Gene LinkOut

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

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