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

Gene ID: 19820, updated on 5-Mar-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; negative regulation of transcription by RNA polymerase II; and regulation of dosage compensation by inactivation of X chromosome. Located in nucleus. Is expressed in several structures, including extraembryonic component; limb; liver; 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, Apr 2022]
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. 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
  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. 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
  4. Deficient spermiogenesis in mice lacking Rlim. Wang F, et al. Elife, 2021 Feb 23. PMID 33620316, Free PMC Article
  5. RNF12 X-Linked Intellectual Disability Mutations Disrupt E3 Ligase Activity and Neural Differentiation. Bustos F, et al. Cell Rep, 2018 May 8. PMID 29742418, Free PMC Article

See all (61) 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)
  • Gene trapped (1) 
  • Targeted (2)  1 citation
  • Endonuclease-mediated (5) 

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 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 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 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 ISO
Inferred from Sequence Orthology
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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