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    RLIM ring finger protein, LIM domain interacting [ Homo sapiens (human) ]

    Gene ID: 51132, updated on 28-Oct-2024

    Summary

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    Official Symbol
    RLIMprovided by HGNC
    Official Full Name
    ring finger protein, LIM domain interactingprovided by HGNC
    Primary source
    HGNC:HGNC:13429
    See related
    Ensembl:ENSG00000131263 MIM:300379; AllianceGenome:HGNC:13429
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MRX61; RNF12; TOKAS; NY-REN-43
    Summary
    The protein encoded by this gene is a RING-H2 zinc finger protein. It has been shown to be an E3 ubiquitin protein ligase that targets LIM domain binding 1 (LDB1/CLIM), and causes proteasome-dependent degradation of LDB1. This protein and LDB1 are co-repressors of LHX1/LIM-1, a homeodomain transcription factor. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Feb 2009]
    Expression
    Ubiquitous expression in bone marrow (RPKM 10.2), brain (RPKM 9.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RLIM in Genome Data Viewer
    Location:
    Xq13.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (74582976..74614624, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (73016616..73048268, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (73802811..73834459, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:73631745-73632397 Neighboring gene uncharacterized LOC105373252 Neighboring gene solute carrier family 16 member 2 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 25 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:73744106-73744606 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:73787669-73788649 Neighboring gene poly(A) binding protein cytoplasmic 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29767 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:73915317-73916516 Neighboring gene RNA, U6 small nuclear 330, pseudogene Neighboring gene neurite extension and migration factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:74097925-74098468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:74098469-74099012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20907

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Syndromic X-linked intellectual disability segregating with a missense variant in RLIM. Tønne E, et al. Eur J Hum Genet, 2015 Dec. PMID 25735484, Free PMC Article
    2. How does the Xist activator Rlim/Rnf12 regulate Xist expression? Wang F, et al. Biochem Soc Trans, 2024 Jun 26. PMID 38747697, Free PMC Article
    3. Functional activity of RLIM/Rnf12 is regulated by phosphorylation-dependent nucleocytoplasmic shuttling. Jiao B, et al. Mol Biol Cell, 2013 Oct. PMID 23904271, Free PMC Article
    4. Kaposi's Sarcoma-Associated Herpesvirus LANA Modulates the Stability of the E3 Ubiquitin Ligase RLIM. Tadmor H, et al. J Virol, 2020 Feb 14. PMID 31801865, Free PMC Article
    5. RLIM Is a Candidate Dosage-Sensitive Gene for Individuals with Varying Duplications of Xq13, Intellectual Disability, and Distinct Facial Features. Palmer EE, et al. Am J Hum Genet, 2020 Dec 3. PMID 33159883, Free PMC Article

    See all (74) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. How does the Xist activator Rlim/Rnf12 regulate Xist expression?
      Title: How does the Xist activator Rlim/Rnf12 regulate Xist expression?
    2. Ring finger protein 12 activates AKT signalling to promote the progression of liver cancer by interacting with EGFR.
      Title: Ring finger protein 12 activates AKT signalling to promote the progression of liver cancer by interacting with EGFR.
    3. A novel RLIM/RNF12 variant disrupts protein stability and function to cause severe Tonne-Kalscheuer syndrome.
      Title: A novel RLIM/RNF12 variant disrupts protein stability and function to cause severe Tonne-Kalscheuer syndrome.
    4. 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.
    5. Sequential stabilization of RNF220 by RLIM and ZC4H2 during cerebellum development and Shh-group medulloblastoma progression.
      Title: Sequential stabilization of RNF220 by RLIM and ZC4H2 during cerebellum development and Shh-group medulloblastoma progression.
    6. RNF12 is regulated by AKT phosphorylation and promotes TGF-beta driven breast cancer metastasis.
      Title: RNF12 is regulated by AKT phosphorylation and promotes TGF-β driven breast cancer metastasis.
    7. RLIM Is a Candidate Dosage-Sensitive Gene for Individuals with Varying Duplications of Xq13, Intellectual Disability, and Distinct Facial Features.
      Title: RLIM Is a Candidate Dosage-Sensitive Gene for Individuals with Varying Duplications of Xq13, Intellectual Disability, and Distinct Facial Features.
    8. The RING Domain of RING Finger 12 Efficiently Builds Degradative Ubiquitin Chains.
      Title: The RING Domain of RING Finger 12 Efficiently Builds Degradative Ubiquitin Chains.
    9. Kaposi's Sarcoma-Associated Herpesvirus LANA Modulates the Stability of the E3 Ubiquitin Ligase RLIM.
      Title: Kaposi's Sarcoma-Associated Herpesvirus LANA Modulates the Stability of the E3 Ubiquitin Ligase RLIM.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Intellectual disability, X-linked 61
    MedGen: C4283894 OMIM: 300978 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ25923, FLJ41093, FLJ42887, FLJ45986, MGC15161, DKFZp686N06224

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription corepressor activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin-protein transferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein ubiquitination ISS
    Inferred from Sequence or Structural Similarity
    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 
    involved_in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of transcription repressor complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase RLIM
    Names
    E3 ubiquitin-protein ligase RNF12
    LIM domain-interacting RING finger protein
    R-LIM
    RING finger LIM domain-binding protein
    RING-type E3 ubiquitin transferase RLIM
    renal carcinoma antigen NY-REN-43
    ring finger protein 12
    ring zinc finger LIM domain binding protein
    ring zinc finger protein NY-REN-43antigen
    NP_057204.2
    NP_899196.1

    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.

    Genomic

    1. NG_013258.1 RefSeqGene

      Range
      5003..36651
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_016120.4 → NP_057204.2  E3 ubiquitin-protein ligase RLIM

      See identical proteins and their annotated locations for NP_057204.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) lacks an alternate exon in the 5' UTR, compared to variant 2, and may represent the more abundant form. Both variants encode the same protein.
      Source sequence(s)
      AK127880, AL513007, BC013357, BF686000
      Consensus CDS
      CCDS14427.1
      UniProtKB/Swiss-Prot
      B2RBQ1, D3DTE0, Q96D38, Q9NVW2, Q9Y598
      Related
      ENSP00000328059.6, ENST00000332687.11
      Conserved Domains (2) summary
      PHA03307
      Location:159 → 348
      PHA03307; transcriptional regulator ICP4; Provisional
      cl17238
      Location:568 → 612
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    2. NM_183353.3 → NP_899196.1  E3 ubiquitin-protein ligase RLIM

      See identical proteins and their annotated locations for NP_899196.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longer transcript. Both variants encode the same protein.
      Source sequence(s)
      AK127880, AL513007, AL712605, BC013357, BF686000
      Consensus CDS
      CCDS14427.1
      UniProtKB/Swiss-Prot
      B2RBQ1, D3DTE0, Q96D38, Q9NVW2, Q9Y598
      Related
      ENSP00000253571.3, ENST00000349225.2
      Conserved Domains (2) summary
      PHA03307
      Location:159 → 348
      PHA03307; transcriptional regulator ICP4; Provisional
      cl17238
      Location:568 → 612
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      74582976..74614624 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      73016616..73048268 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NVW2.3 GenPept UniProtKB/Swiss-Prot:Q9NVW2

    Gene LinkOut

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

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