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

Gene ID: 51132, updated on 5-Mar-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
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Genomic context

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Location:
Xq13.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (74582976..74614624, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (73016616..73048268, complement)
105.20220307 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
  • 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. A novel RLIM/RNF12 variant disrupts protein stability and function to cause severe Tonne-Kalscheuer syndrome. Bustos F, et al. Sci Rep, 2021 May 5. PMID 33953269, Free PMC Article
  2. 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
  3. 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
  4. 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
  5. 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

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. These findings uncover a novel mechanism for the regulation of BRF1 and reveal RNF12 as an important regulator of Pol III-dependent transcription.
    Title: RNF12 catalyzes BRF1 ubiquitination and regulates RNA polymerase III-dependent transcription.
Submit: New GeneRIF Correction See all GeneRIFs (20)

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
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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_2023_10

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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