U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

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

    Gene ID: 51132, updated on 1-Jul-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RLIM in Genome Data Viewer
    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_016120.4NP_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:159348
      PHA03307; transcriptional regulator ICP4; Provisional
      cl17238
      Location:568612
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
    2. NM_183353.3NP_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:159348
      PHA03307; transcriptional regulator ICP4; Provisional
      cl17238
      Location:568612
      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)