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Aliases for RLIM Gene

Aliases for RLIM Gene

  • Ring Finger Protein, LIM Domain Interacting 2 3
  • LIM Domain-Interacting RING Finger Protein 3 4
  • Ring Zinc Finger Protein NY-REN-43antigen 2 3
  • RING Finger LIM Domain-Binding Protein 3 4
  • Renal Carcinoma Antigen NY-REN-43 3 4
  • Ring Finger Protein 12 2 3
  • RNF12 3 4
  • R-LIM 3 4
  • Ring Zinc Finger LIM Domain Binding Protein 3
  • LIM Domain Interacting Ring Finger Protein 2
  • E3 Ubiquitin-Protein Ligase RNF12 3
  • E3 Ubiquitin-Protein Ligase RLIM 3
  • RING Finger Protein 12 4
  • EC 6.3.2.- 4
  • NY-REN-43 3
  • EC 6.3.2 64
  • RNF12, 6

External Ids for RLIM Gene

Previous Symbols for RLIM Gene

  • RNF12

Summaries for RLIM Gene

Entrez Gene Summary for RLIM Gene

  • 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]

GeneCards Summary for RLIM Gene

RLIM (Ring Finger Protein, LIM Domain Interacting) is a Protein Coding gene. GO annotations related to this gene include ubiquitin-protein transferase activity and transcription corepressor activity. An important paralog of this gene is RNF38.

UniProtKB/Swiss-Prot for RLIM Gene

  • E3 ubiquitin-protein ligase. Acts as a negative coregulator for LIM homeodomain transcription factors by mediating the ubiquitination and subsequent degradation of LIM cofactors LDB1 and LDB2 and by mediating the recruitment the SIN3a/histone deacetylase corepressor complex. Ubiquitination and degradation of LIM cofactors LDB1 and LDB2 allows DNA-bound LIM homeodomain transcription factors to interact with other protein partners such as RLIM. Plays a role in telomere length-mediated growth suppression by mediating the ubiquitination and degradation of TERF1. By targeting ZFP42 for degradation, acts as an activator of random inactivation of X chromosome in the embryo, a stochastic process in which one X chromosome is inactivated to minimize sex-related dosage differences of X-encoded genes in somatic cells of female placental mammals.

Gene Wiki entry for RLIM Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RLIM Gene

Genomics for RLIM Gene

Genomic Location for RLIM Gene

Start:
74,582,976 bp from pter
End:
74,614,626 bp from pter
Size:
31,651 bases
Orientation:
Minus strand

Genomic View for RLIM Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for RLIM Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RLIM Gene

Regulatory Elements for RLIM Gene

Proteins for RLIM Gene

  • Protein details for RLIM Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NVW2-RNF12_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase RLIM
    Protein Accession:
    Q9NVW2
    Secondary Accessions:
    • B2RBQ1
    • D3DTE0
    • Q96D38
    • Q9Y598

    Protein attributes for RLIM Gene

    Size:
    624 amino acids
    Molecular mass:
    68549 Da
    Quaternary structure:
    • Interacts with LIM/homeobox factors such as LHX3. Interacts with LDB1, LDB2 and SIN3A (By similarity). Interacts with LIMK1 (By similarity). Interacts (via N-terminus) with TERF1. Interacts (via C-terminus) with ESR1.
    Miscellaneous:
    • Acts as a positive coregulator of ESR1-mediated transcription in breast cancer cells
    SequenceCaution:
    • Sequence=AAD42875.1; Type=Frameshift; Positions=134, 142; Evidence={ECO:0000305};

    Alternative splice isoforms for RLIM Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RLIM Gene

Proteomics data for RLIM Gene at MOPED

Post-translational modifications for RLIM Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys550, Lys568, and Lys582

Other Protein References for RLIM Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains for RLIM Gene

Gene Families for RLIM Gene

HGNC:
  • RNF :RING-type (C3HC4) zinc fingers

Protein Domains for RLIM Gene

InterPro:
Blocks:
ProtoNet:

UniProtKB/Swiss-Prot:

RNF12_HUMAN
Family:
  • Belongs to the RNF12 family.:
    • Q9NVW2
Similarity:
  • Contains 1 RING-type zinc finger.:
    • Q9NVW2
genes like me logo Genes that share domains with RLIM: view

Function for RLIM Gene

Molecular function for RLIM Gene

UniProtKB/Swiss-Prot Function: E3 ubiquitin-protein ligase. Acts as a negative coregulator for LIM homeodomain transcription factors by mediating the ubiquitination and subsequent degradation of LIM cofactors LDB1 and LDB2 and by mediating the recruitment the SIN3a/histone deacetylase corepressor complex. Ubiquitination and degradation of LIM cofactors LDB1 and LDB2 allows DNA-bound LIM homeodomain transcription factors to interact with other protein partners such as RLIM. Plays a role in telomere length-mediated growth suppression by mediating the ubiquitination and degradation of TERF1. By targeting ZFP42 for degradation, acts as an activator of random inactivation of X chromosome in the embryo, a stochastic process in which one X chromosome is inactivated to minimize sex-related dosage differences of X-encoded genes in somatic cells of female placental mammals.

Enzyme Numbers (IUBMB) for RLIM Gene

Gene Ontology (GO) - Molecular Function for RLIM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003714 transcription corepressor activity NAS 11013082
GO:0004842 ubiquitin-protein transferase activity ISS --
GO:0005515 protein binding --
GO:0008270 zinc ion binding IEA --
GO:0016874 ligase activity IEA --
genes like me logo Genes that share ontologies with RLIM: view
genes like me logo Genes that share phenotypes with RLIM: view

Animal Models for RLIM Gene

MGI Knock Outs for RLIM:

miRNA for RLIM Gene

No data available for Transcription Factor Targeting and HOMER Transcription for RLIM Gene

Localization for RLIM Gene

Subcellular locations from UniProtKB/Swiss-Prot for RLIM Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RLIM Gene COMPARTMENTS Subcellular localization image for RLIM gene
Compartment Confidence
nucleus 5
cytosol 3

Gene Ontology (GO) - Cellular Components for RLIM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IDA --
GO:0017053 transcriptional repressor complex NAS 11013082
genes like me logo Genes that share ontologies with RLIM: view

Pathways for RLIM Gene

SuperPathways for RLIM Gene

No Data Available

UniProtKB/Swiss-Prot Q9NVW2-RNF12_HUMAN

  • Pathway: Protein modification; protein ubiquitination

Gene Ontology (GO) - Biological Process for RLIM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006511 ubiquitin-dependent protein catabolic process ISS --
GO:0016567 protein ubiquitination ISS --
GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity IEA --
genes like me logo Genes that share ontologies with RLIM: view

No data available for Pathways by source for RLIM Gene

Transcripts for RLIM Gene

mRNA/cDNA for RLIM Gene

Unigene Clusters for RLIM Gene

Ring finger protein, LIM domain interacting:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for RLIM Gene

No ASD Table

Relevant External Links for RLIM Gene

GeneLoc Exon Structure for
RLIM
ECgene alternative splicing isoforms for
RLIM

Expression for RLIM Gene

mRNA expression in normal human tissues for RLIM Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for RLIM Gene

SOURCE GeneReport for Unigene cluster for RLIM Gene Hs.653288

mRNA Expression by UniProt/SwissProt for RLIM Gene

Q9NVW2-RNF12_HUMAN
Tissue specificity: Expressed in many tissues
genes like me logo Genes that share expressions with RLIM: view

Orthologs for RLIM Gene

This gene was present in the common ancestor of animals.

Orthologs for RLIM Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RLIM 36
  • 98.23 (n)
  • 98.39 (a)
RLIM 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RLIM 37
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RLIM 36
  • 94.93 (n)
  • 96.96 (a)
RLIM 37
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rlim 36
  • 86.56 (n)
  • 88.48 (a)
Rlim 16
Rlim 37
  • 89 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 37
  • 68 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Rlim 36
  • 85.46 (n)
  • 88.39 (a)
chicken
(Gallus gallus)
Aves RLIM 36
  • 79.55 (n)
  • 79.09 (a)
RLIM 37
  • 80 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 37
  • 72 (a)
ManyToMany
African clawed frog
(Xenopus laevis)
Amphibia Xl.29450 36
tropical clawed frog
(Silurana tropicalis)
Amphibia rlim 36
  • 80.06 (n)
  • 91.45 (a)
Str.6791 36
zebrafish
(Danio rerio)
Actinopterygii CR383680.1 37
  • 60 (a)
ManyToMany
LOC562487 36
  • 76.4 (n)
  • 86.73 (a)
si:ch211-59o9.10 37
  • 23 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta mura 37
  • 11 (a)
OneToMany
Species with no ortholog for RLIM:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RLIM Gene

ENSEMBL:
Gene Tree for RLIM (if available)
TreeFam:
Gene Tree for RLIM (if available)

Paralogs for RLIM Gene

Paralogs for RLIM Gene

Selected SIMAP similar genes for RLIM Gene using alignment to 2 proteins:

Pseudogenes.org Pseudogenes for RLIM Gene

genes like me logo Genes that share paralogs with RLIM: view

Variants for RLIM Gene

Sequence variations from dbSNP and Humsavar for RLIM Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs1044974 -- 74,585,749(-) CCCTT(C/T)TCCGA utr-variant-3-prime
rs1052436 -- 74,591,321(-) GAGTC(A/G)TTGCT utr-variant-3-prime
rs1926863 -- 74,601,519(-) GGGGG(G/T)TTTGT intron-variant
rs2767392 -- 74,597,899(+) gattt(A/T)ttttc intron-variant
rs2819591 -- 74,602,872(+) ATTTA(G/T)AGAGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RLIM Gene

Variant ID Type Subtype PubMed ID
nsv521472 CNV Gain 19592680
esv2740232 CNV Deletion 23290073

Relevant External Links for RLIM Gene

HapMap Linkage Disequilibrium report
RLIM
Human Gene Mutation Database (HGMD)
RLIM
Locus Specific Mutation Databases (LSDB)
RLIM

Disorders for RLIM Gene

(1) University of Copenhagen DISEASES for RLIM Gene

genes like me logo Genes that share disorders with RLIM: view

No data available for UniProtKB/Swiss-Prot for RLIM Gene

Publications for RLIM Gene

  1. Functional characterization of the gene encoding RLIM, the corepressor of LIM homeodomain transcription factors. (PMID: 11013082) Ostendorff H.P. … Bach I. (Genomics 2000) 3 4 23
  2. Regulation of estrogen-dependent transcription by the LIM cofactors CLIM and RLIM in breast cancer. (PMID: 19117995) Johnsen S.A. … Bach I. (Cancer Res. 2009) 3 4 23
  3. Antigens recognized by autologous antibody in patients with renal- cell carcinoma. (PMID: 10508479) Scanlan M.J. … Old L.J. (Int. J. Cancer 1999) 2 3 4
  4. Ubiquitin ligase RLIM modulates telomere length homeostasis through a proteolysis of TRF1. (PMID: 19164295) Her Y.R. … Chung I.K. (J. Biol. Chem. 2009) 3 4
  5. RLIM inhibits functional activity of LIM homeodomain transcription factors via recruitment of the histone deacetylase complex. (PMID: 10431247) Bach I. … Rosenfeld M.G. (Nat. Genet. 1999) 3 23

Products for RLIM Gene

Sources for RLIM Gene

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