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Aliases for RLIM Gene

Aliases for RLIM Gene

  • Ring Finger Protein, LIM Domain Interacting 2 3 5
  • LIM Domain-Interacting RING Finger Protein 3 4
  • Ring Zinc Finger Protein NY-REN-43antigen 2 3
  • RING-Type E3 Ubiquitin Transferase RLIM 3 4
  • RING Finger LIM Domain-Binding Protein 3 4
  • Renal Carcinoma Antigen NY-REN-43 3 4
  • E3 Ubiquitin-Protein Ligase RLIM 2 3
  • 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
  • RING Finger Protein 12 4
  • EC 2.3.2.27 4
  • NY-REN-43 3
  • EC 6.3.2 61
  • MRX61 3

External Ids for RLIM Gene

Previous HGNC Symbols for RLIM Gene

  • RNF12

Previous GeneCards Identifiers for RLIM Gene

  • GC0XM073726
  • GC0XM073803
  • GC0XM067438

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. Diseases associated with RLIM include Mental Retardation, X-Linked 61 and Non-Syndromic X-Linked Intellectual Disability. Among its related pathways are Innate Immune System and Class I MHC mediated antigen processing and presentation. GO annotations related to this gene include ligase activity and transcription corepressor activity. An important paralog of this gene is RNF6.

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 CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RLIM Gene

Genomics for RLIM Gene

Regulatory Elements for RLIM Gene

Enhancers for RLIM Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XG074534 1.4 FANTOM5 Ensembl ENCODE 2 +78.6 78554 3.8 PKNOX1 ZNF133 FEZF1 RAD21 YY1 GLIS2 SCRT2 EGR2 ZNF263 ZNF654 SLC16A2 RLIM PIR45746 PIR50185
GH0XG074289 1.4 FANTOM5 ENCODE 1.7 +322.9 322887 4.5 HDGF PKNOX1 ATF1 ARNT SIN3A BRCA1 YY1 GTF3C2 GLIS2 KLF7 RAB11FIP1P1 RN7SL648P JPX ENSG00000271533 RLIM MIR374A GC0XM074296 ENSG00000277922
GH0XG074121 0.4 FANTOM5 2.9 +493.5 493457 0.3 RLIM ENSG00000280375 DDX3P1
GH0XG074612 1 ENCODE 0.7 +0.4 428 3.0 PKNOX1 ATF1 CREB3L1 ARID4B SIN3A DMAP1 YY1 GLIS2 ELK1 ZNF143 UPRT RLIM PABPC1P3
GH0XG074130 0.4 FANTOM5 1.7 +483.9 483911 0.5 RLIM DDX3P2 PIR48767
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RLIM on UCSC Golden Path with GeneCards custom track

Promoters for RLIM Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000247282 626 2800 PKNOX1 FOXA2 ATF1 CREB3L1 ARID4B SIN3A DMAP1 YY1 ELK1 ZNF143

Genomic Location for RLIM Gene

Chromosome:
X
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

Genes around RLIM on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RLIM Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RLIM Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

Selected DME Specific Peptides for RLIM Gene

Q9NVW2:
  • QRGNQSWRAVSRTNPNSGDFRFSLEINVNR
  • SLAQFFLLNEDD
  • DQPRGLTKEQIDNL
  • SQMDRLDREEAFYQFVNNL
  • DSIIDWLNSVRQTGNTTRS
  • GQRPPTIVLDLQVRRVRPG
  • KLRKLPCSHE
  • PNNTVTYESERGGFRRTFSRSERAGVRTYVSTIRIPIRR
  • RGQRRARSRSPD
  • EGSSRTR

Post-translational modifications for RLIM Gene

  • Ubiquitination at Lys9, Lys550, Lys568, and isoforms=2582
  • Modification sites at PhosphoSitePlus

Other Protein References for RLIM Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for RLIM Gene

Gene Families for RLIM Gene

Protein Domains for RLIM Gene

Suggested Antigen Peptide Sequences for RLIM Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NVW2

UniProtKB/Swiss-Prot:

RNF12_HUMAN :
  • Belongs to the RNF12 family.
Family:
  • Belongs to the RNF12 family.
genes like me logo Genes that share domains with RLIM: view

Function for RLIM Gene

Molecular function for RLIM Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.
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 TAS --
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RLIM: view
genes like me logo Genes that share phenotypes with RLIM: view

Human Phenotype Ontology for RLIM Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for RLIM Gene

MGI Knock Outs for RLIM:

Animal Model Products

CRISPR Products

miRNA for RLIM Gene

miRTarBase miRNAs that target RLIM

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

Localization for RLIM Gene

Subcellular locations from UniProtKB/Swiss-Prot for RLIM Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RLIM gene
Compartment Confidence
nucleus 5
cytosol 5

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:0005829 cytosol TAS --
GO:0017053 transcriptional repressor complex NAS 11013082
genes like me logo Genes that share ontologies with RLIM: view

Pathways & Interactions for RLIM Gene

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

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:0000209 protein polyubiquitination TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006511 ubiquitin-dependent protein catabolic process ISS --
genes like me logo Genes that share ontologies with RLIM: view

No data available for SIGNOR curated interactions 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:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE for RLIM Gene

Protein differential expression in normal tissues from HIPED for RLIM Gene

This gene is overexpressed in Plasma (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for RLIM Gene



Protein tissue co-expression partners for RLIM Gene

NURSA nuclear receptor signaling pathways regulating expression of RLIM Gene:

RLIM

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.

Evidence on tissue expression from TISSUES for RLIM Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with RLIM: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RLIM Gene

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 34 35
  • 98.23 (n)
cow
(Bos Taurus)
Mammalia RLIM 35
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RLIM 34 35
  • 94.93 (n)
mouse
(Mus musculus)
Mammalia Rlim 34 16 35
  • 86.56 (n)
rat
(Rattus norvegicus)
Mammalia Rlim 34
  • 85.46 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 68 (a)
ManyToMany
chicken
(Gallus gallus)
Aves RLIM 34 35
  • 79.55 (n)
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 72 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia rlim 34
  • 80.06 (n)
Str.6791 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.29450 34
zebrafish
(Danio rerio)
Actinopterygii LOC562487 34
  • 76.4 (n)
CR383680.1 35
  • 60 (a)
ManyToMany
si:ch211-59o9.10 35
  • 23 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta mura 35
  • 11 (a)
OneToMany
Species where no ortholog for RLIM was found in the sources mined by GeneCards:
  • 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

(7) 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
rs786205133 Pathogenic, Mental retardation, X-linked 61 (MRX61) [MIM:300978] 74,592,248(-) CACCT(A/G)TGAAA reference, missense
VAR_077827 Mental retardation, X-linked 61 (MRX61) [MIM:300978]
VAR_077828 Mental retardation, X-linked 61 (MRX61) [MIM:300978]
VAR_077829 Mental retardation, X-linked 61 (MRX61) [MIM:300978]
rs193920920 Uncertain significance 74,593,055(-) AGGAG(-/A)CTCTT reference, frameshift-variant

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

Variant ID Type Subtype PubMed ID
esv2740232 CNV deletion 23290073
nsv521472 CNV gain 19592680

Variation tolerance for RLIM Gene

Residual Variation Intolerance Score: 38.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.58; 12.55% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RLIM Gene

Human Gene Mutation Database (HGMD)
RLIM
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RLIM

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RLIM Gene

Disorders for RLIM Gene

MalaCards: The human disease database

(3) MalaCards diseases for RLIM Gene - From: ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search RLIM in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RNF12_HUMAN
  • Mental retardation, X-linked 61 (MRX61) [MIM:300978]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Intellectual deficiency is the only primary symptom of non-syndromic X-linked mental retardation, while syndromic mental retardation presents with associated physical, neurological and/or psychiatric manifestations. {ECO:0000269 PubMed:25644381, ECO:0000269 PubMed:25735484}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for RLIM

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RLIM
genes like me logo Genes that share disorders with RLIM: view

No data available for Genatlas for RLIM Gene

Publications for RLIM Gene

  1. 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 22 64
  2. 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 22 64
  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 64
  4. Syndromic X-linked intellectual disability segregating with a missense variant in RLIM. (PMID: 25735484) TA … Fiskerstrand T. (Eur. J. Hum. Genet. 2015) 3 4 64
  5. 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 64

Products for RLIM Gene

Sources for RLIM Gene

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