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Aliases for RNF4 Gene

Aliases for RNF4 Gene

  • Ring Finger Protein 4 2 3
  • RING-Type E3 Ubiquitin Transferase RNF4 3 4
  • RING Finger Protein 4 4 5
  • SNURF 3 4
  • Small Nuclear RING Finger Protein 3
  • Small Nuclear Ring Finger Protein 4
  • E3 Ubiquitin-Protein Ligase RNF4 3
  • E3 Ubiquitin Ligase RNF4 3
  • Protein SNURF 4
  • EC 2.3.2.27 4
  • RES4-26 3
  • SLX5 3

External Ids for RNF4 Gene

Previous GeneCards Identifiers for RNF4 Gene

  • GC04P002465
  • GC04P002337
  • GC04P002432
  • GC04P002438
  • GC04P002463
  • GC04P002410

Summaries for RNF4 Gene

Entrez Gene Summary for RNF4 Gene

  • The protein encoded by this gene contains a RING finger motif and acts as a transcription regulator. This protein has been shown to interact with, and inhibit the activity of, TRPS1, a transcription suppressor of GATA-mediated transcription. Transcription repressor ZNF278/PATZ is found to interact with this protein, and thus reduce the enhancement of androgen receptor-dependent transcription mediated by this protein. Studies of the mouse and rat counterparts suggested a role of this protein in spermatogenesis. A pseudogene of this gene is found on chromosome 1.[provided by RefSeq, Jul 2010]

GeneCards Summary for RNF4 Gene

RNF4 (Ring Finger Protein 4) is a Protein Coding gene. Among its related pathways are Innate Immune System and DNA Double-Strand Break Repair. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and ligase activity.

UniProtKB/Swiss-Prot for RNF4 Gene

  • E3 ubiquitin-protein ligase which binds polysumoylated chains covalently attached to proteins and mediates Lys-6-, Lys-11-, Lys-48- and Lys-63-linked polyubiquitination of those substrates and their subsequent targeting to the proteasome for degradation. Regulates the degradation of several proteins including PML and the transcriptional activator PEA3. Involved in chromosome alignment and spindle assembly, it regulates the kinetochore CENPH-CENPI-CENPK complex by targeting polysumoylated CENPI to proteasomal degradation. Regulates the cellular responses to hypoxia and heat shock through degradation of respectively EPAS1 and PARP1. Alternatively, it may also bind DNA/nucleosomes and have a more direct role in the regulation of transcription for instance enhancing basal transcription and steroid receptor-mediated transcriptional activation.

Gene Wiki entry for RNF4 Gene

Additional gene information for RNF4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RNF4 Gene

Genomics for RNF4 Gene

GeneHancer (GH) Regulatory Elements for RNF4 Gene

Promoters and enhancers for RNF4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04I002467 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 571 +7.7 7702 4.6 PKNOX1 FOXA2 SMAD1 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B E2F8 RNF4 FAM193A NOP14-AS1 NELFA HAUS3 TMEM129 ZFYVE28 SH3BP2 GC04M002457 GC04P002484
GH04I002462 Promoter/Enhancer 1.3 Ensembl ENCODE 557 +0.6 602 1.2 ELF3 RB1 SIN3A ZNF48 RAD21 ZNF335 ZNF121 ZNF143 THAP11 SMARCA5 RNF4 GC04M002457 LOC105374353 ZFYVE28 CFAP99
GH04I002479 Promoter/Enhancer 1 EPDnew dbSUPER 550.4 +17.3 17324 0.1 ZFHX2 GLIS1 SP2 EGR2 RNF4 GC04P002484 GC04M002457
GH04I001867 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 20.5 -591.0 -591030 7 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 SLC30A9 POLR2B NSD2 GC04M001869 HAUS3 RNF4 NELFA CRIPAK GAK FAM193A CTBP1-AS2 MAEA
GH04I002489 Enhancer 1.1 Ensembl ENCODE dbSUPER 46.5 +27.9 27887 1.8 BACH1 CEBPG ZBTB40 ZNF766 GATA3 TRIM24 ZNF600 ZNF197 E2F5 CEBPB RNF4 HAUS3 NELFA FAM193A ENSG00000270195 LOC105374353 ZFYVE28 ENSG00000251148 MXD4 POLN
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RNF4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RNF4 gene promoter:

Genomic Locations for RNF4 Gene

Genomic Locations for RNF4 Gene
chr4:2,462,220-2,625,320
(GRCh38/hg38)
Size:
163,101 bases
Orientation:
Plus strand
chr4:2,463,947-2,627,047
(GRCh37/hg19)

Genomic View for RNF4 Gene

Genes around RNF4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNF4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNF4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNF4 Gene

Proteins for RNF4 Gene

  • Protein details for RNF4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P78317-RNF4_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase RNF4
    Protein Accession:
    P78317
    Secondary Accessions:
    • B2R6D6
    • D6RF58
    • Q49AR8

    Protein attributes for RNF4 Gene

    Size:
    190 amino acids
    Molecular mass:
    21319 Da
    Quaternary structure:
    • Homodimer (via RING-type zinc finger domain). Interacts with GSC2 (By similarity). Interacts with AR/the androgen receptor and TBP (By similarity). Interacts with TCF20 (By similarity). Interacts with PATZ1. Interacts with TRPS1; negatively regulates TRPS1 transcriptional repressor activity. Interacts with PML; SUMO1-dependent. Interacts with PML; SUMO2-dependent. Interacts with PARP1. Interacts with PML (isoform PML-1, isoform PML-2, isoform PML-3, isoform PML-4, isoform PML-5 and isoform PML-6).

    Three dimensional structures from OCA and Proteopedia for RNF4 Gene

    Alternative splice isoforms for RNF4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RNF4 Gene

Post-translational modifications for RNF4 Gene

No data available for DME Specific Peptides for RNF4 Gene

Domains & Families for RNF4 Gene

Gene Families for RNF4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for RNF4 Gene

Suggested Antigen Peptide Sequences for RNF4 Gene

Graphical View of Domain Structure for InterPro Entry

P78317

UniProtKB/Swiss-Prot:

RNF4_HUMAN :
  • The SUMO interaction motifs (SIMs) mediates the binding to polysumoylated substrate.
Domain:
  • The SUMO interaction motifs (SIMs) mediates the binding to polysumoylated substrate.
  • The RING-type zinc finger domain is required for the ubiquitination of polysumoylated substrates.
genes like me logo Genes that share domains with RNF4: view

Function for RNF4 Gene

Molecular function for RNF4 Gene

GENATLAS Biochemistry:
RING finger protein 4,abundantly expressed in fetal tissues,involved in the protein and DNA association in the nucleus of the cell
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 which binds polysumoylated chains covalently attached to proteins and mediates Lys-6-, Lys-11-, Lys-48- and Lys-63-linked polyubiquitination of those substrates and their subsequent targeting to the proteasome for degradation. Regulates the degradation of several proteins including PML and the transcriptional activator PEA3. Involved in chromosome alignment and spindle assembly, it regulates the kinetochore CENPH-CENPI-CENPK complex by targeting polysumoylated CENPI to proteasomal degradation. Regulates the cellular responses to hypoxia and heat shock through degradation of respectively EPAS1 and PARP1. Alternatively, it may also bind DNA/nucleosomes and have a more direct role in the regulation of transcription for instance enhancing basal transcription and steroid receptor-mediated transcriptional activation.

Enzyme Numbers (IUBMB) for RNF4 Gene

Phenotypes From GWAS Catalog for RNF4 Gene

Gene Ontology (GO) - Molecular Function for RNF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding ISS --
GO:0003700 DNA binding transcription factor activity TAS 9710597
GO:0003713 transcription coactivator activity NAS 15572661
GO:0004842 ubiquitin-protein transferase activity ISS --
GO:0005515 protein binding IPI 12885770
genes like me logo Genes that share ontologies with RNF4: view
genes like me logo Genes that share phenotypes with RNF4: view

Animal Model Products

Clone Products

  • Addgene plasmids for RNF4

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RNF4 Gene

Localization for RNF4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RNF4 Gene

Cytoplasm. Nucleus. Nucleus, PML body. Nucleus, nucleoplasm.

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 RNF4 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for RNF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 12885770
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA,IDA 12885770
GO:0016605 colocalizes_with PML body IDA,IEA 20943951
genes like me logo Genes that share ontologies with RNF4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RNF4 Gene

Pathways & Interactions for RNF4 Gene

genes like me logo Genes that share pathways with RNF4: view

UniProtKB/Swiss-Prot P78317-RNF4_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

SIGNOR curated interactions for RNF4 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for RNF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016567 protein ubiquitination IBA --
GO:0030521 androgen receptor signaling pathway NAS 15572661
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process IMP 18408734
genes like me logo Genes that share ontologies with RNF4: view

Drugs & Compounds for RNF4 Gene

(3) Drugs for RNF4 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for RNF4 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with RNF4: view

Transcripts for RNF4 Gene

Unigene Clusters for RNF4 Gene

Ring finger protein 4:
Representative Sequences:

Clone Products

  • Addgene plasmids for RNF4

Alternative Splicing Database (ASD) splice patterns (SP) for RNF4 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c
SP1: -
SP2: -
SP3: - - - - - - -
SP4:
SP5:
SP6: -

Relevant External Links for RNF4 Gene

GeneLoc Exon Structure for
RNF4
ECgene alternative splicing isoforms for
RNF4

Expression for RNF4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RNF4 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RNF4 Gene



NURSA nuclear receptor signaling pathways regulating expression of RNF4 Gene:

RNF4

SOURCE GeneReport for Unigene cluster for RNF4 Gene:

Hs.66394

mRNA Expression by UniProt/SwissProt for RNF4 Gene:

P78317-RNF4_HUMAN
Tissue specificity: Widely expressed at low levels in many tissues; highly expressed in testis.

Evidence on tissue expression from TISSUES for RNF4 Gene

  • Nervous system(4.9)
  • Skin(4.5)
  • Kidney(2.5)
genes like me logo Genes that share expression patterns with RNF4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for RNF4 Gene

Orthologs for RNF4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RNF4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RNF4 33 34
  • 99.47 (n)
dog
(Canis familiaris)
Mammalia RNF4 33 34
  • 89.12 (n)
mouse
(Mus musculus)
Mammalia Rnf4 33 16 34
  • 88.95 (n)
rat
(Rattus norvegicus)
Mammalia Rnf4 33
  • 88.59 (n)
cow
(Bos Taurus)
Mammalia RNF4 33 34
  • 84.41 (n)
oppossum
(Monodelphis domestica)
Mammalia RNF4 34
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RNF4 34
  • 64 (a)
OneToOne
chicken
(Gallus gallus)
Aves RNF4 33 34
  • 70.37 (n)
lizard
(Anolis carolinensis)
Reptilia RNF4 34
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rnf4 33
  • 61.72 (n)
Str.2024 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.5794 33
zebrafish
(Danio rerio)
Actinopterygii im:7142942 33
  • 53.33 (n)
RNF4 34
  • 47 (a)
OneToOne
Dr.17303 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8525 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5143 34
  • 23 (a)
OneToOne
Species where no ortholog for RNF4 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 RNF4 Gene

ENSEMBL:
Gene Tree for RNF4 (if available)
TreeFam:
Gene Tree for RNF4 (if available)

Paralogs for RNF4 Gene

Pseudogenes.org Pseudogenes for RNF4 Gene

genes like me logo Genes that share paralogs with RNF4: view

No data available for Paralogs for RNF4 Gene

Variants for RNF4 Gene

Sequence variations from dbSNP and Humsavar for RNF4 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000069242 -- 2,510,627(+) C/T intron_variant
rs1000103975 -- 2,496,483(+) T/C intron_variant
rs1000158727 -- 2,502,025(+) T/C intron_variant
rs1000185629 -- 2,495,511(+) T/G intron_variant
rs1000330839 -- 2,500,396(+) T/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RNF4 Gene

Variant ID Type Subtype PubMed ID
esv25411 CNV loss 19812545
esv2726835 CNV deletion 23290073
esv2726853 CNV deletion 23290073
esv2823 CNV loss 18987735
esv3599403 CNV loss 21293372
nsv1009347 CNV gain 25217958
nsv1010352 CNV gain 25217958
nsv1123740 CNV deletion 24896259
nsv290753 CNV deletion 16902084
nsv518472 CNV loss 19592680
nsv967718 CNV duplication 23825009

Variation tolerance for RNF4 Gene

Residual Variation Intolerance Score: 82% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.85; 17.82% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RNF4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNF4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RNF4 Gene

Disorders for RNF4 Gene

Additional Disease Information for RNF4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for RNF4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RNF4 Gene

Publications for RNF4 Gene

  1. RNF4 is a poly-SUMO-specific E3 ubiquitin ligase required for arsenic-induced PML degradation. (PMID: 18408734) Tatham MH … Hay RT (Nature cell biology 2008) 3 4 22 58
  2. SUMO-1 promotes association of SNURF (RNF4) with PML nuclear bodies. (PMID: 15707587) Häkli M … Palvimo JJ (Experimental cell research 2005) 3 4 22 58
  3. The RING finger protein RNF4, a co-regulator of transcription, interacts with the TRPS1 transcription factor. (PMID: 12885770) Kaiser FJ … Lüdecke HJ (The Journal of biological chemistry 2003) 3 4 22 58
  4. Identification and characterization of a novel RING-finger gene (RNF4) mapping at 4p16.3. (PMID: 9479498) Chiariotti L … Bruni CB (Genomics 1998) 2 3 4 58
  5. Requirement of PML SUMO interacting motif for RNF4- or arsenic trioxide-induced degradation of nuclear PML isoforms. (PMID: 23028697) Maroui MA … Chelbi-Alix MK (PloS one 2012) 3 4 58

Products for RNF4 Gene

  • Addgene plasmids for RNF4

Sources for RNF4 Gene

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