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Aliases for RYBP Gene

Aliases for RYBP Gene

  • RING1 And YY1 Binding Protein 2 3 5
  • Death Effector Domain-Associated Factor 2 3 4
  • Apoptin-Associating Protein 1 2 3 4
  • YY1 And E4TF1 Associated Factor 1 2 3
  • Ring1 Interactor RYBP 2 3
  • DED-Associated Factor 3 4
  • APAP-1 3 4
  • DEDAF 3 4
  • YEAF1 3 4
  • YY1 And E4TF1-Associated Factor 1 4
  • RING1 And YY1-Binding Protein 3
  • AAP1 3

External Ids for RYBP Gene

Previous GeneCards Identifiers for RYBP Gene

  • GC03M070917
  • GC03M072035
  • GC03M072229
  • GC03M072344
  • GC03M072506

Summaries for RYBP Gene

GeneCards Summary for RYBP Gene

RYBP (RING1 And YY1 Binding Protein) is a Protein Coding gene. Among its related pathways are E2F transcription factor network and Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include transcription corepressor activity. An important paralog of this gene is YAF2.

UniProtKB/Swiss-Prot for RYBP Gene

  • Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1-like complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A Lys-119, rendering chromatin heritably changed in its expressibility (PubMed:25519132). Component of a PRC1-like complex that mediates monoubiquitination of histone H2A Lys-119 on the X chromosome and is required for normal silencing of one copy of the X chromosome in XX females. May stimulate ubiquitination of histone H2A Lys-119 by recruiting the complex to target sites (By similarity). Inhibits ubiquitination and subsequent degradation of TP53, and thereby plays a role in regulating transcription of TP53 target genes (PubMed:19098711). May also regulate the ubiquitin-mediated proteasomal degradation of other proteins like FANK1 to regulate apoptosis (PubMed:14765135, PubMed:27060496). May be implicated in the regulation of the transcription as a repressor of the transcriptional activity of E4TF1 (PubMed:11953439). May bind to DNA (By similarity).

Gene Wiki entry for RYBP Gene

Additional gene information for RYBP Gene

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

Genomics for RYBP Gene

GeneHancer (GH) Regulatory Elements for RYBP Gene

Promoters and enhancers for RYBP 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
GH03I072445 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 579.8 -0.6 -583 4.4 PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 ZNF2 ZNF766 ZNF207 ZNF143 RYBP SHQ1 LOC105377160
GH03I072076 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 27.6 +366.4 366424 6.9 HDGF ATF1 PKNOX1 SMAD1 FEZF1 YBX1 IRF4 YY1 TCF12 ZNF766 RYBP PROK2 GPR27 EIF4E3 LINC00877 FOXP1 ENSG00000276471 ENSG00000273461
GH03I072099 Promoter/Enhancer 1.9 FANTOM5 Ensembl ENCODE dbSUPER 18.2 +345.8 345769 3.7 PKNOX1 MZF1 SIN3A BMI1 IRF4 RAD21 GLIS2 SCRT2 ZNF143 ATF7 RYBP EIF4E3 PROK2 LINC00877 GPR27 CCDC137P LINC00870
GH03I072482 Enhancer 1.4 FANTOM5 Ensembl ENCODE 22.5 -36.5 -36479 1.2 HDAC1 NFRKB FEZF1 BATF IRF4 RAD21 RARA RFX5 YY1 ZNF335 RYBP RNU1-62P GC03P072480 ENSG00000244345
GH03I072268 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 18.5 +176.4 176405 3.6 PKNOX1 ATF1 ETS1 YY1 TCF12 ZNF766 FOS ATF7 RXRA JUNB RYBP LINC00877 LOC105377158 ENSG00000242618
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RYBP on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for RYBP Gene

Genomic Locations for RYBP Gene
chr3:72,371,825-72,446,623
(GRCh38/hg38)
Size:
74,799 bases
Orientation:
Minus strand
chr3:72,420,976-72,496,069
(GRCh37/hg19)

Genomic View for RYBP Gene

Genes around RYBP on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for RYBP Gene

Proteins for RYBP Gene

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

    Protein Symbol:
    Q8N488-RYBP_HUMAN
    Recommended name:
    RING1 and YY1-binding protein
    Protein Accession:
    Q8N488
    Secondary Accessions:
    • Q9P2W5
    • Q9UMW4

    Protein attributes for RYBP Gene

    Size:
    228 amino acids
    Molecular mass:
    24822 Da
    Quaternary structure:
    • Monomer. Component of repressive BCOR complex containing Polycomb group subcomplex at least composed of BCOR, PCGF1, RING1 and RNF2/RING2 (PubMed:16943429). Component of PCR1-like complexes (PubMed:26687479, PubMed:20696397). Interacts with PCGF1 (PubMed:26687479). Part of a PCR1-like complex that contains AUTS2, PCGF5, RNF2, CSNK2B AND RYBP (PubMed:25519132). Interacts with RNF2; the interaction is direct (PubMed:20696397). Interacts with CBX2, YAF2, RING1 and RNF2 (By similarity). Interacts with ubiquitin and ubiquitinated proteins (By similarity). Interacts with ubiquitinated histone H2A (By similarity). Interacts with apoptin, DEDD, FADD, CASP8, CASP10, YY1 and GABPB1 (PubMed:11395500, PubMed:11953439, PubMed:14765135). Together with GABPB1 and YY1, it forms a ternary complex, probably being the bridge factor between these two transcription factors (PubMed:11953439). Interacts with MDM2, and thereby inhibits ubiquitination of TP53 (PubMed:19098711). Identified in a ternary complex containing MDM2, TP53 and RYBP (PubMed:19098711). Interacts with FANK1; may prevent the ubiquitin-mediated proteasomal degradation of FANK1 (PubMed:27060496). Interacts with IFT57 (By similarity).
    SequenceCaution:
    • Sequence=AAK63197.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAO73587.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA89486.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RYBP Gene

neXtProt entry for RYBP Gene

Post-translational modifications for RYBP Gene

Other Protein References for RYBP Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RYBP Gene

Domains & Families for RYBP Gene

Gene Families for RYBP Gene

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

Protein Domains for RYBP Gene

Suggested Antigen Peptide Sequences for RYBP Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8N488

UniProtKB/Swiss-Prot:

RYBP_HUMAN :
  • Intrinsically unstructured in the absence of binding partners. Folds upon binding to DNA or RNF2 (By similarity).
Domain:
  • Intrinsically unstructured in the absence of binding partners. Folds upon binding to DNA or RNF2 (By similarity).
genes like me logo Genes that share domains with RYBP: view

Function for RYBP Gene

Molecular function for RYBP Gene

UniProtKB/Swiss-Prot Function:
Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1-like complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A Lys-119, rendering chromatin heritably changed in its expressibility (PubMed:25519132). Component of a PRC1-like complex that mediates monoubiquitination of histone H2A Lys-119 on the X chromosome and is required for normal silencing of one copy of the X chromosome in XX females. May stimulate ubiquitination of histone H2A Lys-119 by recruiting the complex to target sites (By similarity). Inhibits ubiquitination and subsequent degradation of TP53, and thereby plays a role in regulating transcription of TP53 target genes (PubMed:19098711). May also regulate the ubiquitin-mediated proteasomal degradation of other proteins like FANK1 to regulate apoptosis (PubMed:14765135, PubMed:27060496). May be implicated in the regulation of the transcription as a repressor of the transcriptional activity of E4TF1 (PubMed:11953439). May bind to DNA (By similarity).

Phenotypes From GWAS Catalog for RYBP Gene

Gene Ontology (GO) - Molecular Function for RYBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003714 transcription corepressor activity IEA --
GO:0005515 protein binding IPI 16189514
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RYBP: view
genes like me logo Genes that share phenotypes with RYBP: view

Animal Model Products

miRNA for RYBP Gene

miRTarBase miRNAs that target RYBP

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RYBP Gene

Localization for RYBP Gene

Subcellular locations from UniProtKB/Swiss-Prot for RYBP Gene

Nucleus. Cytoplasm. Nucleus, nucleoplasm. Note=Primarily found in the nucleus. Detected in a punctate pattern likely to represent Polycomb group (PcG) bodies (By similarity). {ECO:0000250 UniProtKB:Q8CCI5}.

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 RYBP gene
Compartment Confidence
nucleus 5
mitochondrion 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RYBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 27060496
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0031519 colocalizes_with PcG protein complex IDA 16943429
genes like me logo Genes that share ontologies with RYBP: view

Pathways & Interactions for RYBP Gene

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

Pathways by source for RYBP Gene

1 Cell Signaling Technology pathway for RYBP Gene
1 BioSystems pathway for RYBP Gene

SIGNOR curated interactions for RYBP Gene

Inactivates:

Gene Ontology (GO) - Biological Process for RYBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006915 apoptotic process IEA --
GO:0007275 multicellular organism development TAS 10369680
genes like me logo Genes that share ontologies with RYBP: view

Drugs & Compounds for RYBP Gene

No Compound Related Data Available

Transcripts for RYBP Gene

mRNA/cDNA for RYBP Gene

(1) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(430) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RYBP Gene

RING1 and YY1 binding protein:
Representative Sequences:

Clone Products

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

No ASD Table

Relevant External Links for RYBP Gene

GeneLoc Exon Structure for
RYBP
ECgene alternative splicing isoforms for
RYBP

Expression for RYBP Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RYBP Gene

This gene is overexpressed in Whole Blood (x4.1).

Protein differential expression in normal tissues from HIPED for RYBP Gene

This gene is overexpressed in Testis (12.6), Peripheral blood mononuclear cells (12.5), Blymphocyte (7.0), Fetal testis (6.2), and Retina (6.0).

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



Protein tissue co-expression partners for RYBP Gene

NURSA nuclear receptor signaling pathways regulating expression of RYBP Gene:

RYBP

SOURCE GeneReport for Unigene cluster for RYBP Gene:

Hs.7910

mRNA Expression by UniProt/SwissProt for RYBP Gene:

Q8N488-RYBP_HUMAN
Tissue specificity: Widely expressed with highest levels in lymphoid tissues and placenta.

Evidence on tissue expression from TISSUES for RYBP Gene

  • Nervous system(4.7)
  • Muscle(4.1)
  • Lung(2.3)
genes like me logo Genes that share expression patterns with RYBP: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for RYBP Gene

Orthologs for RYBP Gene

This gene was present in the common ancestor of animals.

Orthologs for RYBP Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RYBP 33 34
  • 99.85 (n)
cow
(Bos Taurus)
Mammalia RYBP 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RYBP 33 34
  • 97.25 (n)
mouse
(Mus musculus)
Mammalia Rybp 33 34
  • 93.71 (n)
Rybp-ps 16
platypus
(Ornithorhynchus anatinus)
Mammalia RYBP 34
  • 93 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RYBP 34
  • 87 (a)
OneToOne
chicken
(Gallus gallus)
Aves RYBP 33 34
  • 87.52 (n)
lizard
(Anolis carolinensis)
Reptilia RYBP 34
  • 90 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.7862 33
zebrafish
(Danio rerio)
Actinopterygii rybpb 33 34
  • 77.23 (n)
rybpa 34
  • 38 (a)
OneToMany
rybp 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12272 33
fruit fly
(Drosophila melanogaster)
Insecta RYBP 34
  • 51 (a)
OneToMany
Species where no ortholog for RYBP 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)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RYBP Gene

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

Paralogs for RYBP Gene

Paralogs for RYBP Gene

(1) SIMAP similar genes for RYBP Gene using alignment to 2 proteins:

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

Variants for RYBP Gene

Sequence variations from dbSNP and Humsavar for RYBP Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000008590 -- 72,438,495(-) A/T intron_variant
rs1000046401 -- 72,394,988(-) A/G intron_variant
rs1000146249 -- 72,410,939(-) G/A intron_variant
rs1000165018 -- 72,434,031(-) T/A intron_variant
rs1000339555 -- 72,411,495(-) T/C intron_variant

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

Variant ID Type Subtype PubMed ID
esv1338763 CNV deletion 17803354
esv3303471 CNV mobile element insertion 20981092
esv3325196 CNV insertion 20981092
esv990953 CNV deletion 20482838
nsv954886 CNV duplication 24416366

Additional Variant Information for RYBP Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for RYBP Gene

Disorders for RYBP Gene

Additional Disease Information for RYBP

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

No disorders were found for RYBP Gene.

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

Publications for RYBP Gene

  1. Polycomb group and SCF ubiquitin ligases are found in a novel BCOR complex that is recruited to BCL6 targets. (PMID: 16943429) Gearhart MD … Bardwell VJ (Molecular and cellular biology 2006) 3 4 22 58
  2. The death effector domain-associated factor plays distinct regulatory roles in the nucleus and cytoplasm. (PMID: 11395500) Zheng L … Lenardo MJ (The Journal of biological chemistry 2001) 3 4 22 58
  3. Proapoptotic RYBP interacts with FANK1 and induces tumor cell apoptosis through the AP-1 signaling pathway. (PMID: 27060496) Ma W … Chen D (Cellular signalling 2016) 3 4 58
  4. The variant Polycomb Repressor Complex 1 component PCGF1 interacts with a pluripotency sub-network that includes DPPA4, a regulator of embryogenesis. (PMID: 26687479) Oliviero G … Cagney G (Scientific reports 2015) 3 4 58
  5. An AUTS2-Polycomb complex activates gene expression in the CNS. (PMID: 25519132) Gao Z … Reinberg D (Nature 2014) 3 4 58

Products for RYBP Gene

Sources for RYBP Gene

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