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

External Ids for RYBP Gene

Previous GeneCards Identifiers for RYBP Gene

  • GC03M070917
  • GC03M072035
  • GC03M072229
  • GC03M072344
  • GC03M072506
  • GC03M072420

Summaries for RYBP Gene

GeneCards Summary for RYBP Gene

RYBP (RING1 And YY1 Binding Protein) is a Protein Coding gene. Diseases associated with RYBP include Kidney Leiomyosarcoma and Lymphoma, Hodgkin, Classic. 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 Summary 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). May play a role in the repression of tumor growth and metastasis in breast cancer by down-regulating SRRM3 (PubMed:27748911).

Gene Wiki entry for RYBP Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RYBP Gene

Genomics for RYBP Gene

GeneHancer (GH) Regulatory Elements Pubs

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
GH03J072444 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 279.7 -0.3 -268 5 ZNF207 MYC NCOR1 IKZF1 ZNF600 JUND ZNF592 ZNF223 POLR2A ZIC2 RYBP HSALNG0026813 lnc-GXYLT2-10 SHQ1 MG828644 GXYLT2
GH03J072076 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 27.6 +366.4 366424 6.9 BCLAF1 ZNF207 NCOR1 POLR2A NFIC SMAD5 HES1 BHLHE40 FEZF1 ZNF341 RYBP PROK2 GPR27 EIF4E3 LINC00877 FOXP1 ENSG00000276471 ENSG00000273461
GH03J072099 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 18.2 +345.9 345870 3.9 BCLAF1 SP1 ZNF600 CEBPA POLR2A ZIC2 BCL11A CTCF FOXA1 SIN3A LINC00877 RYBP EIF4E3 PROK2 GPR27 CCDC137P LINC00870
GH03J072455 Enhancer 1 FANTOM5 Ensembl ENCODE 35.5 -8.3 -8278 4.6 CEBPA YY1 CTCF BHLHE40 RXRA TAL1 PRDM10 JUND HNF4A RAD21 RYBP HSALNG0026815 MG828644 GXYLT2
GH03J072268 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 18.5 +176.4 176405 3.6 MYC NCOR1 IKZF1 JUND ZNF592 ZMYM3 ATF2 CEBPA ATF3 YY1 RYBP RF01061-115 AB372778-022 LINC00877 PROK2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RYBP on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RYBP

Top Transcription factor binding sites by QIAGEN in the RYBP gene promoter:
  • AP-2alpha
  • AP-2alpha isoform 2
  • AP-2alpha isoform 3
  • AP-2alpha isoform 4
  • AP-2alphaA

Genomic Locations for RYBP Gene

Latest Assembly
chr3:72,371,825-72,446,623
(GRCh38/hg38)
Size:
74,799 bases
Orientation:
Minus strand

Previous Assembly
chr3:72,423,744-72,495,774
(GRCh37/hg19 by Entrez Gene)
Size:
72,031 bases
Orientation:
Minus strand

chr3:72,420,976-72,496,069
(GRCh37/hg19 by Ensembl)
Size:
75,094 bases
Orientation:
Minus strand

Alternative Locations (GRCh38/hg38)

  • chr3(PATCHES):49,167-122,044 (-)

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=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAO73587.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAA89486.1; Type=Erroneous initiation; Note=Truncated N-terminus.; 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

InterPro:
Blocks:
  • Zn-finger, Ran-binding

Suggested Antigen Peptide Sequences for RYBP Gene

GenScript: Design optimal peptide antigens:
  • YY1 and E4TF1-associated factor 1 (RYBP_HUMAN)

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). May play a role in the repression of tumor growth and metastasis in breast cancer by down-regulating SRRM3 (PubMed:27748911).

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 IBA 21873635
GO:0003712 transcription coregulator activity IBA 21873635
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 Models for RYBP Gene

MGI Knock Outs for RYBP:
  • Rybp Rybp<tm1Nisa>

miRNA for RYBP Gene

miRTarBase miRNAs that target RYBP

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RYBP

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
plasma membrane 1
extracellular 1
cytoskeleton 1

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 IBA,IDA 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 BioSystems pathway for RYBP Gene
1 Cell Signaling Technology 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:0006355 regulation of transcription, DNA-templated IBA 21873635
GO:0006915 apoptotic process IEA --
GO:0007275 multicellular organism development TAS 10369680
GO:0032435 negative regulation of proteasomal ubiquitin-dependent protein catabolic process IMP 27060496
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 :
9 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RYBP

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

No ASD Table

Relevant External Links for RYBP Gene

GeneLoc Exon Structure for
RYBP

Expression for RYBP Gene

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



Protein tissue co-expression partners for RYBP Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RYBP

SOURCE GeneReport for Unigene cluster for RYBP Gene:

Hs.7910

mRNA Expression by UniProt/SwissProt for RYBP Gene:

Q8N488-RYBP_HUMAN
Tissue specificity: Down-regulated in breast cancer tissues and in several breast cancer cell lines (at protein level) (PubMed:27748911). Widely expressed with highest levels in lymphoid tissues and placenta.

Evidence on tissue expression from TISSUES for RYBP Gene

  • Nervous system(4.7)
  • Muscle(4.4)
  • Lung(2.7)
  • Blood(2.2)
  • Kidney(2)
  • Skin(2)
genes like me logo Genes that share expression patterns with RYBP: view

Primer products for research

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 29 30
  • 99.85 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RYBP 30
  • 99 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia RYBP 29 30
  • 97.25 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Rybp 29 16 30
  • 93.71 (n)
OneToOne
Rybp-ps 16
Platypus
(Ornithorhynchus anatinus)
Mammalia RYBP 30
  • 93 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia RYBP 30
  • 87 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RYBP 29 30
  • 87.52 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RYBP 30
  • 90 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.7862 29
Zebrafish
(Danio rerio)
Actinopterygii rybpb 29 30
  • 77.23 (n)
OneToMany
rybpa 30
  • 38 (a)
OneToMany
rybp 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12272 29
Fruit Fly
(Drosophila melanogaster)
Insecta RYBP 30
  • 51 (a)
OneToMany
Species where no ortholog for RYBP was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for RYBP: view image
Alliance of Genome Resources:
Additional Orthologs for RYBP

Paralogs for RYBP Gene

Paralogs for RYBP Gene

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

  • RYBP_HUMAN
  • L8ECE1_HUMAN
genes like me logo Genes that share paralogs with RYBP: view

Variants for RYBP Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RYBP Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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
Leiden Open Variation Database (LOVD)
RYBP

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Variation tolerance for RYBP Gene

Disorders for RYBP Gene

MalaCards: The human disease database

(3) MalaCards diseases for RYBP Gene - From: COP and GCD

Disorder Aliases PubMed IDs
kidney leiomyosarcoma
  • leiomyosarcoma of kidney
lymphoma, hodgkin, classic
  • chl
breast cancer
  • breast cancer, familial
- elite association - COSMIC cancer census association via MalaCards
Search RYBP in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RYBP

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with RYBP: view

No data available for 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
  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
  3. RING1 and YY1 binding protein suppresses breast cancer growth and metastasis. (PMID: 27748911) Zhou H … Wang S (International journal of oncology 2016) 3 4
  4. 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
  5. 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

Products for RYBP Gene

Sources for RYBP Gene