RIPPLY3 Gene (Protein Coding)

Ripply Transcriptional Repressor 3

GC21P037006
GIFtS:
30
See more...

Aliases for RIPPLY3 Gene

Aliases for RIPPLY3 Gene

  • Ripply Transcriptional Repressor 3 2 3 5
  • Down Syndrome Critical Region Protein 6 3 4
  • Down Syndrome Critical Region Gene 6 2 3
  • Protein Ripply3 3 4
  • DSCR6 3 4
  • Ripply3 Homolog (Zebrafish) 2
  • Ripply3 Homolog 3
  • RIPPLY3 5

External Ids for RIPPLY3 Gene

Previous HGNC Symbols for RIPPLY3 Gene

  • DSCR6

Previous GeneCards Identifiers for RIPPLY3 Gene

  • GC21P038379

Summaries for RIPPLY3 Gene

GeneCards Summary for RIPPLY3 Gene

RIPPLY3 (Ripply Transcriptional Repressor 3) is a Protein Coding gene. Diseases associated with RIPPLY3 include Down Syndrome and Cardiomyopathy, Dilated, 1J. An important paralog of this gene is RIPPLY1.

UniProtKB/Swiss-Prot Summary for RIPPLY3 Gene

  • Acts as a transcriptional corepressor. Negative regulator of the transcriptional activity of TBX1. Plays a role in the development of the pharyngeal apparatus and derivatives (By similarity).

Additional gene information for RIPPLY3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RIPPLY3 Gene

Genomics for RIPPLY3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RIPPLY3 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
GH21J037007 Promoter 1.1 EPDnew Ensembl 250.7 +0.7 651 1.6 ELF1 ZBTB48 ZBTB33 L3MBTL2 ZNF202 EZH2 ZFX MTA1 RAD21 ZBTB20 RIPPLY3 HLCS ENSG00000242553 SETD4 MORC3 DYRK1A RIMKLBP1 piR-50437-421 PIGP
GH21J036976 Promoter/Enhancer 1.4 FANTOM5 Ensembl ENCODE 12.1 -29.0 -28997 1.1 TBP DEK CTCF BHLHE40 ARNT REST NFATC3 VEZF1 NBN IRF4 HLCS TTC3 RIPPLY3 PIGP DYRK1A lnc-PIGP-2 hsa-miR-5095-325 SIM2
GH21J037082 Enhancer 0.9 Ensembl 11.5 +77.4 77351 2.2 CEBPA FOXA1 HOMEZ THAP11 CEBPB FOXA2 SMAD4 SAP130 RXRA MIER3 TTC3 PIGP MRPL20P1 HLCS ENSG00000207416 RIPPLY3 TTC3-AS1 ENSG00000242553 VPS26C HSALNG0132978
GH21J037026 Enhancer 0.4 Ensembl 13.1 +20.6 20551 0.2 ZBTB17 POLR2A SREBF1 RIPPLY3 MRPL20P1 ENSG00000207416 HLCS piR-50437-421 PIGP
GH21J036707 Promoter/Enhancer 1.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 1.3 -298.8 -298849 5 CTCF ZIC2 CBX8 MAX ZNF189 ZNF148 POLR2A EZH2 RAD21 USF1 SIM2 RIPPLY3 ENSG00000224269 HSALNG0132958 LOC107985492 HLCS
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RIPPLY3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RIPPLY3

Genomic Locations for RIPPLY3 Gene

Latest Assembly
chr21:37,006,150-37,019,662
(GRCh38/hg38)
Size:
13,513 bases
Orientation:
Plus strand

Previous Assembly
chr21:38,378,450-38,391,962
(GRCh37/hg19 by Entrez Gene)
Size:
13,513 bases
Orientation:
Plus strand

chr21:38,378,450-38,391,959
(GRCh37/hg19 by Ensembl)
Size:
13,510 bases
Orientation:
Plus strand

Genomic View for RIPPLY3 Gene

Genes around RIPPLY3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RIPPLY3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RIPPLY3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RIPPLY3 Gene

Proteins for RIPPLY3 Gene

Products:

  1. Antibodies for research
  2. Protein products for research
  3. Assay products for research

  • Protein details for RIPPLY3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P57055-DSCR6_HUMAN
    Recommended name:
    Protein ripply3
    Protein Accession:
    P57055

    Protein attributes for RIPPLY3 Gene

    Size:
    190 amino acids
    Molecular mass:
    20368 Da
    Quaternary structure:
    • Interacts with TBX1.

    Alternative splice isoforms for RIPPLY3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RIPPLY3 Gene

Protein Expression for RIPPLY3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for RIPPLY3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RIPPLY3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RIPPLY3 Gene

Domains & Families for RIPPLY3 Gene

Gene Families for RIPPLY3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RIPPLY3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RIPPLY3 Gene

GenScript: Design optimal peptide antigens:
  • Down syndrome critical region protein 6 (DSCR6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P57055

UniProtKB/Swiss-Prot:

DSCR6_HUMAN :
  • The Ripply homology domain and the WRPW motif are both necessary for its transcriptional corepressor activity on the transcription activator TBX1.
  • Belongs to the ripply family.
Domain:
  • The Ripply homology domain and the WRPW motif are both necessary for its transcriptional corepressor activity on the transcription activator TBX1.
  • The WRPW motif is required for binding to tle/groucho proteins.
Family:
  • Belongs to the ripply family.
genes like me logo Genes that share domains with RIPPLY3: view

Function for RIPPLY3 Gene

Products:

  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for RIPPLY3 Gene

UniProtKB/Swiss-Prot Function:
Acts as a transcriptional corepressor. Negative regulator of the transcriptional activity of TBX1. Plays a role in the development of the pharyngeal apparatus and derivatives (By similarity).

Phenotypes From GWAS Catalog for RIPPLY3 Gene

Gene Ontology (GO) - Molecular Function for RIPPLY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 30241482
genes like me logo Genes that share ontologies with RIPPLY3: view
genes like me logo Genes that share phenotypes with RIPPLY3: view

Animal Models for RIPPLY3 Gene

MGI Knock Outs for RIPPLY3:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RIPPLY3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RIPPLY3 Gene

Localization for RIPPLY3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RIPPLY3 Gene

Nucleus.

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 RIPPLY3 gene
Compartment Confidence
nucleus 4
cytosol 2
extracellular 1
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for RIPPLY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,NAS 10814524
genes like me logo Genes that share ontologies with RIPPLY3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RIPPLY3 Gene

Pathways & Interactions for RIPPLY3 Gene

PathCards logo

SuperPathways for RIPPLY3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RIPPLY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA,IBA 21873635
GO:0007275 multicellular organism development IEA --
GO:0007507 heart development IEA --
GO:0008150 biological_process ND --
GO:0008285 negative regulation of cell proliferation IEA --
genes like me logo Genes that share ontologies with RIPPLY3: view

No data available for Pathways by source and SIGNOR curated interactions for RIPPLY3 Gene

Drugs & Compounds for RIPPLY3 Gene

Products:

  1. Drug products for research
No Compound Related Data Available

Transcripts for RIPPLY3 Gene

Products:

  1. CRISPR products for research
  2. miRNA products for research
  3. Inhibitory RNAs for research
  4. Clone products for research

mRNA/cDNA for RIPPLY3 Gene

3 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
3 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 RIPPLY3

Alternative Splicing Database (ASD) splice patterns (SP) for RIPPLY3 Gene

No ASD Table

Relevant External Links for RIPPLY3 Gene

GeneLoc Exon Structure for
RIPPLY3

Expression for RIPPLY3 Gene

Products:

  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RIPPLY3 Gene

mRNA expression in normal human tissues for RIPPLY3 Gene
mRNA expression by GTEx for RIPPLY3 GenemRNA expression by BioGPS for RIPPLY3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RIPPLY3 Gene

This gene is overexpressed in Brain - Putamen (basal ganglia) (x5.2), Prostate (x4.7), Bladder (x4.5), and Brain - Caudate (basal ganglia) (x4.1).

Protein differential expression in normal tissues from HIPED for RIPPLY3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (53.2) and Platelet (15.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for RIPPLY3 Gene



Protein tissue co-expression partners for RIPPLY3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RIPPLY3

mRNA Expression by UniProt/SwissProt for RIPPLY3 Gene:

P57055-DSCR6_HUMAN
Tissue specificity: Expressed at a low level in fetal kidney and fetal brain.

Evidence on tissue expression from TISSUES for RIPPLY3 Gene

  • Nervous system(4.3)
  • Eye(4)
genes like me logo Genes that share expression patterns with RIPPLY3: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for RIPPLY3 Gene

Orthologs for RIPPLY3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RIPPLY3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia DSCR6 30
  • 99.12 (n)
RIPPLY3 31
  • 98 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia DSCR6 30
  • 74.13 (n)
RIPPLY3 31
  • 60 (a)
 OneToOne
Cow
(Bos Taurus)
 Mammalia RIPPLY3 30 31
  • 71.56 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Ripply3 30 17 31
  • 68.28 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Ripply3 30
  • 68.04 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia RIPPLY3 31
  • 55 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves DSCR6 30
  • 58.67 (n)
RIPPLY3 31
  • 51 (a)
 OneToOne
Zebrafish
(Danio rerio)
 Actinopterygii ripply3 31
  • 37 (a)
 OneToOne
Species where no ortholog for RIPPLY3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • 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 RIPPLY3 Gene

ENSEMBL:
Gene Tree for RIPPLY3 (if available)
TreeFam:
Gene Tree for RIPPLY3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RIPPLY3: view image

Paralogs for RIPPLY3 Gene

Paralogs for RIPPLY3 Gene

Pseudogenes.org Pseudogenes for RIPPLY3 Gene

genes like me logo Genes that share paralogs with RIPPLY3: view

Variants for RIPPLY3 Gene

Products:

  1. SNP Genotyping and Copy Number Assays for research

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RIPPLY3 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 RIPPLY3 Gene

Variant ID Type Subtype PubMed ID
esv2751929 CNV gain 17911159
esv2763684 CNV gain+loss 21179565
esv3568184 CNV loss 25503493

Variation tolerance for RIPPLY3 Gene

Residual Variation Intolerance Score: 84.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.22; 40.01% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RIPPLY3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RIPPLY3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RIPPLY3 Gene

Disorders for RIPPLY3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for RIPPLY3 Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RIPPLY3

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 RIPPLY3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RIPPLY3 Gene

Publications for RIPPLY3 Gene

  1. Isolation of two novel genes, DSCR5 and DSCR6, from Down syndrome critical region on human chromosome 21q22.2. (PMID: 10814524) Shibuya K … Shimizu N (Biochemical and biophysical research communications 2000) 2 3 4
  2. RIPPLY3 is a retinoic acid-inducible repressor required for setting the borders of the pre-placodal ectoderm. (PMID: 22354841) Janesick A … Blumberg B (Development (Cambridge, England) 2012) 2 3
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. A loss-of-function mutation p.T52S in RIPPLY3 is a potential predisposing genetic risk factor for Chinese Han conotruncal heart defect patients without the 22q11.2 deletion/duplication. (PMID: 30241482) Hong N … Sun K (Journal of translational medicine 2018) 3
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3

ExternalLinks

View latest publications for RIPPLY3 gene in Mastermind

Products for RIPPLY3 Gene

Sources for RIPPLY3 Gene