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RIPPLY3 Gene

protein-coding   GIFtS: 30
GCID: GC21P038379

Ripply Transcriptional Repressor 3

(Previous names: Down syndrome critical region gene 6, ripply3 homolog (zebrafish))
(Previous symbol: DSCR6)
  See RIPPLY3-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Ripply Transcriptional Repressor 31 2     Ripply3 Homolog (Zebrafish)1
DSCR61 2 3 5     Protein Ripply32
Down Syndrome Critical Region Gene 61 2     Ripply3 Homolog2
Down Syndrome Critical Region Protein 62 3     

External Ids:    HGNC: 30471   Entrez Gene: 538202   Ensembl: ENSG000001831457   OMIM: 6098925   UniProtKB: P570553   
ORGUL members:         

Export aliases for RIPPLY3 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for RIPPLY3 Gene:
RIPPLY3 (ripply transcriptional repressor 3) is a protein-coding gene. Diseases associated with RIPPLY3 include down syndrome.

UniProtKB/Swiss-Prot: DSCR6_HUMAN, P57055
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)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Search for regulatory transcription factor binding sites for RIPPLY3
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for RIPPLY3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RIPPLY3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 21q22.2   Ensembl cytogenetic band:  21q22.13   HGNC cytogenetic band: 21q22.2

RIPPLY3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RIPPLY3 gene location

GeneLoc information about chromosome 21         GeneLoc Exon Structure

GeneLoc location for GC21P038379:  view genomic region     (about GC identifiers)

Start:
38,378,450 bp from pter      End:
38,391,959 bp from pter
Size:
13,510 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: DSCR6_HUMAN, P57055 (See protein sequence)
Recommended Name: Protein ripply3  
Size: 190 amino acids; 20368 Da
Subunit: Interacts with TBX1 (By similarity)
Alternative splicing: 2 isoforms:  P57055-1   P57055-2   

Explore the universe of human proteins at neXtProt for RIPPLY3: NX_P57055

Explore proteomics data for RIPPLY3 at MOPED


See RIPPLY3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_061835.1  
ENSEMBL proteins: 
 ENSP00000331734  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR028127 Ripply_fam

Graphical View of Domain Structure for InterPro Entry P57055

ProtoNet protein and cluster: P57055

UniProtKB/Swiss-Prot: DSCR6_HUMAN, P57055
Domain: The Ripply homology domain and the WRPW motif are both necessary for its transcriptional corepressor
activity on the transcription activator TBX1 (By similarity)
Domain: The WRPW motif is required for binding to tle/groucho proteins (By similarity)
Similarity: Belongs to the ripply family


Find genes that share domains with RIPPLY3           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: DSCR6_HUMAN, P57055
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)

     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding ----
     
Find genes that share ontologies with RIPPLY3           About GenesLikeMe


Phenotypes:
     9 MGI mutant phenotypes (inferred from 1 allele(MGI details for Ripply3):
 cardiovascular system  cellular  craniofacial  embryogenesis  endocrine/exocrine gland 
 hematopoietic system  homeostasis/metabolism  immune system  mortality/aging 

Find genes that share phenotypes with RIPPLY3           About GenesLikeMe

Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
DSCR6_HUMAN, P57055: Nucleus (By similarity)

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus NAS10814524

Find genes that share ontologies with RIPPLY3           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RIPPLY3
Interactions:

    Search GeneGlobe Interaction Network for RIPPLY3

Gene Ontology (GO): 5 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000122negative regulation of transcription from RNA polymerase II promoter IEA--
GO:0006351transcription, DNA-templated IEA--
GO:0007507heart development IEA--
GO:0008150biological_process ND--
GO:0060037pharyngeal system development IEA--

Find genes that share ontologies with RIPPLY3           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for RIPPLY3 (DSCR6)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for RIPPLY3 gene: 
NM_018962.2  

3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000485272(uc011aec.2 uc010gnd.3) ENST00000490393 ENST00000329553(uc002yvv.3)

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8 AceView cDNA sequences:

AW664559 NM_018962 AW270732 AB037159 AI688564 AB037158 AB037160 AB037161 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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RIPPLY3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
RIPPLY3 Expression
About this image


RIPPLY3 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 Endoderm (Gastrulation Derivatives)
         Definitive endoderm-like cells
 
 Neural Tube (Nervous System)
         Floor plate-like cells
RIPPLY3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

RIPPLY3 Protein Expression

UniProtKB/Swiss-Prot: DSCR6_HUMAN, P57055
Tissue specificity: Expressed at a low level in fetal kidney and fetal brain

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In Situ
Assay Products:
 

 
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of chordates.

Orthologs for RIPPLY3 gene from Selected species (see all 8)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ripply31 , 5 ripply3 homolog (zebrafish)1, 5 68.28(n)1
64.52(a)1
  16 (55.17 cM)5
1707651  NM_133229.21  NP_573492.21 
 943284205 
chicken
(Gallus gallus)
Aves DSCR61 Down syndrome critical region gene 6 58.67(n)
48(a)
  101749102  XM_004934542.1  XP_004934599.1 
zebrafish
(Danio rerio)
Actinopterygii ripply36
ripply3
37(a)
1 ↔ 1
10(162944-166288) ENSDARG00000036974


ENSEMBL Gene Tree for RIPPLY3 (if available)
TreeFam Gene Tree for RIPPLY3 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for RIPPLY3 gene

Find genes that share paralogs with RIPPLY3           About GenesLikeMe


1 Pseudogenes.org Pseudogene for RIPPLY3
PGOHUM00000247774


(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for RIPPLY3 (see all 368)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 21 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1127650451,2
C--28930538(+) TGGCAT/-TTTTT 1 -- int11Minor allele frequency- -:0.50CSA 2
rs1845290271,2
--38377004(+) CACCGC/TGCCCT 1 -- us2k10--------
rs1890091781,2
--38377059(+) TGGTAA/CCTTAT 1 -- us2k10--------
rs16218351,2
C,H--38377108(+) TAGCCT/GCCTCC 1 -- us2k16Minor allele frequency- G:0.00NS EA NA 422
rs2018054031,2
--38377219(+) TCTTC-/GGATTT 1 -- us2k10--------
rs713285381,2
C--38377221(+) TTCGAT/-TTTTT 1 -- us2k11Minor allele frequency- -:0.50NA 2
rs771671751,2
C,F--38377221(+) CTTCGA/GTTTTT 1 -- us2k12Minor allele frequency- G:0.19WA 120
rs1418887711,2
--38377247(+) TTGAGA/GCAGAG 1 -- us2k10--------
rs1462664191,2
--38377320(+) CTCCCA/GAGTTC 1 -- us2k10--------
rs1149327081,2
F--38377412(+) TCTTAG/ATGGAT 1 -- us2k11Minor allele frequency- A:0.05WA 118

HapMap Linkage Disequilibrium report for RIPPLY3 (38378450 - 38391959 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for RIPPLY3: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing RIPPLY3
DNA2.0 Custom Variant and Variant Library Synthesis for RIPPLY3

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 609892    OMIM disorders: --

1 disease for RIPPLY3:    
About MalaCards
down syndrome


Find genes that share disorders with RIPPLY3           About GenesLikeMe


Export disorders for RIPPLY3 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for RIPPLY3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with RIPPLY3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Isolation of two novel genes, DSCR5 and DSCR6, from Down syndrome critical region on human chromosome 21q22.2. (PubMed id 10814524)1, 2, 3 Shibuya K....Shimizu N. (Biochem. Biophys. Res. Commun. 2000)
  2. RIPPLY3 is a retinoic acid-inducible repressor required for setting the borders of the pre-placodal ectoderm. (PubMed id 22354841)1, 3 Janesick A....Blumberg B. (Development 2012)
  3. Groucho-associated transcriptional repressor ripply1 is required for proper transition from the presomitic mesoderm to somites. (PubMed id 16326386)2 Kawamura A....Takada S. (Dev. Cell 2005)
  4. The DNA sequence of human chromosome 21. (PubMed id 10830953)1 Hattori M.... Yaspo M.-L. (Nature 2000)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 53820 HGNC: 3047 AceView: DSCR6 Ensembl:ENSG00000183145 euGenes: HUgn53820
ECgene: RIPPLY3 H-InvDB: RIPPLY3

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for RIPPLY3 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for RIPPLY3 gene:
Search GeneIP for patents involving RIPPLY3

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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 Browse ESI BIO Cell Lines and PureStem Progenitors for RIPPLY3
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 SwitchGear 3'UTR luciferase reporter plasmids for RIPPLY3
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 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RIPPLY3
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RIPPLY3
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for RIPPLY3
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Customized transgenic rodents for:
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 Search Addgene for plasmids for RIPPLY3
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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