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RIPPLY1 Gene

protein-coding   GIFtS: 40
GCID: GC0XM106143

Ripply Transcriptional Repressor 1

(Previous name: ripply1 homolog (zebrafish))
  See 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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Aliases
Ripply Transcriptional Repressor 11 2
Ripply1 Homolog (Zebrafish)1
Protein Ripply12
Ripply1 Homolog2

External Ids:    HGNC: 251171   Entrez Gene: 921292   Ensembl: ENSG000001472237   OMIM: 3005755   UniProtKB: Q0D2K33   

Export aliases for RIPPLY1 gene to outside databases

Previous GC identifers: GC0XM106029 GC0XM095771


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RIPPLY1 Gene:
This gene encodes a protein similar to a zebrafish protein which acts as a transcriptional repressor in and is
required for somite segmentation in zebrafish embryos (PMID: 16326386). Multiple transcript variants encoding
different isoforms have been found for this gene. (provided by RefSeq, Aug 2011)

GeneCards Summary for RIPPLY1 Gene:
RIPPLY1 (ripply transcriptional repressor 1) is a protein-coding gene. Diseases associated with RIPPLY1 include pancreatitis. An important paralog of this gene is RIPPLY2.

UniProtKB/Swiss-Prot: RIPP1_HUMAN, Q0D2K3
Function: Plays a role in somitogenesis. Essential for transcriptional repression of the segmental patterning
genes, thus terminating the segmentation program in the presomitic mesoderm, and also required for the
maintenance of rostrocaudal polarity in somites (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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RefSeq DNA sequence:
NC_000023.11  NC_018934.2  NT_011651.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the RIPPLY1 gene promoter:
         STAT1   AML1a   STAT1beta   STAT1alpha   AREB6   STAT2   FOXO1a   STAT3   FOXO1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RIPPLY1


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

Entrez Gene cytogenetic band: Xq22.3   Ensembl cytogenetic band:  Xq22.3   HGNC cytogenetic band: Xq22.3

RIPPLY1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RIPPLY1 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM106143:  view genomic region     (about GC identifiers)

Start:
106,143,293 bp from pter      End:
106,146,565 bp from pter
Size:
3,273 bases      Orientation:
minus 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: RIPP1_HUMAN, Q0D2K3 (See protein sequence)
Recommended Name: Protein ripply1  
Size: 151 amino acids; 16379 Da
Sequence caution: Sequence=AAI10437.1; Type=Miscellaneous discrepancy; Note=Intron retention; Sequence=CAI40159.1;
Type=Erroneous initiation; Sequence=CAI40160.1; Type=Erroneous initiation;
Secondary accessions: A0JP63 Q0VGB3 Q5JRB8 Q5JRB9
Alternative splicing: 2 isoforms:  Q0D2K3-1   Q0D2K3-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for RIPPLY1: NX_Q0D2K3

Explore proteomics data for RIPPLY1 at MOPED


See RIPPLY1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001165177.1  NP_612391.1  

ENSEMBL proteins: 
 ENSP00000276173   ENSP00000400539  

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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 Q0D2K3

ProtoNet protein and cluster: Q0D2K3

UniProtKB/Swiss-Prot: RIPP1_HUMAN, Q0D2K3
Domain: The ripply homology domain is required for transcriptional repression (By similarity)
Domain: The WRPW motif is required for binding to TLE/GROUCHO proteins (By similarity)
Similarity: Belongs to the ripply family


RIPPLY1 for domains           About GeneDecksing


(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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: RIPP1_HUMAN, Q0D2K3
Function: Plays a role in somitogenesis. Essential for transcriptional repression of the segmental patterning
genes, thus terminating the segmentation program in the presomitic mesoderm, and also required for the
maintenance of rostrocaudal polarity in somites (By similarity)

Phenotypes:
     3 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Ripply1):

 embryogenesis  no phenotypic analysis  skeleton 

RIPPLY1 for phenotypes           About GeneDecksing

Animal Models:
     MGI mouse knock-out Ripply1tm1.1Sjt for RIPPLY1

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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
RIPP1_HUMAN, Q0D2K3: Nucleus (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus4
extracellular2
cytosol1

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

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus ISS--

RIPPLY1 for ontologies           About GeneDecksing


(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 RIPPLY1
Interactions:

    Search GeneGlobe Interaction Network for RIPPLY1

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

GO IDQualified GO termEvidencePubMed IDs
GO:0001757somite specification ISS--
GO:0006351transcription, DNA-templated IEA--
GO:0009880embryonic pattern specification ISS--
GO:0032525somite rostral/caudal axis specification ISS--
GO:0045892negative regulation of transcription, DNA-templated ISS--

RIPPLY1 for ontologies           About GeneDecksing



(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 RIPPLY1 (RIPP1)



(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,
Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for RIPPLY1 gene (2 alternative transcripts): 
NM_001171706.1  NM_138382.2  

Unigene Cluster for RIPPLY1:

Ripply1 homolog (zebrafish)
Hs.334726  [show with all ESTs]
Unigene Representative Sequence: NM_138382
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000276173(uc004emr.2 uc004ems.2) ENST00000411805
miRNA
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hsa-miR-629* hsa-miR-4279
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Additional mRNA sequence: 

BC007652.1 BC101998.1 BC105691.1 BC105692.1 BC127250.1 

3 DOTS entries:

DT.40112895  DT.100014175  DT.100746819 

13 AceView cDNA sequences:

BC009313 BC007652 BE378966 N51709 AW452146 CF529346 CF529342 BX106639 
CB989767 AI910686 N51797 BU595706 BF307611 

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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RIPPLY1 expression in normal human tissues (normalized intensities)      RIPPLY1 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CAAGGTTGGG
RIPPLY1 Expression
About this image


RIPPLY1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 
 NULL (Uncategorized)
         Mesoderm-like cells
RIPPLY1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

RIPPLY1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.334726
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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 RIPPLY1 gene from Selected species (see all 7)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ripply15 ripply1 homolog (zebrafish)   --   X (61.35 cM) 139779549 
chicken
(Gallus gallus)
Aves RIPPLY16
ripply transcriptional repressor 1
43(a)
1 ↔ 1
4(10917000-10918178)
zebrafish
(Danio rerio)
Actinopterygii ripply16
ripply1
36(a)
1 ↔ 1
21(36930713-36937075) ENSDARG00000054103


ENSEMBL Gene Tree for RIPPLY1 (if available)
TreeFam Gene Tree for RIPPLY1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for RIPPLY1 gene
RIPPLY22  
1 SIMAP similar gene for RIPPLY1 using alignment to 1 protein entry:     RIPP1_HUMAN:
RIPPLY2

RIPPLY1 for paralogs           About GeneDecksing



(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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Structural Variations
     Database of Genomic Variants (DGV) 1 variation for RIPPLY1:    About this table    
Variant IDTypeSubtypePubMed ID
esv2752312CNV Gain17911159

Locus Specific Mutation Databases (LSDB): RIPPLY1

Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 300575    OMIM disorders: --

1 disease for RIPPLY1:    About MalaCards
pancreatitis


RIPPLY1 for disorders           About GeneDecksing


Export disorders for RIPPLY1 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 RIPPLY1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with RIPPLY1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Groucho-associated transcriptional repressor ripply1 is required for proper transition from the presomitic mesoderm to somites. (PubMed id 16326386)1, 2 Kawamura A....Takada S. (Dev. Cell 2005)
  2. Common genetic variants in the CLDN2 and PRSS1-PRSS2 loci alter risk for alcohol-related and sporadic pancreatitis. (PubMed id 23143602)1 Whitcomb D.C....Devlin B. (Nat. Genet. 2012)
  3. Analysis of Ripply1/2-deficient mouse embryos reveals a mechanism underlying the rostro-caudal patterning within a somite. (PubMed id 20346937)1 Takahashi J....Takada S. (Dev. Biol. 2010)
  4. The DNA sequence of the human X chromosome. (PubMed id 15772651)2 Ross M.T.... Bentley D.R. (Nature 2005)
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(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: 92129 HGNC: 25117 AceView: LOC92129 Ensembl:ENSG00000147223 euGenes: HUgn92129
ECgene: RIPPLY1 H-InvDB: RIPPLY1

(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 RIPPLY1 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 RIPPLY1 gene:
Search GeneIP for patents involving RIPPLY1

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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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 Protein Production and Purification
 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RIPPLY1
 Browse SwitchGear 3'UTR luciferase reporter plasmids for RIPPLY1
 Browse SwitchGear Promoter luciferase reporter plasmids for RIPPLY1
 Search ThermoFisher Antibodies for RIPPLY1
 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RIPPLY1
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RIPPLY1
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for RIPPLY1
 Search LSBio for Antibodies for RIPPLY1
Customized transgenic rodents for:
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 Biomarker expression
 Off-target effect monitoring
 Translational medicine
 Tissue-specific gene expresssion
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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

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