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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RIPPLY1 Gene

protein-coding   GIFtS: 39
GCID: GC0XM106143

ripply1 homolog (zebrafish)
  Search for RIPPLY1
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Biological research products
for RIPPLY1    

Aliases
for RIPPLY1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Ripply1 Homolog (Zebrafish)1 2
Protein Ripply12

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


Summaries
for RIPPLY1 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for RIPPLY1:
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)

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)




Genomic Views
for RIPPLY1 gene

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.1  NT_011651.17  
Regulatory elements:
   SABiosciences 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
   Search SABiosciences Chromatin IP Primers for RIPPLY1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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

Proteins
for RIPPLY1 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: RIPP1_HUMAN, Q0D2K3 (See protein sequence)
Recommended Name: Protein ripply1  
Size: 151 amino acids; 16379 Da
Subcellular location: Nucleus (By similarity)
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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q0D2K3

    • RIPPLY1 Protein expression data from MOPED and PaxDb:    About this image 
    RIPPLY1 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001165177.1  NP_612391.1  

    ENSEMBL proteins: 
     ENSP00000276173   ENSP00000400539  

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    Uscn Proteins for RIPPLY1

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

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

    RIPPLY1 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for RIPPLY1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    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


    Function
    for RIPPLY1 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    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:
         Mouse knock-out Ripply1tm1.1Sjt for RIPPLY1
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for RIPPLY1 

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    hsa-miR-629* hsa-miR-4279
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    Pathways & Interactions
    for RIPPLY1 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RIPPLY1

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

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

    RIPPLY1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for RIPPLY1 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RIPPLY1
    Search CenterWatch for drugs/clinical trials and news about RIPPLY1 / RIPP1 

    Transcripts
    for RIPPLY1 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    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

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    2 QIAGEN miScript miRNA Assays for microRNAs that regulate RIPPLY1:
    hsa-miR-629* hsa-miR-4279
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    Inhib. RNA
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    Clone
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RIPPLY1
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    Additional cDNA sequence: 

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

    3 DOTS entries:

    DT.40112895  DT.100014175  DT.100746819 

    13 AceView cDNA sequences:

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

    GeneLoc Exon Structure


    Expression
    for RIPPLY1 gene

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RIPPLY1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CAAGGTTGGG
    RIPPLY1 Expression
    About this image

    RIPPLY1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table

    Stem Cell Differentiation: 2 LifeMap Cells 
    NameCategory
    PureStem™ progenitor U31 (Embryonic Progenitor Cell)
    Mesoderm-like cells (Derivation of cardio...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See RIPPLY1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RIPPLY1

    SOURCE GeneReport for Unigene cluster: Hs.334726
        SABiosciences Custom PCR Arrays for RIPPLY1
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    In Situ
    Assay Products:     
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    Orthologs
    for RIPPLY1 gene

    (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)
    About This Section
    This gene was present in the common ancestor of chordates.

    Orthologs for RIPPLY1 gene from 3/8 species (see all 8)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Ripply11 , 5 ripply1 homolog (zebrafish)1, 5 69.98(n)1
    62.25(a)1    		   X (61.35 cM)5
    6224731  NM_001037915.21  NP_001033004.11 
     1397795495 
    chicken
    (Gallus gallus)    		 Aves RIPPLY11 ripply1 homolog (zebrafish) 65.26(n)
    54.74(a)    		   771630  XM_001234886.2  XP_001234887.2 
    zebrafish
    (Danio rerio)    		 Actinopterygii ripply11 ripply1 60.93(n)
    54.84(a)    		   654446  NM_001039108.1  NP_001034197.1 


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

    Paralogs
    for RIPPLY1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RIPPLY1 gene
    DSCR62  RIPPLY22  
    1 SIMAP similar gene for RIPPLY1 using alignment to 1 protein entry:     RIPP1_HUMAN:
    RIPPLY2

    RIPPLY1 for paralogs           About GeneDecksing



    Genomic Variants
    for RIPPLY1 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for RIPPLY1
         1 CNV: 8310
    Locus Specific Mutation Databases (LSDB): RIPPLY1
    SABiosciences Cancer Mutation PCR Assays
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    Disorders / Diseases
    for RIPPLY1 gene

    (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.)
    About This Section
    RIPPLY1 for disorders           About MalaCards

    RIPPLY1 for disorders           About GeneDecksing

    OMIM gene information: 300575    OMIM disorders: --


    Export disorders for RIPPLY1 gene to outside databases

    Publications
    for RIPPLY1 gene

    (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)
    About This Section

    PubMed articles for RIPPLY1 gene integrated from 9 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. (2005)
    2. 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. (2010)
    3. The DNA sequence of the human X chromosome. (PubMed id 15772651)2 Ross M.T.... Bentley D.R. (2005)
    4. 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. (2004)
    5. 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. (2002)

    External Searches for RIPPLY1 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing RIPPLY1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 92129 HGNC: 25117 AceView: LOC92129 Ensembl:ENSG00000147223 euGenes: HUgn92129
    ECgene: RIPPLY1 H-InvDB: RIPPLY1

    Other Databases showing RIPPLY1 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing RIPPLY1 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for RIPPLY1 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for RIPPLY1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		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



    Products
    for RIPPLY1 gene

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    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
    About This Section

     
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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013 , 14 May 2013

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    von Willebrand factor
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