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    RIPPLY1 ripply transcriptional repressor 1 [ Homo sapiens (human) ]

    Gene ID: 92129, updated on 2-Nov-2024

    Summary

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    Official Symbol
    RIPPLY1provided by HGNC
    Official Full Name
    ripply transcriptional repressor 1provided by HGNC
    Primary source
    HGNC:HGNC:25117
    See related
    Ensembl:ENSG00000147223 MIM:300575; AllianceGenome:HGNC:25117
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    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]
    Expression
    Biased expression in liver (RPKM 2.2), kidney (RPKM 1.1) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RIPPLY1 in Genome Data Viewer
    Location:
    Xq22.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (106900063..106903341, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (105336573..105339851, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (106143293..106146571, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ring finger protein 128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:105969778-105970366 Neighboring gene TBC1 domain family member 8B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:106137885-106138409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:106176295-106176796 Neighboring gene claudin 2 Neighboring gene Sharpr-MPRA regulatory region 10711 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:106209370-106209870 Neighboring gene MORC family CW-type zinc finger 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20926 Neighboring gene NANOG hESC enhancer GRCh37_chrX:106261730-106262231 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 40

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Common genetic variants in the CLDN2 and PRSS1-PRSS2 loci alter risk for alcohol-related and sporadic pancreatitis. Whitcomb DC, et al. Nat Genet, 2012 Dec. PMID 23143602, Free PMC Article
    2. Analysis of Ripply1/2-deficient mouse embryos reveals a mechanism underlying the rostro-caudal patterning within a somite. Takahashi J, et al. Dev Biol, 2010 Jun 15. PMID 20346937
    3. Groucho-associated transcriptional repressor ripply1 is required for proper transition from the presomitic mesoderm to somites. Kawamura A, et al. Dev Cell, 2005 Dec. PMID 16326386
    4. A proteome-scale map of the human interactome network. Rolland T, et al. Cell, 2014 Nov 20. PMID 25416956, Free PMC Article
    5. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Common genetic variants in the CLDN2 and PRSS1-PRSS2 loci alter risk for alcohol-related and sporadic pancreatitis.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in embryonic pattern specification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in embryonic pattern specification ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in somite rostral/caudal axis specification ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in somite specification ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    protein ripply1
    Names
    ripply1 homolog

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_022934.1 RefSeqGene

      Range
      4991..8269
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001171706.2 → NP_001165177.1  protein ripply1 isoform 2

      See identical proteins and their annotated locations for NP_001165177.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two in-frame exons in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AL591849, BC007652, BC105691, BX106639
      Consensus CDS
      CCDS55471.1
      UniProtKB/Swiss-Prot
      Q0D2K3
      Related
      ENSP00000400539.1, ENST00000411805.1
      Conserved Domains (1) summary
      pfam14998
      Location:52 → 84
      Ripply; Transcription Regulator

    2. NM_138382.3 → NP_612391.1  protein ripply1 isoform 1

      See identical proteins and their annotated locations for NP_612391.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL591849, BC007652, BC105691
      Consensus CDS
      CCDS48145.1
      UniProtKB/Swiss-Prot
      A0JP63, Q0D2K3, Q0VGB3, Q5JRB8, Q5JRB9
      Related
      ENSP00000276173.4, ENST00000276173.5
      Conserved Domains (1) summary
      pfam14998
      Location:56 → 131
      Ripply; Transcription Regulator

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      106900063..106903341 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      105336573..105339851 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q0D2K3.1 GenPept UniProtKB/Swiss-Prot:Q0D2K3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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