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    RIPPLY2 ripply transcriptional repressor 2 [ Homo sapiens (human) ]

    Gene ID: 134701, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RIPPLY2provided by HGNC
    Official Full Name
    ripply transcriptional repressor 2provided by HGNC
    Primary source
    HGNC:HGNC:21390
    See related
    Ensembl:ENSG00000203877 MIM:609891; AllianceGenome:HGNC:21390
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SCDO6; C6orf159; dJ237I15.1
    Summary
    This gene encodes a nuclear protein that belongs to a novel family of proteins required for vertebrate somitogenesis. Members of this family have a tetrapeptide WRPW motif that is required for interaction with the transcriptional repressor Groucho and a carboxy-terminal Ripply homology domain/Bowline-DSCR-Ledgerline conserved region required for transcriptional repression. Null mutant mice die soon after birth and display defects in axial skeleton segmentation due to defective somitogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
    Expression
    Biased expression in brain (RPKM 3.1), adrenal (RPKM 0.4) and 5 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RIPPLY2 in Genome Data Viewer
    Location:
    6q14.2
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (83853229..83857515)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (85076512..85080798)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (84562948..84567234)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene synaptosome associated protein 91 Neighboring gene Sharpr-MPRA regulatory region 13924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17359 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17360 Neighboring gene uncharacterized LOC105377879 Neighboring gene MPRA-validated peak5930 silencer Neighboring gene RIPPLY2-CYB5R4 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17361 Neighboring gene Sharpr-MPRA regulatory region 3398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17362 Neighboring gene cytochrome b5 reductase 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:84615227-84615728 Neighboring gene CRISPRi-validated cis-regulatory element chr6.3721 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:84686166-84687365 Neighboring gene MPRA-validated peak5932 silencer Neighboring gene long intergenic non-protein coding RNA 2857

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Congenital cervical spine malformation due to bi-allelic RIPPLY2 variants in spondylocostal dysostosis type 6. Wegler M, et al. Clin Genet, 2021 Apr. PMID 33410135
    2. Rare variants in the notch signaling pathway describe a novel type of autosomal recessive Klippel-Feil syndrome. Karaca E, et al. Am J Med Genet A, 2015 Nov. PMID 26238661, Free PMC Article
    3. Congenital posterior cervical spine malformation due to biallelic c.240-4T>G RIPPLY2 variant: A discrete entity. Serey-Gaut M, et al. Am J Med Genet A, 2020 Jun. PMID 32212228
    4. Compound heterozygous mutations in RIPPLY2 associated with vertebral segmentation defects. McInerney-Leo AM, et al. Hum Mol Genet, 2015 Mar 1. PMID 25343988
    5. Novel cleft susceptibility genes in chromosome 6q. Letra A, et al. J Dent Res, 2010 Sep. PMID 20511563, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Congenital cervical spine malformation due to bi-allelic RIPPLY2 variants in spondylocostal dysostosis type 6.
      Title: Congenital cervical spine malformation due to bi-allelic RIPPLY2 variants in spondylocostal dysostosis type 6.
    2. Congenital posterior cervical spine malformation due to biallelic c.240-4T>G RIPPLY2 variant: A discrete entity.
      Title: Congenital posterior cervical spine malformation due to biallelic c.240-4T>G RIPPLY2 variant: A discrete entity.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Novel cleft susceptibility genes in chromosome 6q.
    5. Compares Ripply proteins in zebrafish, mouse, human, and amphioxus.
      Title: Groucho-associated transcriptional repressor ripply1 is required for proper transition from the presomitic mesoderm to somites.
    6. Functional analysis of the mouse Ripply2 ortholog.
      Title: Ripply2 is essential for precise somite formation during mouse early development.
    Submit: New GeneRIF Correction

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough RIPPLY2-CYB5R4

    Readthrough gene: RIPPLY2-CYB5R4, Included gene: CYB5R4

    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 Notch signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in bone morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in determination of left/right symmetry IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in embryonic pattern specification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ossification IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in post-anal tail morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in somite rostral/caudal axis specification ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in somitogenesis 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 ripply2
    Names
    ripply2 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_046722.1 RefSeqGene

      Range
      5095..9250
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001009994.3 → NP_001009994.1  protein ripply2 isoform 1

      See identical proteins and their annotated locations for NP_001009994.1

      Status: REVIEWED

      Source sequence(s)
      AL139232
      Consensus CDS
      CCDS34493.1
      UniProtKB/Swiss-Prot
      Q5TAB6, Q5TAB7
      Related
      ENSP00000358703.1, ENST00000369689.6
      Conserved Domains (1) summary
      pfam14998
      Location:36 → 121
      Ripply; Transcription Regulator

    2. NM_001400899.1 → NP_001387828.1  protein ripply2 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL139232

    3. NM_001400900.1 → NP_001387829.1  protein ripply2 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL139232

    RNA

    1. NR_103525.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' exon structure. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
      Source sequence(s)
      AI279191, BM782014
      Related
      ENST00000369687.2

    2. NR_174622.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL139232

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      83853229..83857515
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      85076512..85080798
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5TAB7.1 GenPept UniProtKB/Swiss-Prot:Q5TAB7

    Gene LinkOut

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

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