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

Gene ID: 134701, updated on 27-Nov-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: 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. 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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