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    RIPPLY3 ripply transcriptional repressor 3 [ Homo sapiens (human) ]

    Gene ID: 53820, updated on 2-Nov-2024

    Summary

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    Official Symbol
    RIPPLY3provided by HGNC
    Official Full Name
    ripply transcriptional repressor 3provided by HGNC
    Primary source
    HGNC:HGNC:3047
    See related
    Ensembl:ENSG00000183145 MIM:609892; AllianceGenome:HGNC:3047
    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
    Also known as
    DSCR6
    Summary
    Predicted to be involved in embryonic pattern specification and negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of cell population proliferation. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See RIPPLY3 in Genome Data Viewer
    Location:
    21q22.13
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (37006150..37019662)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (35388362..35401872)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (38378450..38391962)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene holocarboxylase synthetase Neighboring gene ReSE screen-validated silencer GRCh37_chr21:38338431-38338761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13291 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13292 Neighboring gene HLCS antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13293 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38378343-38378843 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18442 Neighboring gene mitochondrial ribosomal protein L20 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:38406966-38407130 Neighboring gene uncharacterized LOC124905017 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38414477-38414978 Neighboring gene RNA, U6 small nuclear 696, pseudogene

    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. A loss-of-function mutation p.T52S in RIPPLY3 is a potential predisposing genetic risk factor for Chinese Han conotruncal heart defect patients without the 22q11.2 deletion/duplication. Hong N, et al. J Transl Med, 2018 Sep 21. PMID 30241482, Free PMC Article
    2. Isolation of two novel genes, DSCR5 and DSCR6, from Down syndrome critical region on human chromosome 21q22.2. Shibuya K, et al. Biochem Biophys Res Commun, 2000 May 19. PMID 10814524
    3. RIPPLY3 is a retinoic acid-inducible repressor required for setting the borders of the pre-placodal ectoderm. Janesick A, et al. Development, 2012 Mar. PMID 22354841, Free PMC Article
    4. The DNA sequence of human chromosome 21. Hattori M, et al. Nature, 2000 May 18. PMID 10830953
    5. TNF-α inhibits glucocorticoid receptor-induced gene expression by reshaping the GR nuclear cofactor profile. Dendoncker K, et al. Proc Natl Acad Sci U S A, 2019 Jun 25. PMID 31182584, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. deleterious variants in RIPPLY3 are potential molecular mechanisms involved in the pathogenesis of human Conotruncal heart defect.
      Title: A loss-of-function mutation p.T52S in RIPPLY3 is a potential predisposing genetic risk factor for Chinese Han conotruncal heart defect patients without the 22q11.2 deletion/duplication.
    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)

    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 biological_process ND
    No biological Data available
    more info
    		  
    involved_in cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in embryonic pattern specification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in heart development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in pharyngeal system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein ripply3
    Names
    Down syndrome critical region gene 6
    down syndrome critical region protein 6
    ripply3 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.

    mRNA and Protein(s)

    1. NM_001317768.2 → NP_001304697.1  protein ripply3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate exon in the 5' UTR which results in the use of a downstream start codon compared to variant 1. The enocoded isoform (2) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AB037159, AP000704
      UniProtKB/Swiss-Prot
      P57055
      Related
      ENST00000485272.5
      Conserved Domains (1) summary
      pfam14998
      Location:1 → 33
      Ripply; Transcription Regulator

    2. NM_001317777.1 → NP_001304706.1  protein ripply3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate exon and lacks an exon in it's 5' UTR which results in the use of a downstream start codon compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2 and 3 encode the same isoform (2)
      Source sequence(s)
      AB037160, AP000704
      UniProtKB/Swiss-Prot
      P57055
      Related
      ENST00000490393.1
      Conserved Domains (1) summary
      pfam14998
      Location:1 → 33
      Ripply; Transcription Regulator

    3. NM_018962.3 → NP_061835.1  protein ripply3 isoform 1

      See identical proteins and their annotated locations for NP_061835.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB037158, AP000704
      Consensus CDS
      CCDS13648.1
      UniProtKB/Swiss-Prot
      P57055
      Related
      ENSP00000331734.2, ENST00000329553.3
      Conserved Domains (1) summary
      pfam14998
      Location:38 → 117
      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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      37006150..37019662
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      35388362..35401872
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P57055.1 GenPept UniProtKB/Swiss-Prot:P57055

    Gene LinkOut

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

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