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

Gene ID: 53820, updated on 5-Mar-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, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
21q22.13
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (37006150..37019662)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (35388362..35401872)
105.20220307 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
  • 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 (8) 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_2023_10

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

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