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

Gene ID: 92129, updated on 28-Oct-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.

Chemical Information
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