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    RAVER1 ribonucleoprotein, PTB binding 1 [ Homo sapiens (human) ]

    Gene ID: 125950, updated on 27-Nov-2024

    Summary

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    Official Symbol
    RAVER1provided by HGNC
    Official Full Name
    ribonucleoprotein, PTB binding 1provided by HGNC
    Primary source
    HGNC:HGNC:30296
    See related
    Ensembl:ENSG00000161847 MIM:609950; AllianceGenome:HGNC:30296
    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
    Enables RNA binding activity. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
    Expression
    Ubiquitous expression in spleen (RPKM 11.2), bone marrow (RPKM 11.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RAVER1 in Genome Data Viewer
    Location:
    19p13.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (10316212..10333529, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (10442322..10459641, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10426888..10444205, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:10415538-10416737 Neighboring gene FDX2-ZGLP1 readthrough Neighboring gene zinc finger GATA like protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10064 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:10427579-10427770 Neighboring gene ferredoxin 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:10430834-10431047 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10442682-10443598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10443599-10444515 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10445230-10445848 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10448906-10449654 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13960 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10450403-10451150 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10451151-10451898 Neighboring gene intercellular adhesion molecule 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10463923-10464686 Neighboring gene tyrosine kinase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10474734-10475234 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10491214-10491877

    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. RAVER1 hinders lethal EMT and modulates miR/RISC activity by the control of alternative splicing. Wedler A, et al. Nucleic Acids Res, 2024 Apr 24. PMID 38300787, Free PMC Article
    2. Functional characterization of the ribonucleoprotein, PTB-binding 1/Raver1 promoter region. Romanelli MG, et al. Gene, 2007 Dec 15. PMID 17931803
    3. CRISPRi links COVID-19 GWAS loci to LZTFL1 and RAVER1. Fink-Baldauf IM, et al. EBioMedicine, 2022 Jan. PMID 34998241, Free PMC Article
    4. Raver1 interactions with vinculin and RNA suggest a feed-forward pathway in directing mRNA to focal adhesions. Lee JH, et al. Structure, 2009 Jun 10. PMID 19523901, Free PMC Article
    5. The metavinculin tail domain directs constitutive interactions with raver1 and vinculin RNA. Lee JH, et al. J Mol Biol, 2012 Oct 5. PMID 22709580, Free PMC Article

    See all (104) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RAVER1 hinders lethal EMT and modulates miR/RISC activity by the control of alternative splicing.
      Title: RAVER1 hinders lethal EMT and modulates miR/RISC activity by the control of alternative splicing.
    2. CRISPRi links COVID-19 GWAS loci to LZTFL1 and RAVER1.
      Title: CRISPRi links COVID-19 GWAS loci to LZTFL1 and RAVER1.
    3. RAVER1 specifically regulates MDA5 activity, revealing a mechanism of differential regulation of MDA5- and RIG-I-mediated innate antiviral response.
      Title: RAVER1 is a coactivator of MDA5-mediated cellular antiviral response.
    4. These binding assays show that raver1 forms a ternary complex with metavinculin and vinculin mRNA.
      Title: The metavinculin tail domain directs constitutive interactions with raver1 and vinculin RNA.
    5. 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.
    6. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Polymorphisms in innate immunity genes and risk of childhood leukemia.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Risk of meningioma and common variation in genes related to innate immunity.
    8. RAVER1 interactions with vinculin and RNA suggest a feed forward pathway in directing messenger RNA to focal adhesions.
      Title: Raver1 interactions with vinculin and RNA suggest a feed-forward pathway in directing mRNA to focal adhesions.
    9. Raver1 gene promoter region shares common features of ubiquitously expressed gene with the interacting splicing regulator PTB
      Title: Functional characterization of the ribonucleoprotein, PTB-binding 1/Raver1 promoter region.
    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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify ribonucleoprotein PTB-binding 1 protein (RAVER1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify ribonucleoprotein PTB-binding 1 protein (RAVER1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify ribonucleoprotein PTB-binding 1 protein (RAVER1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify ribonucleoprotein PTB-binding 1 protein (RAVER1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1978

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ribonucleoprotein PTB-binding 1
    Names
    protein raver-1

    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_001366174.1 → NP_001353103.1  ribonucleoprotein PTB-binding 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC011511, AC114271
      Conserved Domains (4) summary
      cd12663
      Location:59 → 129
      RRM1_RAVER1; RNA recognition motif 1 in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)
      cd12665
      Location:133 → 209
      RRM2_RAVER1; RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)
      cd12667
      Location:219 → 306
      RRM3_RAVER1; RNA recognition motif 3 in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)
      cl26464
      Location:364 → 612
      Atrophin-1; Atrophin-1 family

    2. NM_133452.3 → NP_597709.3  ribonucleoprotein PTB-binding 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      BC037565, BX401103, CR746909, DB446023
      Consensus CDS
      CCDS45960.2
      UniProtKB/TrEMBL
      A0A087WZ13
      Related
      ENSP00000482277.1, ENST00000617231.5
      Conserved Domains (4) summary
      cd12663
      Location:59 → 129
      RRM1_RAVER1; RNA recognition motif 1 in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)
      cd12665
      Location:133 → 209
      RRM2_RAVER1; RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)
      cd12667
      Location:219 → 306
      RRM3_RAVER1; RNA recognition motif 3 in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)
      cl26464
      Location:364 → 635
      Atrophin-1; Atrophin-1 family

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      10316212..10333529 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438143.1 → XP_047294099.1  ribonucleoprotein PTB-binding 1 isoform X3

    2. XM_047438141.1 → XP_047294097.1  ribonucleoprotein PTB-binding 1 isoform X1

    3. XM_047438142.1 → XP_047294098.1  ribonucleoprotein PTB-binding 1 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      10442322..10459641 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319743.1 → XP_054175718.1  ribonucleoprotein PTB-binding 1 isoform X4

    2. XM_054319746.1 → XP_054175721.1  ribonucleoprotein PTB-binding 1 isoform X3

    3. XM_054319744.1 → XP_054175719.1  ribonucleoprotein PTB-binding 1 isoform X1

    4. XM_054319745.1 → XP_054175720.1  ribonucleoprotein PTB-binding 1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IY67.1 GenPept UniProtKB/Swiss-Prot:Q8IY67

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