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

Gene ID: 125950, updated on 3-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
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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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