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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RAVER1 Gene

protein-coding   GIFtS: 49
GCID: GC19M010426

ribonucleoprotein, PTB-binding 1

 Explore 2 diseases affiliated with
RAVER1 via our new
 Human Malady Compendium 
Biological research products
for RAVER1
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Ribonucleoprotein, PTB-Binding 11 2
KIAA19781 3 5
Protein Raver-12 3
Ribonucleoprotein PTB-Binding 12

External Ids:    HGNC: 302961   Entrez Gene: 1259502   Ensembl: ENSG000001618477   OMIM: 6099505   UniProtKB: Q8IY673   

Export aliases for RAVER1 gene to outside databases

Previous GC identifers: GC19U990309 GC19M010649 GC19M010272 GC19M010287 GC19M010007


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: RAVR1_HUMAN, Q8IY67
Function: Cooperates with PTBP1 to modulate regulated alternative splicing events. Promotes exon skipping. Cooperates
with PTBP1 to modulate switching between mutually exclusive exons during maturation of the TPM1 pre-mRNA (By
similarity)

Gene Wiki entry for RAVER1


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NC_018930.1  NT_011295.11  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RAVER1 gene promoter:
         HEN1   Sp1   Bach2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRAVER1 promoter sequence
   Search SABiosciences Chromatin IP Primers for RAVER1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RAVER1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19p13.2   Ensembl cytogenetic band:  19p13.2   HGNC cytogenetic band: 19p13.2

RAVER1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RAVER1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M010426:  view genomic region     (about GC identifiers)

Start:
10,426,888 bp from pter      End:
10,444,316 bp from pter
Size:
17,429 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: RAVR1_HUMAN, Q8IY67 (See protein sequence)
Recommended Name: Ribonucleoprotein PTB-binding 1  
Size: 606 amino acids; 63877 Da
Subunit: Interacts with PTBP1, RAVER2, VCL and ACTN1. Part of a complex containing RAVER1, VCL and ACTN1 (By
similarity)
Subcellular location: Nucleus (By similarity). Cytoplasm (By similarity). Note=Nuclear, in perinucleolar structures.
Shuttles between nucleus and cytoplasm. Cytoplasm, at focal contacts and cell-cell contacts. Associated with myotubes
during muscle differentiation (By similarity)
Sequence caution: Sequence=AAH37565.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact;
Sequence=BAB85564.1; Type=Miscellaneous discrepancy; Note=Intron retention;
4 PDB 3D structures from and Proteopedia for RAVER1:
3H2U (3D)        3H2V (3D)        3SMZ (3D)        3VF0 (3D)    
Secondary accessions: A6NMU4 Q8IY60 Q8TF24
Alternative splicing: 3 isoforms:  Q8IY67-1   Q8IY67-2   Q8IY67-3   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for RAVER1: NX_Q8IY67

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8IY67

  • RAVER1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_597709.2  
    ENSEMBL proteins: 
     ENSP00000293677   ENSP00000465532   ENSP00000468375   ENSP00000465753  

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    Uscn Proteins for RAVER1

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IEA--


    RAVER1 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for RAVER1


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    RAVER1 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR012677 Nucleotide-bd_a/b_plait
     IPR000504 RRM_dom

    Graphical View of Domain Structure for InterPro Entry Q8IY67

    ProtoNet protein and cluster: Q8IY67

    1 Blocks protein family: IPB000504 RNA-binding region RNP-1 (RNA recognition motif)

    UniProtKB/Swiss-Prot: RAVR1_HUMAN, Q8IY67
    Similarity: Contains 3 RRM (RNA recognition motif) domains


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: RAVR1_HUMAN, Q8IY67
    Function: Cooperates with PTBP1 to modulate regulated alternative splicing events. Promotes exon skipping. Cooperates
    with PTBP1 to modulate switching between mutually exclusive exons during maturation of the TPM1 pre-mRNA (By
    similarity)

    miRNA
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    hsa-miR-4291 hsa-miR-3910 hsa-miR-520d-5p hsa-miR-4267 hsa-miR-124 hsa-miR-133a hsa-miR-506 hsa-miR-1252
    SwitchGear 3'UTR luciferase reporter plasmidRAVER1 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for RAVER1 (see all 7)
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RAVER1

    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0003676nucleic acid binding ----
    GO:0003723RNA binding IEA--


    RAVER1 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for RAVER1:
     Increased gamma-H2AX phosphory 

    Animal Models:
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Raver1):
     cellular  nervous system 

    RAVER1 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for RAVER1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 13)

    5/536 Interacting proteins for RAVER1 (Q8IY672, 3 ENSP000002936774) via UniProtKB, MINT, STRING, and/or I2D (see all 536)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PTBP1P265992, 3, ENSP000003494284MINT-7947479 I2D: score=2 STRING: ENSP00000349428
    PTBP3O957582, 3, ENSP000003633734MINT-7947479 I2D: score=1 STRING: ENSP00000363373
    ACTN4O437073, ENSP000002526994I2D: score=1 STRING: ENSP00000252699
    TERF2Q155543, ENSP000002549424I2D: score=1 STRING: ENSP00000254942
    TOB1P506163, ENSP000002689574I2D: score=1 STRING: ENSP00000268957
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RAVER1
    Search CenterWatch for drugs/clinical trials and news about RAVER1 / RAVR1 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RAVER1 gene: 
    NM_133452.2  

    Unigene Cluster for RAVER1:

    Ribonucleoprotein, PTB-binding 1
    Hs.707428  [show with all ESTs]
    Unigene Representative Sequence: NM_133452
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000293677(uc002mnz.3 uc002moa.3) ENST00000592208 ENST00000585935
    ENST00000593136 ENST00000591969

    miRNA
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    hsa-miR-4291 hsa-miR-3910 hsa-miR-520d-5p hsa-miR-4267 hsa-miR-124 hsa-miR-133a hsa-miR-506 hsa-miR-1252
    SwitchGear 3'UTR luciferase reporter plasmidRAVER1 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    BC037565.1 BC128436.1 

    12 DOTS entries:

    DT.100874796  DT.99948727  DT.95120195  DT.100037615  DT.65284621  DT.95278145  DT.40109149  DT.92443801 
    DT.100719881  DT.121422198  DT.92443804  DT.97815111 

    24/529 AceView cDNA sequences (see all 529):

    CA424713 BM310518 BQ719653 BU508490 CR590853 BM665154 AI498122 CA426759 
    BU732531 AW631239 C01301 BQ109567 AA706413 BQ709668 CF135584 CK823014 
    AK096830 BC046121 BQ430683 BQ926069 BQ065822 BI333296 BQ548716 BQ446829 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for RAVER1    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
    SP1:                                                                                                
    SP2:                                                                                                
    SP3:                          -                                                                     
    SP4:                                                                                                
    SP5:                    -                                                                           


    ECgene alternative splicing isoforms for RAVER1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RAVER1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See RAVER1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RAVER1

    SOURCE GeneReport for Unigene cluster: Hs.707428
        SABiosciences Custom PCR Arrays for RAVER1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RAVER1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for RAVER1 gene from 4/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Raver11 , 5 ribonucleoprotein, PTB-binding 11, 5 84.44(n)1
    89.04(a)1
      9 (7.71 cM)5
    717661  NM_027911.31  NP_082187.11 
     210741685 
    lizard
    (Anolis carolinensis)
    Reptilia RAVER16
    --
    58(a)
    1 → many
    2(27795537-27836341)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.308982 Xenopus laevis transcribed sequences 75.56(n)    CB208172.1 
    zebrafish
    (Danio rerio)
    Actinopterygii raver16
    ribonucleoprotein, PTB-binding 1
    49(a)
    1 → many
    3(46597752-46625119)


    ENSEMBL Gene Tree for RAVER1 (if available)
    TreeFam Gene Tree for RAVER1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RAVER1 gene
    ENSG000002673032  RAVER22  
    1 SIMAP similar gene for RAVER1 using alignment to 5 protein entries:     RAVR1_HUMAN (see all proteins):
    RAVER2

    RAVER1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/286 NCBI SNPs in RAVER1 are shown (see all 286    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs344705201,2
    C--10015963(+) CATAA-/TTTTTT 1 -- int11Minor allele frequency- T:0.00NA 2
    rs774389951,2
    C,F,--10428788(+) ACCAAC/ACNNNN 1 -- int12Minor allele frequency- A:0.09WA NA 238
    rs124591441,2
    C,F,A,H,--10428790(+) CAACCC/TCTGCC 1 -- int118Minor allele frequency- T:0.19NS EA NA WA 2132
    rs1877842211,2
    --10428803(+) CACCCC/GAGCTT 1 -- int10--------
    rs1475894401,2
    --10428992(+) GGGGG-/CCCCCCCC 1 GG cds10--------
    rs2814271,2
    C,F,H,--10429120(+) CCCTCC/TGCCTC 1 -- int1 trp311Minor allele frequency- T:0.25NA WA CSA EA 257
    rs1929000021,2
    --10429184(+) CATGCA/GCCACC 1 -- int10--------
    rs1845876911,2
    --10429225(+) GAGACA/GGGGTT 1 -- int10--------
    rs1898574851,2
    --10429253(+) CTGGTC/TTCACA 1 -- int10--------
    rs1454924381,2
    --10429402(+) ACCCGC/TCTCCT 1 -- int10--------

    HapMap Linkage Disequilibrium report for RAVER1 (10426888 - 10444316 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for RAVER1
         2 CNVs: 29686 29685

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    RAVER1 for disorders           About GeneDecksing

    OMIM gene information: 609950    OMIM disorders: --

    2 diseases for RAVER1:    About MalaCards
    meningioma    leukemia

    Human Genome Epidemiology (HuGE) Navigator: RAVER1 (7 documents)

    Export disorders for RAVER1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for RAVER1 gene, integrated from 9 sources (see all 33):
    (articles sorted by number of sources associating them with RAVER1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Prediction of the coding sequences of unidentified human genes. XXII. The complete sequences of 50 new cDNA clones which code for large proteins. (PubMed id 11853319)1, 2, 3 Nagase T.... Ohara O. (2001)
    2. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243)1, 2 Beausoleil S.A.... Gygi S.P. (2006)
    3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    5. Raver1, a dual compartment protein, is a ligand for P TB/hnRNPI and microfilament attachment proteins. (PubMed id 11724819)1, 3 HA1ttelmaier S....Jockusch B.M. (2001)
    6. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    7. The metavinculin tail domain directs constitutive inte ractions with raver1 and vinculin RNA. (PubMed id 22709580)1 Lee J.H....Izard T. (2012)
    8. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    9. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    10. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 125950 HGNC: 30296 AceView: ICAM3andMGC19604andRAVER1 Ensembl:ENSG00000161847 euGenes: HUgn125950
    ECgene: RAVER1 H-InvDB: RAVER1

    (According to HUGE)
    About This Section
    HUGE: KIAA1978

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for RAVER1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RAVER1 gene:
    Search GeneIP for patents involving RAVER1

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