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

RAI2 Gene

protein-coding   GIFtS: 53
GCID: GC0XM017818

retinoic acid induced 2

 Explore 4 diseases affiliated with
RAI2 via our new
 Human Malady Compendium 
Biological research products
for RAI2
    

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

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Retinoic Acid Induced 21 2
Retinoic Acid-Induced Protein 22

External Ids:    HGNC: 98351   Entrez Gene: 107422   Ensembl: ENSG000001318317   OMIM: 3002175   UniProtKB: Q9Y5P33   
ORGUL members:         
NONCODE:n409188 n409187    

Export aliases for RAI2 gene to outside databases

Previous GC identifers: GC0XM017362 GC0XM016484 GC0XM017020 GC0XM017179 GC0XM017578 GC0XM017728 GC0XM015576


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

Entrez Gene summary for RAI2:
Retinoic acid plays a critical role in development, cellular growth, and differentiation. The specific function of this
retinoic acid-induced gene has not yet been determined but it may play a role in development. The chromosomal location
of this gene designates it to be a candidate for diseases such as Nance-Horan syndrome, sensorineural deafness,
non-specific X-linked mental retardation, oral-facial-digital syndrome, and Fried syndrome. Alternate splicing results
in multiple transcript variants. (provided by RefSeq, Feb 2010)

Gene Wiki entry for RAI2


(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_000023.10  NC_018934.1  NT_167197.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RAI2 gene promoter:
         HFH-3   C/EBPbeta   Sox5   Lmo2   CUTL1   HNF-1A   RORalpha1   FOXI1   E2F-1   HNF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRAI2 promoter sequence
   Search SABiosciences Chromatin IP Primers for RAI2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RAI2


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

Entrez Gene cytogenetic band: Xp22   Ensembl cytogenetic band:  Xp22.13   HGNC cytogenetic band: Xp22

RAI2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RAI2 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM017818:  view genomic region     (about GC identifiers)

Start:
17,818,169 bp from pter      End:
17,879,457 bp from pter
Size:
61,289 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: RAI2_HUMAN, Q9Y5P3 (See protein sequence)
Recommended Name: Retinoic acid-induced protein 2  
Size: 530 amino acids; 57180 Da
Secondary accessions: B1B1K2 Q8N6X7

Explore the universe of human proteins at neXtProt for RAI2: NX_Q9Y5P3

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9Y5P3

  • RAI2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (4 alternative transcripts): 
    NP_001166203.1  NP_001166210.1  NP_001166214.1  NP_068557.3  

    ENSEMBL proteins: 
     ENSP00000333456   ENSP00000353106   ENSP00000444210   ENSP00000401323   ENSP00000392578  

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    Uscn Proteins for RAI2

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--


    RAI2 for ontologies           About GeneDecksing



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

    RAI2 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR026092 RAI2/SOBP

    Graphical View of Domain Structure for InterPro Entry Q9Y5P3

    ProtoNet protein and cluster: Q9Y5P3


    (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:
         Genatlas biochemistry entry for RAI2:
    retinoic acid induced 2,expressed in heart,brain,placenta,lung,skeletal muscle,kidney,pancreas and retina,excluded as
    causing-disease gene in Nance-Horan syndrome

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    hsa-miR-301b hsa-miR-320a hsa-miR-495 hsa-miR-320d hsa-miR-301a hsa-miR-3666 hsa-miR-3647-3p hsa-miR-320b
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    Inhib. RNA
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0005515protein binding IPI16713569


    RAI2 for ontologies           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:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RAI2

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    5 Interacting proteins for RAI2 (Q9Y5P31, 2, 3 ENSP000003334564) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SGTBQ96EQ02, 3, ENSP000003703954MINT-67571 I2D: score=4 STRING: ENSP00000370395
    UBQLN4Q9NRR51, 3, ENSP000003572924EBI-746228,EBI-722657 I2D: score=1 STRING: ENSP00000357292
    CTBP2P565453, ENSP000003118254I2D: score=3 STRING: ENSP00000311825
    --Q5SQP83, 2MINT-66799 I2D: score=1 
    --Q5SQP83, 2MINT-66799 I2D: score=1 
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0009790embryo development NAS10049581


    RAI2 for ontologies           About GeneDecksing



    (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 RAI2
    Search CenterWatch for drugs/clinical trials and news about RAI2 

    (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,
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    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 RAI2 gene (4 alternative transcripts): 
    NM_001172732.1  NM_001172739.1  NM_001172743.1  NM_021785.4  

    Unigene Cluster for RAI2:

    Retinoic acid induced 2
    Hs.446680  [show with all ESTs]
    Unigene Representative Sequence: NR_033348
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000331511 ENST00000360011(uc004cyf.3 uc004cyg.3) ENST00000545871(uc022btl.1 uc004cyh.4)
    ENST00000451717(uc010nfa.3) ENST00000415486(uc011miy.2)

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    8/15 QIAGEN miScript miRNA Assays for microRNAs that regulate RAI2 (see all 15):
    hsa-miR-301b hsa-miR-320a hsa-miR-495 hsa-miR-320d hsa-miR-301a hsa-miR-3666 hsa-miR-3647-3p hsa-miR-320b
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    Inhib. RNA
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    Additional cDNA sequence: 

    AK056214.1 AK298873.1 AK314631.1 BC027937.1 NR_033348.1 NR_033349.1 

    8 DOTS entries:

    DT.121309261  DT.100035785  DT.100738675  DT.112527  DT.97825189  DT.99956029  DT.100719714  DT.121309272 

    24/56 AceView cDNA sequences (see all 56):

    CR592976 AA045082 NM_021785 AI014566 BX118803 BE670727 BE503005 AI696330 
    BU728108 AI961859 AA121289 AI937418 BU076739 AA128005 W00683 BX382061 
    BC027937 C01114 AL709687 CD673707 BP375960 BX389771 AA343822 AA121303 

    GeneLoc Exon Structure

    5/6 Alternative Splicing Database (ASD) splice patterns (SP) for RAI2 (see all 6)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d · 6e ^ 7a · 7b
    SP1:                                      -           -     -     -     -               
    SP2:                    -     -     -                                                   
    SP3:                    -     -           -                                             
    SP4:                          -           -                                             
    SP5:                                      -                                             


    ECgene alternative splicing isoforms for RAI2

    (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

    RAI2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTCCCAATCA

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

    About this image

    RAI2 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    2 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    HeartEndocardiumEndocardial Tube CellsEndocardium
    KidneyMetanephric MesenchymeMetanephric Mesenchyme CellsKidney
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Early limb mesenchymal cells (ELM cells) (Primary Cell)Bone, Cartilage, Limb

    See RAI2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RAI2

    SOURCE GeneReport for Unigene cluster: Hs.446680
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    In Situ
    Assay Products:
     

     
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    (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 animals.

    Orthologs for RAI2 gene from 5/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rai21 , 5 retinoic acid induced 21, 5 87.65(n)1
    89.98(a)1
      X (74.07 cM)5
    240041  NM_001103367.11  NP_001096837.11 
     1617170695 
    chicken
    (Gallus gallus)
    Aves RAI21 retinoic acid induced 2 70.03(n)
    66.6(a)
      418614  XM_416813.3  XP_416813.1 
    lizard
    (Anolis carolinensis)
    Reptilia RAI26
    --
    61(a)
    1 ↔ 1
    3(122789810-122791474)
    zebrafish
    (Danio rerio)
    Actinopterygii CABZ01118120.16
    --
    36(a)
    1 ↔ 1
    23(45081002-45082591)
    fruit fly
    (Drosophila melanogaster)
    Insecta Sobp6
    Sine oculis-binding protein
    9(a)
    1 → many
    2R(7714668-7727035)


    ENSEMBL Gene Tree for RAI2 (if available)
    TreeFam Gene Tree for RAI2 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RAI2 gene
    SOBP2  

    RAI2 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

    10/628 NCBI SNPs in RAI2 are shown (see all 628    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1911862751,2
    --17817775(+) AGGAAG/TCAGGT 6 -- ds50010--------
    rs1828275831,2
    --17817849(+) ACACAC/TCCAAG 6 -- ds50010--------
    rs1871184991,2
    --17817862(+) CTATAC/TGAACT 6 -- ds50010--------
    rs1436663241,2
    C,--17817899(+) CACCTC/TGCTGT 6 -- ds50010--------
    rs1915592391,2
    --17818165(+) TGCAAC/TCAATT 6 -- ds50010--------
    rs1821887411,2
    --17818418(+) CACCTC/TTCCAT 6 -- ut31 nc-transcript-variant0--------
    rs1404310811,2
    C,F,--17818594(+) GTGTAT/CTTCCT 10 /I /V mis11Minor allele frequency- C:0.00NA 4552
    rs22136161,2
    C,F,H--17818647(-) CCTTAG/AGAAAC 10 /K /R nc-transcript-variantmis1 ese310Minor allele frequency- A:0.00NA EA NS 1112
    rs1474160081,2
    C,F,--17818711(+) AAGCAC/TGGAGT 10 M V nc-transcript-variantmis11Minor allele frequency- T:0.00NA 4552
    rs1397259591,2
    C,F,--17818722(+) CTTCTC/GTTTTG 10 T R mis11Minor allele frequency- G:0.00NA 4552

    HapMap Linkage Disequilibrium report for RAI2 (17818169 - 17879457 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 8 variations for RAI2
         2 CNVs: 96509 83372
         6 Indels: 83374 83376 83377 96510 83373 83375
    Locus Specific Mutation Databases (LSDB): RAI2

    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for RAI2

    (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

    RAI2 for disorders           About GeneDecksing

    OMIM gene information: 300217    OMIM disorders: --

    4 diseases for RAI2:    About MalaCards
    nance-horan syndrome    oral-facial-digital syndrome    cataract    ataxia


    Export disorders for RAI2 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 RAI2 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with RAI2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of the human homologue (RAI2) of a mouse retinoic acid-induced gene in Xp22. (PubMed id 10049581)1, 2, 3 Walpole S.M.... Trump D. (1999)
    2. Exclusion of RAI2 as the causative gene for Nance-Horan syndrome. (PubMed id 10394933)1, 3, 9 Walpole S.M....Toutain A. (1999)
    3. 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)
    4. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    5. 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)
    6. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    7. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. (PubMed id 16713569)1 Lim J.... Zoghbi H.Y. (2006)
    8. The DNA sequence of the human X chromosome. (PubMed id 15772651)2 Ross M.T.... Bentley D.R. (2005)
    9. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (2005)
    10. Refinement of the X-linked cataract locus (CXN) and g ene analysis for CXN and Nance-Horan syndrome (NHS). (PubMed id 15370543)1 Brooks S....Hardcastle A. (2004)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 10742 HGNC: 9835 AceView: RAI2 Ensembl:ENSG00000131831 euGenes: HUgn10742
    ECgene: RAI2 H-InvDB: RAI2

    (According to HUGE)
    About This Section
      --

    (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 RAI2 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 RAI2 gene:
    Search GeneIP for patents involving RAI2

    GeneCards and IP:
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