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RAG1 Gene

protein-coding   GIFtS: 65
GCID: GC11P036546

Recombination Activating Gene 1

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Recombination Activating Gene 11 2
RING Finger Protein 741 2 3
Recombination Activating Protein 11 2
V(D)J Recombination-Activating Protein 11 2
RAG-12 3
RNF742 3

External Ids:    HGNC: 98311   Entrez Gene: 58962   Ensembl: ENSG000001663497   OMIM: 1796155   UniProtKB: P159183   

Export aliases for RAG1 gene to outside databases

Previous GC identifers: GC11P038146 GC11P037266 GC11P036628 GC11P036553 GC11P036292


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RAG1 Gene:
The protein encoded by this gene is involved in activation of immunoglobulin V-D-J recombination. The encoded
protein is involved in recognition of the DNA substrate, but stable binding and cleavage activity also requires
RAG2. Defects in this gene can be the cause of several diseases. (provided by RefSeq, Jul 2008)

GeneCards Summary for RAG1 Gene:
RAG1 (recombination activating gene 1) is a protein-coding gene. Diseases associated with RAG1 include lymphopenia, and alpha/beta t-cell lymphopenia with gamma/delta t-cell expansion, severe cytomegalovirus infection, and autoimmunity. GO annotations related to this gene include ubiquitin-protein ligase activity and protein homodimerization activity.

UniProtKB/Swiss-Prot: RAG1_HUMAN, P15918
Function: Catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase
during V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell
receptor genes in developing B and T-lymphocytes through rearrangement of different V (variable), in some cases D
(diversity), and J (joining) gene segments. In the RAG complex, RAG1 mediates the DNA-binding to the conserved
recombination signal sequences (RSS) and catalyzes the DNA cleavage activities by introducing a double-strand
break between the RSS and the adjacent coding segment. RAG2 is not a catalytic component but is required for all
known catalytic activities. DNA cleavage occurs in 2 steps: a first nick is introduced in the top strand
immediately upstream of the heptamer, generating a 3'-hydroxyl group that can attack the phosphodiester bond on
the opposite strand in a direct transesterification reaction, thereby creating 4 DNA ends: 2 hairpin coding ends
and 2 blunt, 5'-phosphorylated ends. The chromatin structure plays an essential role in the V(D)J recombination
reactions and the presence of histone H3 trimethylated at 'Lys-4' (H3K4me3) stimulates both the nicking and
haipinning steps. The RAG complex also plays a role in pre-B cell allelic exclusion, a process leading to
expression of a single immunoglobulin heavy chain allele to enforce clonality and monospecific recognition by the
B-cell antigen receptor (BCR) expressed on individual B-lymphocytes. The introduction of DNA breaks by the RAG
complex on one immunoglobulin allele induces ATM-dependent repositioning of the other allele to pericentromeric
heterochromatin, preventing accessibility to the RAG complex and recombination of the second allele. In addition
to its endonuclease activity, RAG1 also acts as a E3 ubiquitin-protein ligase that mediates monoubiquitination of
histone H3. Histone H3 monoubiquitination is required for the joining step of V(D)J recombination. Mediates
polyubiquitination of KPNA1 (By similarity)




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000011.10  NT_009237.19  NC_018922.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the RAG1 gene promoter:
         STAT1   GATA-3   AP-1   ATF-2   FOXD3   STAT1beta   STAT1alpha   GATA-1   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRAG1 promoter sequence
   Search Chromatin IP Primers for RAG1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RAG1


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

Entrez Gene cytogenetic band: 11p13   Ensembl cytogenetic band:  11p12   HGNC cytogenetic band: 11p13

RAG1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RAG1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P036546:  view genomic region     (about GC identifiers)

Start:
36,532,259 bp from pter      End:
36,614,706 bp from pter
Size:
82,448 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: RAG1_HUMAN, P15918 (See protein sequence)
Recommended Name: V(D)J recombination-activating protein 1  
Size: 1043 amino acids; 119097 Da
Cofactor: Binds 1 divalent metal cation per subunit. Magnesium or manganese (By similarity)
Subunit: Homodimer. Component of the RAG complex composed of core components RAG1 and RAG2, and associated
component HMGB1 or HMGB2. Interacts with VPRBP, leading to recruitment of the CUL4A-RBX1-DDB1-DCAF1/VPRBP complex
to ubiquitinate proteins and limit error-prone repair during V(D)J recombination (By similarity)
Sequence caution: Sequence=AAM77798.1; Type=Erroneous gene model prediction;
Secondary accessions: Q8NER2

Explore the universe of human proteins at neXtProt for RAG1: NX_P15918

Explore proteomics data for RAG1 at MOPED

Post-translational modifications: 

  • Autoubiquitinated in the presence of CDC34/UBCH3 (By similarity)1
  • Ubiquitination2 at Lys234
  • Modification sites at PhosphoSitePlus

  • See RAG1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_000439.1  
    ENSEMBL proteins: 
     ENSP00000434610   ENSP00000299440  

    RAG1 Human Recombinant Protein Products:

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    ThermoFisher Antibody for RAG1
    LSBio Antibodies in human, mouse, rat for RAG1

    RAG1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Cloud-Clone Corp. ELISAs for RAG1
    Cloud-Clone Corp. CLIAs for RAG1


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    RNF: RING-type (C3HC4) zinc fingers

    Selected InterPro protein domains (see all 9):
     IPR001841 Znf_RING
     IPR013083 Znf_RING/FYVE/PHD
     IPR015880 Znf_C2H2-like
     IPR017907 Znf_RING_CS
     IPR013087 Znf_C2H2/integrase_DNA-bd

    Graphical View of Domain Structure for InterPro Entry P15918

    ProtoNet protein and cluster: P15918

    1 Blocks protein domain: IPB001841 Zn-finger

    UniProtKB/Swiss-Prot: RAG1_HUMAN, P15918
    Domain: The RING-type zinc finger mediates the E3 ubiquitin-protein ligase activity (By similarity)
    Domain: The NBD (nonamer binding) DNA-binding domain mediates the specific binding to the nonamer RSS motif by
    forming a tightly interwoven homodimer that binds and synapses 2 nonamer elements, with each NBD making contact
    with both DNA molecules. Each RSS is composed of well-conserved heptamer (consensus 5'-CACAGTG-3') and nonamer
    (consensus 5'-ACAAAAACC-3') sequences separated by a spacer of either 12 bp or 23 bp (By similarity)
    Similarity: Belongs to the RAG1 family
    Similarity: Contains 1 NBD (nonamer binding) DNA-binding domain
    Similarity: Contains 1 RAG1-type zinc finger
    Similarity: Contains 1 RING-type zinc finger


    RAG1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RAG1_HUMAN, P15918
    Function: Catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase
    during V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell
    receptor genes in developing B and T-lymphocytes through rearrangement of different V (variable), in some cases D
    (diversity), and J (joining) gene segments. In the RAG complex, RAG1 mediates the DNA-binding to the conserved
    recombination signal sequences (RSS) and catalyzes the DNA cleavage activities by introducing a double-strand
    break between the RSS and the adjacent coding segment. RAG2 is not a catalytic component but is required for all
    known catalytic activities. DNA cleavage occurs in 2 steps: a first nick is introduced in the top strand
    immediately upstream of the heptamer, generating a 3'-hydroxyl group that can attack the phosphodiester bond on
    the opposite strand in a direct transesterification reaction, thereby creating 4 DNA ends: 2 hairpin coding ends
    and 2 blunt, 5'-phosphorylated ends. The chromatin structure plays an essential role in the V(D)J recombination
    reactions and the presence of histone H3 trimethylated at 'Lys-4' (H3K4me3) stimulates both the nicking and
    haipinning steps. The RAG complex also plays a role in pre-B cell allelic exclusion, a process leading to
    expression of a single immunoglobulin heavy chain allele to enforce clonality and monospecific recognition by the
    B-cell antigen receptor (BCR) expressed on individual B-lymphocytes. The introduction of DNA breaks by the RAG
    complex on one immunoglobulin allele induces ATM-dependent repositioning of the other allele to pericentromeric
    heterochromatin, preventing accessibility to the RAG complex and recombination of the second allele. In addition
    to its endonuclease activity, RAG1 also acts as a E3 ubiquitin-protein ligase that mediates monoubiquitination of
    histone H3. Histone H3 monoubiquitination is required for the joining step of V(D)J recombination. Mediates
    polyubiquitination of KPNA1 (By similarity)

         Genatlas biochemistry entry for RAG1:
    recombination V(D)J activating gene 1,acting,in conjuction with RAG2,at a pair of recombination signal sequences
    and making double strand breaks,next to these signals,located 8kb apart from RAG2,convergently oriented

         Gene Ontology (GO): Selected molecular function terms (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding TAS9630231
    GO:0004519endonuclease activity ISS--
    GO:0004842ubiquitin-protein ligase activity ISS--
    GO:0005515protein binding IPI17474147
    GO:0008270zinc ion binding ISS--
         
    RAG1 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for RAG1:
     Increased gamma-H2AX phosphory  Synthetic lethal with Ras 

         Selected MGI mutant phenotypes (inferred from 11 alleles(MGI details for Rag1) (see all 21):
     behavior/neurological  cardiovascular system  cellular  digestive/alimentary  endocrine/exocrine gland 
     growth/size/body  hearing/vestibular/ear  hematopoietic system  homeostasis/metabolism  immune system 
     integument  liver/biliary system  mortality/aging  nervous system  normal 

    RAG1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for RAG1: Rag1tm1Mom Rag1tm1Bal

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RAG1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for RAG1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for RAG1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for RAG1

    miRNA
    Products:
        
    miRTarBase miRNAs that target RAG1:
    hsa-mir-186-5p (MIRT045071)

    Block miRNA regulation of human, mouse, rat RAG1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate RAG1 (see all 36):
    hsa-miR-549 hsa-miR-607 hsa-let-7d hsa-miR-513a-5p hsa-miR-25 hsa-miR-200a hsa-let-7g hsa-miR-141
    SwitchGear 3'UTR luciferase reporter plasmidRAG1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for RAG1
    Predesigned siRNA for gene silencing in human, mouse, rat RAG1

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for RAG1

    Clone
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    GenScript: all cDNA clones in your preferred vector: RAG1 (NM_000448)
    Browse Sino Biological Human cDNA Clones
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RAG1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    RAG1_HUMAN, P15918: Nucleus (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus4
    cytosol2
    mitochondrion2
    plasma membrane2
    extracellular1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ISS--

    RAG1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for RAG1 About    
    See pathways by source

    SuperPathContained pathways About
    1Primary immunodeficiency
    Primary immunodeficiency
    2Lymphocyte Signaling
    Lymphocyte Signaling
    3FoxO signaling pathway
    FoxO signaling pathway

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for RAG1
        Lymphocyte Signaling


    2 Kegg Pathways  (Kegg details for RAG1):
        FoxO signaling pathway
    Primary immunodeficiency


    RAG1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including RAG1: 
              Innate & Adaptive Immune Responses in human mouse rat
              Antigen Presenting Cells in human mouse rat
              T-cell & B-cell Activation in human mouse rat
              Ubiquitin Ligases in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for RAG1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 19)

    Selected Interacting proteins for RAG1 (P159181, 2, 3 ENSP000002994404) via UniProtKB, MINT, STRING, and/or I2D (see all 41)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST4H4P628053, ENSP000003507674I2D: score=1 STRING: ENSP00000350767
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 17):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002250adaptive immune response IEA--
    GO:0002331pre-B cell allelic exclusion ISS--
    GO:0006310DNA recombination TAS9630231
    GO:0006955immune response TAS9630231
    GO:0010390histone monoubiquitination ISS--

    RAG1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
    About This Section

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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for RAG1

    2 HMDB Compounds for RAG1    About this table
    CompoundSynonyms CAS #PubMed Ids
    MagnesiumMagnesium (see all 2)7439-95-4--
    Manganesemanganese 7439-96-5--

    Selected Novoseek inferred chemical compound relationships for RAG1 gene (see all 13)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cytidine 33.3 5 16504994 (1), 15135294 (1), 17174398 (1), 15613101 (1) (see all 5)
    probenecid 11.4 2 8833898 (1), 9232432 (1)
    zinc 8.63 22 19500590 (5), 8676393 (3), 9228952 (2), 19740377 (1) (see all 8)
    estrogen 5.05 1 12853125 (1)
    tcdd 0 2 7516097 (1), 9571985 (1)
    nadh 0 1 16861209 (1)
    12-o-tetradecanoylphorbol 13-acetate 0 2 1396960 (2)
    ionomycin 0 1 1396960 (1)
    alanine 0 1 11971977 (1)
    aspartate 0 1 10678172 (1)



    RAG1 for compounds           About GeneDecksing



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
    About This Section

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    REFSEQ mRNAs for RAG1 gene: 
    NM_000448.2  

    Unigene Cluster for RAG1:

    Recombination activating gene 1
    Hs.73958  [show with all ESTs]
    Unigene Representative Sequence: NM_000448
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000529126 ENST00000534663(uc001mwt.3) ENST00000299440(uc001mwu.4)

    miRNA
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    Block miRNA regulation of human, mouse, rat RAG1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate RAG1 (see all 36):
    hsa-miR-549 hsa-miR-607 hsa-let-7d hsa-miR-513a-5p hsa-miR-25 hsa-miR-200a hsa-let-7g hsa-miR-141
    SwitchGear 3'UTR luciferase reporter plasmidRAG1 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector: RAG1 (NM_000448)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for RAG1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RAG1
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for RAG1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat RAG1
      QuantiTect SYBR Green Assays in human, mouse, rat RAG1
      QuantiFast Probe-based Assays in human, mouse, rat RAG1

    Additional mRNA sequence: M29474.1 

    2 DOTS entries:

    DT.445525  DT.91676360 

    23 AceView cDNA sequences:

    BM469208 BM457041 BC037344 BQ216220 BX456469 T25427 BX644208 NM_000448 
    BG390092 BQ226214 M29474 CD608568 AW063930 T28965 BX414728 CD608566 
    BM193498 BI459026 AV755803 N92955 AA909300 AW950957 AA283244 

    GeneLoc Exon Structure


    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    RAG1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCCTGCTAAA
    RAG1 Expression
    About this image


    RAG1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Blood (Cardiovascular System)    fully expand to see all 5 entries
             Pro B-Cells Hematopoietic Bone Marrow
     
     Thymus (Hematopoietic System)    fully expand to see all 4 entries
             Double Negative 3 Thymocytes Thymus
             Thymus   
     
     Testis (Reproductive System)
    RAG1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RAG1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.73958

    UniProtKB/Swiss-Prot: RAG1_HUMAN, P15918
    Tissue specificity: Maturing lymphoid cells

        Pathway & Disease-focused RT2 Profiler PCR Arrays including RAG1: 
              Innate & Adaptive Immune Responses in human mouse rat
              Antigen Presenting Cells in human mouse rat
              T-cell & B-cell Activation in human mouse rat
              Ubiquitin Ligases in human mouse rat

    Primer
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    QuantiFast Probe-based Assays in human, mouse, rat RAG1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RAG1

    (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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for RAG1 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rag11 , 5 recombination activating gene 11, 5 86.09(n)1
    89.81(a)1
      2 (53.88 cM)5
    193731  NM_009019.21  NP_033045.21 
     1016382825 
    chicken
    (Gallus gallus)
    Aves RAG11 recombination activating gene 1 73.03(n)
    76.8(a)
      423164  NM_001031188.1  NP_001026359.1 
    lizard
    (Anolis carolinensis)
    Reptilia RAG16
    recombination activating gene 1
    74(a)
    1 ↔ 1
    1(53518235-53521375)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia rag11 recombination activating gene 1 69.54(n)
    73.13(a)
      100145555  XM_002937292.1  XP_002937338.1 
    zebrafish
    (Danio rerio)
    Actinopterygii rag12 recombination activating gene 1 76.59(n)   30663  NM_131389.1 


    ENSEMBL Gene Tree for RAG1 (if available)
    TreeFam Gene Tree for RAG1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RAG1 gene
    1 SIMAP similar gene for RAG1 using alignment to 4 protein entries:     RAG1_HUMAN (see all proteins):
    PCGF3

    RAG1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for RAG1 (see all 426)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1048942891,2,,4
    COmenn syndrome (OS)4 pathogenic136524984(+) GGCCCC/TGCCAA 2 R C mis10--------
    rs1048942911,2,,4
    COmenn syndrome (OS)4 pathogenic136524985(+) GCCCCA/G/TCCAAC 3 H R L mis11NA 4002
    rs1048942921,2,,4
    COmenn syndrome (OS)4 pathogenic136525084(+) TGGAGA/GTGTGA 2 D G mis10--------
    rs1415245401,2,,4
    COmenn syndrome (OS)4 untested136525101(+) TGTGCA/GTGACC 2 M V mis11Minor allele frequency- G:0.00NA 4548
    rs1048942851,2,,4
    COmenn syndrome (OS)4 pathogenic136525479(+) GGTTCC/TGCTAT 2 R C mis10--------
    rs1048942841,2,,4
    COmenn syndrome (OS)4 pathogenic136525480(+) GTTCCA/GCTATG 2 H R mis10--------
    rs1994746881,2,,4
    COmenn syndrome (OS)4 untested136525668(+) CAGTCC/TGTTTT 2 R C mis10--------
    rs1048942861,2,,4
    COmenn syndrome (OS)4 pathogenic136526010(+) CACCCA/GTCTGG 2 H R mis10--------
    rs1048942871,2,,4
    CAlpha/beta T-cell lymphopenia, with gamma/delta T-cell expansion, severe cytomegalovirus infection and autoimmunity (T-CMVA)4 pathogenic136526321(+) ATCTCC/TGGAAG 2 R W mis10--------
    rs1048942901,2,,4
    COmenn syndrome (OS)4 pathogenic136526535(+) CCAGTA/GCAGTT 2 Y C mis10--------

    HapMap Linkage Disequilibrium report for RAG1 (36532259 - 36614706 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for RAG1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2422305CNV Duplication17116639
    nsv832123CNV Gain17160897
    nsv467791CNV Gain19166990

    Human Gene Mutation Database (HGMD): RAG1
    Locus Specific Mutation Databases (LSDB): RAG1

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing RAG1
    DNA2.0 Custom Variant and Variant Library Synthesis for RAG1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 179615   
    OMIM disorders: 601457  603554  609889  233650  
    UniProtKB/Swiss-Prot: RAG1_HUMAN, P15918
  • Combined cellular and humoral immune defects with granulomas (CHIDG) [MIM:233650]: Immunodeficiency
    disease with granulomas in the skin, mucous membranes, and internal organs. Other characteristics include
    hypogammaglobulinemia, a diminished number of T and B cells, and sparse thymic tissue on ultrasonography.
    Note=The disease is caused by mutations affecting the gene represented in this entry
  • Severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-negative/NK-cell-positive
    (T(-)B(-)NK(+) SCID) [MIM:601457]: A form of severe combined immunodeficiency (SCID), a genetically and
    clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and
    cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients present in infancy recurrent,
    persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of
    T-cell-mediated cellular immunity due to a defect in T-cell development. Note=The disease is caused by mutations
    affecting the gene represented in this entry
  • Omenn syndrome (OS) [MIM:603554]: Severe immunodeficiency characterized by the presence of activated,
    anergic, oligoclonal T-cells, hypereosinophilia, and high IgE levels. Note=The disease is caused by mutations
    affecting the gene represented in this entry
  • Alpha/beta T-cell lymphopenia, with gamma/delta T-cell expansion, severe cytomegalovirus infection and
    autoimmunity (T-CMVA) [MIM:609889]: An immunological disorder characterized by oligoclonal expansion of TCR
    gamma/delta T-cells, TCR alpha/beta T-cell lymphopenia, severe, disseminated cytomegalovirus infection and
    autoimmune cytopenia. Note=The disease is caused by mutations affecting the gene represented in this entry

  • Selected diseases for RAG1 (see all 47):    
    About MalaCards
    lymphopenia    alpha/beta t-cell lymphopenia with gamma/delta t-cell expansion, severe cytomegalovirus infection, and autoimmunity    cytomegalovirus infection    combined cellular and humoral immune defects with granulomas
    omenn syndrome    recombinase activating gene 1 deficiency    severe combined immunodeficiency, b cell-negative    artemis deficiency
    lymphoblastic lymphoma    hereditary neuropathies    severe combined immunodeficiency    leukemia/lymphoma, t-cell
    ataxia telangiectasia    burkitt's lymphoma    leukopenia    follicular lymphoma
    lymphoblastic leukemia    acute leukemia    non-hodgkin lymphoma    was-related disorders

    2 diseases from the University of Copenhagen DISEASES database for RAG1:
    Omenn syndrome     Severe combined immunodeficiency

    RAG1 for disorders           About GeneDecksing

    Selected Novoseek inferred disease relationships for RAG1 gene (see all 25)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    omenn syndrome 93.8 26 18056378 (3), 19830075 (3), 19011808 (2), 11520796 (2) (see all 17)
    severe combined immunodeficiency 79.6 11 16061569 (2), 15845893 (1), 14726805 (1), 16527199 (1) (see all 10)
    immunodeficiency 38.3 14 11520796 (2), 1428003 (1), 11908269 (1), 16276422 (1) (see all 13)
    t-all 38 4 12446444 (4)
    lymphoblastic leukemia acute 36.2 3 8391873 (1), 7987804 (1), 8445948 (1)
    leukemia 28.3 3 8371592 (1), 18005092 (1), 15611260 (1)
    hereditary neuropathy 28.1 1 15607947 (1)
    leukemia t-cell 21.4 1 17059760 (1)
    lymphoma lymphoblastic 20 1 8391873 (1)
    burkitt lymphoma 18.9 2 8445948 (1)

    Genetic Association Database (GAD): RAG1
    Human Genome Epidemiology (HuGE) Navigator: RAG1 (25 documents)
    Tumor Gene Database (TGDB): RAG1

    Export disorders for RAG1 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)
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    PubMed articles for RAG1 gene, integrated from 10 sources (see all 297):
    (articles sorted by number of sources associating them with RAG1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. RAG-1 interacts with the repeated amino acid motif of the human homologue of the yeast protein SRP1. (PubMed id 8052633)1, 2, 9 Cortes P.... Baltimore D. (Proc. Natl. Acad. Sci. U.S.A. 1994)
    2. Mutations in genes required for T-cell development: IL7R, CD45, IL2RG, JAK3, RAG1, RAG2, ARTEMIS, and ADA and severe combined immunodeficiency: HuGE review. (PubMed id 14726805)1, 4, 9 Kalman L....Buckley R. (Genet. Med. 2004)
    3. Human RAG2, like RAG1, is on chromosome 11 band p13 and therefore not linked to ataxia telangiectasia complementation groups. (PubMed id 1283330)1, 3, 9 Sherrington P.D....Rabbitts T.H. (amp 1992)
    4. A novel immunodeficiency associated with hypomorphic RAG1 mutations and CMV infection. (PubMed id 16276422)1, 2, 9 de Villartay J.-P....Le Deist F. (J. Clin. Invest. 2005)
    5. V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. (PubMed id 11133745)1, 2, 9 Villa A.... Schwarz K. (Blood 2001)
    6. Characterization of immune function and analysis of RAG gene mutations in Omenn syndrome and related disorders. (PubMed id 10606976)1, 2, 9 Wada T.... Yachie A. (Clin. Exp. Immunol. 2000)
    7. Partial V(D)J recombination activity leads to Omenn syndrome. (PubMed id 9630231)1, 2, 9 Villa A....Spanopoulou E. (Cell 1998)
    8. Novel mutations in RAG1/2 and ADA genes in Israeli patients presenting with T-B-SCID or Omenn syndrome. (PubMed id 21624848)1, 2 Dalal I.... Leshinsky-Silver E. (Clin. Immunol. 2011)
    9. Clinical characteristics and molecular analysis of three Chinese children with Omenn syndrome. (PubMed id 21771083)1, 2 Zhang Z.Y.... Yang X.Q. (Pediatr. Allergy Immunol. 2011)
    10. Polymorphisms in DNA repair genes and risk of non-Hodgkin lymphoma in a pooled analysis of three studies. (PubMed id 20813000)1, 4 Shen M....Zheng T. (Br. J. Haematol. 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 5896 HGNC: 9831 AceView: RAG1 Ensembl:ENSG00000166349 euGenes: HUgn5896
    ECgene: RAG1 Kegg: 5896 H-InvDB: RAG1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for RAG1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for RAG1 Genetics and Cytogenetics in Oncology and Haematology
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=RAG1[genesymbol]
    NIEHS-SNPshttp://egp.gs.washington.edu/data/rag1/
    RAG1basehttp://bioinf.uta.fi/RAG1base/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RAG1 gene:
    Search GeneIP for patents involving RAG1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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