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    Rag2 recombination activating 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 295953, updated on 18-Sep-2024

    Summary

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    Official Symbol
    Rag2provided by RGD
    Official Full Name
    recombination activating 2provided by RGD
    Primary source
    RGD:1305588
    See related
    EnsemblRapid:ENSRNOG00000004623 AllianceGenome:RGD:1305588
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable several functions, including phosphatidylinositol phosphate binding activity; phosphatidylinositol-3,4-bisphosphate binding activity; and zinc ion binding activity. Involved in mature B cell differentiation involved in immune response and negative regulation of T cell differentiation in thymus. Predicted to be located in nucleus. Predicted to be part of DNA recombinase complex. Used to study severe combined immunodeficiency. Human ortholog(s) of this gene implicated in Omenn syndrome; combined cellular and humoral immune defects with granulomas; severe combined immunodeficiency; and severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, Nk cell-positive. Orthologous to human RAG2 (recombination activating 2). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Restricted expression toward (RPKM 217.7) See more
    Orthologs
    human mouse all
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    Genomic context

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    See Rag2 in Genome Data Viewer
    Location:
    3q31
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (108357399..108367186)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (87902373..87910227)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (91191837..91200134)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134486296 Neighboring gene uncharacterized LOC103691849 Neighboring gene intraflagellar transport associated protein Neighboring gene recombination activating 1 Neighboring gene TNF receptor associated factor 6

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Sprague Dawley Rag2-Null Rats Created from Engineered Spermatogonial Stem Cells Are Immunodeficient and Permissive to Human Xenografts. Noto FK, et al. Mol Cancer Ther, 2018 Nov. PMID 30206106, Free PMC Article
    2. Identifying conflicting signal in a multigene analysis reveals a highly resolved tree: the phylogeny of Rodentia (Mammalia). DeBry RW. Syst Biol, 2003 Oct. PMID 14530129
    3. The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2. Ramón-Maiques S, et al. Proc Natl Acad Sci U S A, 2007 Nov 27. PMID 18025461, Free PMC Article
    4. A PHD finger motif in the C terminus of RAG2 modulates recombination activity. Elkin SK, et al. J Biol Chem, 2005 Aug 5. PMID 15964836
    5. RAG-2-deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement. Shinkai Y, et al. Cell, 1992 Mar 6. PMID 1547487

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables methylated histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol-3,4,5-trisphosphate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol-3,4-bisphosphate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol-3,5-bisphosphate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol-4,5-bisphosphate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within B cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in B cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within B cell homeostatic proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within B cell lineage commitment ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within DN2 thymocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within T cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in T cell differentiation in thymus ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within T cell lineage commitment ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in V(D)J recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within V(D)J recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in V(D)J recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within defense response to bacterium ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mature B cell differentiation involved in immune response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of T cell differentiation in thymus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of organ growth ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of organ growth ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in pre-B cell allelic exclusion ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of DNA recombinase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    V(D)J recombination-activating protein 2
    Names
    recombination activating gene 2
    recombination activating protein 2

    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_001100528.2 → NP_001093998.1  V(D)J recombination-activating protein 2

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      A6HNM2, G3V6K7
      Related
      ENSRNOP00000006097.4, ENSRNOT00000006097.7
      Conserved Domains (2) summary
      pfam03089
      Location:51 → 388
      RAG2; Recombination activating protein 2
      pfam13341
      Location:414 → 491
      RAG2_PHD; RAG2 PHD domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      108357399..108367186
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063283306.1 → XP_063139376.1  V(D)J recombination-activating protein 2 isoform X1

      UniProtKB/TrEMBL
      A6HNM2, G3V6K7
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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