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    RAG2 recombination activating 2 [ Homo sapiens (human) ]

    Gene ID: 5897, updated on 12-Aug-2018

    Summary

    Official Symbol
    RAG2provided by HGNC
    Official Full Name
    recombination activating 2provided by HGNC
    Primary source
    HGNC:HGNC:9832
    See related
    Ensembl:ENSG00000175097 MIM:179616; Vega:OTTHUMG00000166393
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RAG-2
    Summary
    This gene encodes a protein that is involved in the initiation of V(D)J recombination during B and T cell development. This protein forms a complex with the product of the adjacent recombination activating gene 1, and this complex can form double-strand breaks by cleaving DNA at conserved recombination signal sequences. The recombination activating gene 1 component is thought to contain most of the catalytic activity, while the N-terminal of the recombination activating gene 2 component is thought to form a six-bladed propeller in the active core that serves as a binding scaffold for the tight association of the complex with DNA. A C-terminal plant homeodomain finger-like motif in this protein is necessary for interactions with chromatin components, specifically with histone H3 that is trimethylated at lysine 4. Mutations in this gene cause Omenn syndrome, a form of severe combined immunodeficiency associated with autoimmune-like symptoms. [provided by RefSeq, Jul 2008]
    Expression
    Restricted expression toward thyroid (RPKM 16.6) See more
    Orthologs

    Genomic context

    See RAG2 in Genome Data Viewer
    Location:
    11p12
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (36591943..36598279, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (36613493..36619829, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene TNF receptor associated factor 6 Neighboring gene recombination activating 1 Neighboring gene chromosome 11 open reading frame 74 Neighboring gene uncharacterized LOC107984325 Neighboring gene transforming acidic coiled-coil containing protein 3 pseudogene

    Genomic regions, transcripts, and products

    Expression

    • 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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Vif vif HIV-1 Vif downregulates the expression of recombination activating gene 2 (RAG2) in Vif-expression T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • C-MYB transcription factor network, organism-specific biosystem (from Pathway Interaction Database)
      C-MYB transcription factor network, organism-specific biosystem
      C-MYB transcription factor network
    • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
      Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
    • FoxO signaling pathway, organism-specific biosystem (from KEGG)
      FoxO signaling pathway, organism-specific biosystemThe forkhead box O (FOXO) family of transcription factors regulates the expression of genes in cellular physiological events including apoptosis, cell-cycle control, glucose metabolism, oxidative str...
    • Immune System, organism-specific biosystem (from REACTOME)
      Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
    • Interleukin-7 signaling, organism-specific biosystem (from REACTOME)
      Interleukin-7 signaling, organism-specific biosystemInterleukin-7 (IL7) is produced primarily by T zone fibroblastic reticular cells found in lymphoid organs, and also expressed by non-hematopoietic stromal cells present in other tissues including the...
    • MAPK family signaling cascades, organism-specific biosystem (from REACTOME)
      MAPK family signaling cascades, organism-specific biosystemThe mitogen activated protein kinases (MAPKs) are a family of conserved protein serine threonine kinases that respond to varied extracellular stimuli to activate intracellular processes including gen...
    • MAPK6/MAPK4 signaling, organism-specific biosystem (from REACTOME)
      MAPK6/MAPK4 signaling, organism-specific biosystemMAPK6 and MAPK4 (also known as ERK3 and ERK4) are vertebrate-specific atypical MAP kinases. Atypical MAPK are less well characterized than their conventional counterparts, and are generally classifi...
    • Primary immunodeficiency, organism-specific biosystem (from KEGG)
      Primary immunodeficiency, organism-specific biosystemPrimary immunodeficiencies (PIs) are a heterogeneous group of disorders, which affect cellular and humoral immunity or non-specific host defense mechanisms mediated by complement proteins, and cells ...
    • Primary immunodeficiency, conserved biosystem (from KEGG)
      Primary immunodeficiency, conserved biosystemPrimary immunodeficiencies (PIs) are a heterogeneous group of disorders, which affect cellular and humoral immunity or non-specific host defense mechanisms mediated by complement proteins, and cells ...
    • Signal Transduction, organism-specific biosystem (from REACTOME)
      Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
    • Signaling by Interleukins, organism-specific biosystem (from REACTOME)
      Signaling by Interleukins, organism-specific biosystemInterleukins are low molecular weight proteins that bind to cell surface receptors and act in an autocrine and/or paracrine fashion. They were first identified as factors produced by leukocytes but a...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    methylated histone binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    phosphatidylinositol binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    phosphatidylinositol-3,4,5-trisphosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    phosphatidylinositol-3,4-bisphosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    phosphatidylinositol-3,5-bisphosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    phosphatidylinositol-4,5-bisphosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    ubiquitin protein ligase activity IEA
    Inferred from Electronic Annotation
    more info
     
    zinc ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    B cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    B cell homeostatic proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    B cell lineage commitment IEA
    Inferred from Electronic Annotation
    more info
     
    T cell differentiation in thymus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    T cell lineage commitment IEA
    Inferred from Electronic Annotation
    more info
     
    V(D)J recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    V(D)J recombination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    defense response to bacterium IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of organ growth IEA
    Inferred from Electronic Annotation
    more info
     
    pre-B cell allelic exclusion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    nucleoplasm TAS
    Traceable Author Statement
    more info
     

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_007573.1 RefSeqGene

      Range
      4958..11294
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_99

    mRNA and Protein(s)

    1. NM_000536.3NP_000527.2  V(D)J recombination-activating protein 2

      See identical proteins and their annotated locations for NP_000527.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shortest transcript. Variants 1, 3 and 4 encode the same protein.
      Source sequence(s)
      AK292664, AW058148, BC022397, DB146077
      Consensus CDS
      CCDS7903.1
      UniProtKB/Swiss-Prot
      P55895
      Related
      ENSP00000308620.3, OTTHUMP00000232776, ENST00000311485.7, OTTHUMT00000389536
      Conserved Domains (2) summary
      pfam03089
      Location:51388
      RAG2; Recombination activating protein 2
      pfam13341
      Location:414491
      RAG2_PHD; RAG2 PHD domain
    2. NM_001243785.1NP_001230714.1  V(D)J recombination-activating protein 2

      See identical proteins and their annotated locations for NP_001230714.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) includes an alternate exon in the 5' UTR compared to variant 1. Variants 1, 3 and 4 encode the same protein.
      Source sequence(s)
      AK292664, AW058148, BC022397, DB124002, DB146077
      Consensus CDS
      CCDS7903.1
      UniProtKB/Swiss-Prot
      P55895
      Conserved Domains (2) summary
      pfam03089
      Location:51388
      RAG2; Recombination activating protein 2
      pfam13341
      Location:414491
      RAG2_PHD; RAG2 PHD domain
    3. NM_001243786.1NP_001230715.1  V(D)J recombination-activating protein 2

      See identical proteins and their annotated locations for NP_001230715.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) includes an alternate exon in the 5' UTR compared to variant 1. Variants 1, 3 and 4 encode the same protein.
      Source sequence(s)
      AC139427, AK292664, AW058148, BC022397, DB143931, DB146077
      Consensus CDS
      CCDS7903.1
      UniProtKB/Swiss-Prot
      P55895
      Related
      ENSP00000478672.1, ENST00000618712.4
      Conserved Domains (2) summary
      pfam03089
      Location:51388
      RAG2; Recombination activating protein 2
      pfam13341
      Location:414491
      RAG2_PHD; RAG2 PHD domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

      Range
      36591943..36598279 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_033666.1: Suppressed sequence

      Description
      NR_033666.1: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript.
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