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RAG2 recombination activating 2 [ Homo sapiens (human) ]

Gene ID: 5897, updated on 23-Nov-2023

Summary

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Official Symbol
RAG2provided by HGNC
Official Full Name
recombination activating 2provided by HGNC
Primary source
HGNC:HGNC:9832
See related
Ensembl:ENSG00000175097 MIM:179616; AllianceGenome:HGNC:9832
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
mouse all
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Genomic context

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See RAG2 in Genome Data Viewer
Location:
11p12
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (36590996..36598236, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (36734171..36741410, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (36613493..36619786, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:36522348-36523547 Neighboring gene TNF receptor associated factor 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4633 Neighboring gene recombination activating 1 Neighboring gene NANOG hESC enhancer GRCh37_chr11:36603130-36603633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4634 Neighboring gene intraflagellar transport associated protein Neighboring gene uncharacterized LOC107984325 Neighboring gene transforming acidic coiled-coil containing protein 3 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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 Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Atypical Omenn Syndrome Due to RAG2 Gene Mutation, a Case Report. Pourvali A, et al. Iran J Immunol, 2019 Dec. PMID 31885011
  2. From RAG2 to T Cell Riches and Future Fortunes. Glynn RA, et al. J Immunol, 2019 Mar 1. PMID 30782849
  3. Recombination activity of human recombination-activating gene 2 (RAG2) mutations and correlation with clinical phenotype. Tirosh I, et al. J Allergy Clin Immunol, 2019 Feb. PMID 29772310, Free PMC Article
  4. The Conserved ATM Kinase RAG2-S365 Phosphorylation Site Limits Cleavage Events in Individual Cells Independent of Any Repair Defect. Hewitt SL, et al. Cell Rep, 2017 Oct 24. PMID 29069605, Free PMC Article
  5. Late Onset Hypomorphic RAG2 Deficiency Presentation with Fatal Vaccine-Strain VZV Infection. Dutmer CM, et al. J Clin Immunol, 2015 Nov. PMID 26515615, Free PMC Article

See all (101) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A novel loss of function mutation in the PHD domain of the RAG2 gene, affecting zinc-binding affinity.
    Title: A novel loss of function mutation in the PHD domain of the RAG2 gene, affecting zinc-binding affinity.
  2. Hypomorphic RAG deficiency: impact of disease burden on survival and thymic recovery argues for early diagnosis and HSCT.
    Title: Hypomorphic RAG deficiency: impact of disease burden on survival and thymic recovery argues for early diagnosis and HSCT.
  3. Rag2(-/-) accelerates lipofuscin accumulation in the brain: Implications for human stem cell brain transplantation studies.
    Title: Rag2(-/-) accelerates lipofuscin accumulation in the brain: Implications for human stem cell brain transplantation studies.
  4. Partial RAG deficiency in humans induces dysregulated peripheral lymphocyte development and humoral tolerance defect with accumulation of T-bet(+) B cells.
    Title: Partial RAG deficiency in humans induces dysregulated peripheral lymphocyte development and humoral tolerance defect with accumulation of T-bet(+) B cells.
  5. RAG2 abolishes RAG1 aggregation to facilitate V(D)J recombination.
    Title: RAG2 abolishes RAG1 aggregation to facilitate V(D)J recombination.
  6. Survival-Assured Liver Injury Preconditioning (SALIC) Enables Robust Expansion of Human Hepatocytes in Fah(-/-) Rag2(-/-) IL2rg(-/-) Rats.
    Title: Survival-Assured Liver Injury Preconditioning (SALIC) Enables Robust Expansion of Human Hepatocytes in Fah(-/-) Rag2(-/-) IL2rg(-/-) Rats.
  7. Clinical Manifestations, Mutational Analysis, and Immunological Phenotype in Patients with RAG1/2 Mutations: First Cases Series from Mexico and Description of Two Novel Mutations.
    Title: Clinical Manifestations, Mutational Analysis, and Immunological Phenotype in Patients with RAG1/2 Mutations: First Cases Series from Mexico and Description of Two Novel Mutations.
  8. The Interplay Between Chromatin Architecture and Lineage-Specific Transcription Factors and the Regulation of Rag Gene Expression.
    Title: The Interplay Between Chromatin Architecture and Lineage-Specific Transcription Factors and the Regulation of Rag Gene Expression.
  9. Co-evolution of mutagenic genome editors and vertebrate adaptive immunity.
    Title: Co-evolution of mutagenic genome editors and vertebrate adaptive immunity.
  10. The Clinical and Genetic Spectrum of 82 Patients With RAG Deficiency Including a c.256_257delAA Founder Variant in Slavic Countries.
    Title: The Clinical and Genetic Spectrum of 82 Patients With RAG Deficiency Including a c.256_257delAA Founder Variant in Slavic Countries.
Submit: New GeneRIF Correction See all GeneRIFs (65)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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 PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables methylated histone binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables phosphatidylinositol binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables phosphatidylinositol-3,4,5-trisphosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables phosphatidylinositol-3,4-bisphosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables phosphatidylinositol-3,5-bisphosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables phosphatidylinositol-4,5-bisphosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin protein ligase activity IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in B cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in B cell homeostatic proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in B cell lineage commitment IEA
Inferred from Electronic Annotation
more info
  
involved_in DN2 thymocyte differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in T cell differentiation in thymus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in T cell lineage commitment IEA
Inferred from Electronic Annotation
more info
  
involved_in V(D)J recombination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in V(D)J recombination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in defense response to bacterium IEA
Inferred from Electronic Annotation
more info
  
involved_in mature B cell differentiation involved in immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of T cell differentiation in thymus IEA
Inferred from Electronic Annotation
more info
  
involved_in organ growth IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of organ growth IEA
Inferred from Electronic Annotation
more info
  
involved_in pre-B cell allelic exclusion ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of DNA recombinase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  

General protein information

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

Genomic

  1. NG_007573.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_000536.4 → NP_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
    A8K9E9, P55895, Q8TBL4
    Related
    ENSP00000308620.4, ENST00000311485.8
    Conserved Domains (2) summary
    pfam03089
    Location:51 → 388
    RAG2; Recombination activating protein 2
    pfam13341
    Location:414 → 491
    RAG2_PHD; RAG2 PHD domain

  2. NM_001243785.2 → NP_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
    Consensus CDS
    CCDS7903.1
    UniProtKB/Swiss-Prot
    A8K9E9, P55895, Q8TBL4
    Related
    ENSP00000436895.2, ENST00000527033.6
    Conserved Domains (2) summary
    pfam03089
    Location:51 → 388
    RAG2; Recombination activating protein 2
    pfam13341
    Location:414 → 491
    RAG2_PHD; RAG2 PHD domain

  3. NM_001243786.2 → NP_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
    Consensus CDS
    CCDS7903.1
    UniProtKB/Swiss-Prot
    A8K9E9, P55895, Q8TBL4
    Related
    ENSP00000432174.2, ENST00000532616.2
    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_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    36590996..36598236 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427385.1 → XP_047283341.1  V(D)J recombination-activating protein 2 isoform X1

    UniProtKB/Swiss-Prot
    A8K9E9, P55895, Q8TBL4

  2. XM_047427386.1 → XP_047283342.1  V(D)J recombination-activating protein 2 isoform X1

    UniProtKB/Swiss-Prot
    A8K9E9, P55895, Q8TBL4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    36734171..36741410 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369591.1 → XP_054225566.1  V(D)J recombination-activating protein 2 isoform X1

    UniProtKB/Swiss-Prot
    A8K9E9, P55895, Q8TBL4

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.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P55895.1 GenPept UniProtKB/Swiss-Prot:P55895

Gene LinkOut

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