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Aliases for RAG2 Gene

Aliases for RAG2 Gene

  • Recombination Activating Gene 2 2 3
  • RAG-2 3 4
  • V(D)J Recombination-Activating Protein 2 3

External Ids for RAG2 Gene

Summaries for RAG2 Gene

Entrez Gene Summary for RAG2 Gene

  • 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]

GeneCards Summary for RAG2 Gene

RAG2 (Recombination Activating Gene 2) is a Protein Coding gene. Diseases associated with RAG2 include omenn syndrome and combined cellular and humoral immune defects with granulomas. Among its related pathways are FoxO signaling pathway and C-MYB transcription factor network. GO annotations related to this gene include chromatin binding and methylated histone binding.

UniProtKB/Swiss-Prot for RAG2 Gene

  • Core 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. DNA cleavage by the RAG complex 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 the RAG complex, RAG2 is not the catalytic component but is required for all known catalytic activities mediated by RAG1. It probably acts as a sensor of chromatin state that recruits the RAG complex to H3K4me3 (By similarity).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RAG2 Gene

Genomics for RAG2 Gene

Genomic Location for RAG2 Gene

Start:
36,575,574 bp from pter
End:
36,598,279 bp from pter
Size:
22,706 bases
Orientation:
Minus strand

Genomic View for RAG2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for RAG2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAG2 Gene

Regulatory Elements for RAG2 Gene

Proteins for RAG2 Gene

  • Protein details for RAG2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P55895-RAG2_HUMAN
    Recommended name:
    V(D)J recombination-activating protein 2
    Protein Accession:
    P55895
    Secondary Accessions:
    • A8K9E9
    • Q8TBL4

    Protein attributes for RAG2 Gene

    Size:
    527 amino acids
    Molecular mass:
    59241 Da
    Quaternary structure:
    • Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2.

neXtProt entry for RAG2 Gene

Proteomics data for RAG2 Gene at MOPED

Post-translational modifications for RAG2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RAG2 Gene

No data available for DME Specific Peptides for RAG2 Gene

Domains for RAG2 Gene

Suggested Antigen Peptide Sequences for RAG2 Gene

Graphical View of Domain Structure for InterPro Entry

P55895

UniProtKB/Swiss-Prot:

RAG2_HUMAN
Domain:
  • The atypical PHD-type zinc finger recognizes and binds histone H3 trimethylated on Lys-4 (H3K4me3). The presence Tyr-445 instead of a carboxylate in classical PHD-type zinc fingers results in an enhanced binding to H3K4me3 in presence of dimethylated on Arg-2 (H3R2me2) rather than inhibited. The atypical PHD-type zinc finger also binds various phosphoinositides, such as phosphatidylinositol 3,4-bisphosphate binding (PtdIns(3,4)P2), phosphatidylinositol 3,5-bisphosphate binding (PtdIns(3,5)P2), phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) and phosphatidylinositol 3,4,5-trisphosphate binding (PtdIns(3,4,5)P3) (By similarity).:
    • P55895
Family:
  • Belongs to the RAG2 family.:
    • P55895
Similarity:
  • Contains 1 PHD-type zinc finger.:
    • P55895
genes like me logo Genes that share domains with RAG2: view

No data available for Gene Families for RAG2 Gene

Function for RAG2 Gene

Molecular function for RAG2 Gene

GENATLAS Biochemistry: recombination V(D)J activating gene 2,acting,in conjunction with RAG1,at a pair of recombination signal sequences and making double strand breaks,next to these signals,located 8kb apart from RAG1,convergently oriented
UniProtKB/Swiss-Prot Function: Core 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. DNA cleavage by the RAG complex 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 the RAG complex, RAG2 is not the catalytic component but is required for all known catalytic activities mediated by RAG1. It probably acts as a sensor of chromatin state that recruits the RAG complex to H3K4me3 (By similarity).

Gene Ontology (GO) - Molecular Function for RAG2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding ISS --
GO:0005515 protein binding --
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding ISS --
GO:0005547 phosphatidylinositol-3,4,5-trisphosphate binding ISS --
genes like me logo Genes that share ontologies with RAG2: view
genes like me logo Genes that share phenotypes with RAG2: view

Animal Models for RAG2 Gene

MGI Knock Outs for RAG2:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for RAG2 Gene

Localization for RAG2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAG2 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RAG2 Gene COMPARTMENTS Subcellular localization image for RAG2 gene
Compartment Confidence
nucleus 5
plasma membrane 2
cytosol 1
endoplasmic reticulum 1
extracellular 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for RAG2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with RAG2: view

Pathways for RAG2 Gene

genes like me logo Genes that share pathways with RAG2: view

Pathways by source for RAG2 Gene

1 BioSystems pathway for RAG2 Gene
2 KEGG pathways for RAG2 Gene

Gene Ontology (GO) - Biological Process for RAG2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002326 B cell lineage commitment IEA --
GO:0002331 pre-B cell allelic exclusion ISS --
GO:0002358 B cell homeostatic proliferation IEA --
GO:0002360 T cell lineage commitment IEA --
GO:0006310 DNA recombination --
genes like me logo Genes that share ontologies with RAG2: view

Compounds for RAG2 Gene

(6) Novoseek inferred chemical compound relationships for RAG2 Gene

Compound -log(P) Hits PubMed IDs
cytidine 41.5 4
probenecid 14.8 2
zinc 0 2
serine 0 1
caffeine 0 1
genes like me logo Genes that share compounds with RAG2: view

Transcripts for RAG2 Gene

mRNA/cDNA for RAG2 Gene

Unigene Clusters for RAG2 Gene

Recombination activating gene 2:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for RAG2 Gene

No ASD Table

Relevant External Links for RAG2 Gene

GeneLoc Exon Structure for
RAG2
ECgene alternative splicing isoforms for
RAG2

Expression for RAG2 Gene

mRNA expression in normal human tissues for RAG2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RAG2 Gene

This gene is overexpressed in Thyroid (53.0).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for RAG2 Gene

SOURCE GeneReport for Unigene cluster for RAG2 Gene Hs.714519

mRNA Expression by UniProt/SwissProt for RAG2 Gene

P55895-RAG2_HUMAN
Tissue specificity: Cells of the B- and T-lymphocyte lineages
genes like me logo Genes that share expressions with RAG2: view

Orthologs for RAG2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RAG2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RAG2 35
  • 99.81 (n)
  • 99.43 (a)
RAG2 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RAG2 35
  • 90.7 (n)
  • 91.08 (a)
RAG2 36
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RAG2 35
  • 89.88 (n)
  • 88.99 (a)
RAG2 36
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rag2 35
  • 87.54 (n)
  • 88.43 (a)
Rag2 16
Rag2 36
  • 88 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RAG2 36
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RAG2 36
  • 79 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rag2 35
  • 87.98 (n)
  • 89.18 (a)
chicken
(Gallus gallus)
Aves RAG2 35
  • 72.62 (n)
  • 72.81 (a)
RAG2 36
  • 73 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RAG2 36
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rag2 35
  • 66.54 (n)
  • 61.46 (a)
zebrafish
(Danio rerio)
Actinopterygii rag2 35
  • 57.7 (n)
  • 51.91 (a)
rag2 36
  • 51 (a)
OneToOne
Species with no ortholog for RAG2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RAG2 Gene

ENSEMBL:
Gene Tree for RAG2 (if available)
TreeFam:
Gene Tree for RAG2 (if available)

Paralogs for RAG2 Gene

No data available for Paralogs for RAG2 Gene

Variants for RAG2 Gene

Sequence variations from dbSNP and Humsavar for RAG2 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs3084298 -- 36,591,599(+) TAACT(-/AC)ACACA downstream-variant-500B
rs3740956 -- 36,592,208(+) CTTTA(C/T)TGGCT utr-variant-3-prime
rs10636125 -- 36,591,626(+) CACAC(-/ACAC)TCACA downstream-variant-500B
rs10836573 -- 36,592,257(+) AGACT(C/T)ATATA utr-variant-3-prime
rs11828016 -- 36,591,572(+) TATTC(A/G)CTGGC downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for RAG2 Gene

Variant ID Type Subtype PubMed ID
esv2422305 CNV Duplication 17116639
nsv467791 CNV Gain 19166990
nsv832123 CNV Gain 17160897

Relevant External Links for RAG2 Gene

HapMap Linkage Disequilibrium report
RAG2
Human Gene Mutation Database (HGMD)
RAG2
Locus Specific Mutation Databases (LSDB)
RAG2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RAG2 Gene

Disorders for RAG2 Gene

(3) OMIM Diseases for RAG2 Gene (179616)

UniProtKB/Swiss-Prot

RAG2_HUMAN
  • 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. {ECO:0000269 PubMed:18463379}. 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. {ECO:0000269 PubMed:8810255}. 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. {ECO:0000269 PubMed:9630231}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(3) University of Copenhagen DISEASES for RAG2 Gene

(12) Novoseek inferred disease relationships for RAG2 Gene

Disease -log(P) Hits PubMed IDs
omenn syndrome 92.6 16
severe combined immunodeficiency 75.6 9
immunodeficiency 35.5 10
leukemia 20.9 2
leukemia t-cell 15.7 1

Relevant External Links for RAG2

Genetic Association Database (GAD)
RAG2
Human Genome Epidemiology (HuGE) Navigator
RAG2
genes like me logo Genes that share disorders with RAG2: view

Publications for RAG2 Gene

  1. Expression of human recombination activating genes (RAG1 and RAG2) in neoplastic lymphoid cells: correlation with cell differentiation and antigen receptor expression. (PMID: 1832998) Bories J.C. … Sigaux F. (Blood 1991) 3 4 23
  2. Human RAG2, like RAG1, is on chromosome 11 band p13 and therefore not linked to ataxia telangiectasia complementation groups. (PMID: 1283330) Sherrington P.D. … Rabbitts T.H. (Genes Chromosomes Cancer 1992) 2 3 23
  3. Sequence and chromosome assignment to 11p13-p12 of human RAG genes. (PMID: 1428003) Ichihara Y. … Kurosawa Y. (Immunol. Lett. 1992) 3 4 23
  4. Partial V(D)J recombination activity leads to Omenn syndrome. (PMID: 9630231) Villa A. … Spanopoulou E. (Cell 1998) 3 4 23
  5. Mutations in genes required for T-cell development: IL7R, CD45, IL2RG, JAK3, RAG1, RAG2, ARTEMIS, and ADA and severe combined immunodeficiency: HuGE review. (PMID: 14726805) Kalman L. … Buckley R. (Genet. Med. 2004) 3 23 48

Products for RAG2 Gene

Sources for RAG2 Gene

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