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RAG2 recombination activating 2 [ Homo sapiens (human) ]

Gene ID: 5897, updated on 8-Dec-2019

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
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
109.20190905 current GRCh38.p13 (GCF_000001405.39) 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 intraflagellar transport associated protein 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What'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
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
 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
DNA recombinase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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_000536.4NP_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, ENST00000311485.7
    Conserved Domains (2) summary
    pfam03089
    Location:51388
    RAG2; Recombination activating protein 2
    pfam13341
    Location:414491
    RAG2_PHD; RAG2 PHD domain
  2. NM_001243785.2NP_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
    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 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 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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