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RAG2 recombination activating 2 [ Homo sapiens (human) ]

Gene ID: 5897, updated on 4-Jan-2025

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; 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
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Genomic context

See RAG2 in Genome Data Viewer
Location:
11p12
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (36590996..36598236, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (36734171..36741410, complement)
RS_2024_09 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

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

EBI GWAS Catalog

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

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 PubChem

Interactions

General gene information

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding  
enables methylated histone binding  
enables phosphatidylinositol binding  
enables phosphatidylinositol-3,4,5-trisphosphate binding  
enables phosphatidylinositol-3,4-bisphosphate binding  
enables phosphatidylinositol-3,5-bisphosphate binding  
enables phosphatidylinositol-4,5-bisphosphate binding  
enables sequence-specific DNA binding  
enables zinc ion binding  
Process Evidence Code Pubs
involved_in B cell differentiation  
involved_in B cell homeostatic proliferation  
involved_in B cell lineage commitment  
involved_in DN2 thymocyte differentiation  
involved_in T cell differentiation in thymus  
involved_in T cell lineage commitment  
involved_in V(D)J recombination  
involved_in V(D)J recombination  
involved_in chromatin organization  
involved_in defense response to bacterium  
involved_in mature B cell differentiation involved in immune response  
involved_in negative regulation of T cell differentiation in thymus  
involved_in organ growth  
involved_in positive regulation of organ growth  
involved_in pre-B cell allelic exclusion  
Component Evidence Code Pubs
part_of DNA recombinase complex  
located_in nucleoplasm  

General protein information

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_000536.4NP_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
    A8K9E9, P55895, Q8TBL4
    Related
    ENSP00000308620.4, ENST00000311485.8
    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
    A8K9E9, P55895, Q8TBL4
    Related
    ENSP00000436895.2, ENST00000527033.6
    Conserved Domains (2) summary
    pfam03089
    Location:51388
    RAG2; Recombination activating protein 2
    pfam13341
    Location:414491
    RAG2_PHD; RAG2 PHD domain
  3. NM_001243786.2NP_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:51388
    RAG2; Recombination activating protein 2
    pfam13341
    Location:414491
    RAG2_PHD; RAG2 PHD domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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_047427385.1XP_047283341.1  V(D)J recombination-activating protein 2 isoform X1

    UniProtKB/Swiss-Prot
    A8K9E9, P55895, Q8TBL4
  2. XM_047427386.1XP_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_054369591.1XP_054225566.1  V(D)J recombination-activating protein 2 isoform X1

    UniProtKB/Swiss-Prot
    A8K9E9, P55895, Q8TBL4

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