RAG2 recombination activating 2 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

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_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

From variant of uncertain significance to likely pathogenic in two siblings with atypical RAG2 Deficiency: a case report and review of the literature.
Title: From variant of uncertain significance to likely pathogenic in two siblings with atypical RAG2 Deficiency: a case report and review of the literature.
Heterogeneity in RAG1 and RAG2 deficiency: 35 cases from a single-centre.
Title: Heterogeneity in RAG1 and RAG2 deficiency: 35 cases from a single-centre.
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.
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.
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.
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.
RAG2 abolishes RAG1 aggregation to facilitate V(D)J recombination.
Title: RAG2 abolishes RAG1 aggregation to facilitate V(D)J recombination.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (67)

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

Associated conditions

Description	Tests
Combined immunodeficiency with skin granulomas MedGen: C2673536 OMIM: 233650 GeneReviews: Not available	not available
Histiocytic medullary reticulosis MedGen: C2700553 OMIM: 603554 GeneReviews: Not available	not available
Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive MedGen: C1832322 OMIM: 601457 GeneReviews: Not available	not available

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC102178P2 (e-PCR)
- UniSTS:270081

RAG2 (e-PCR)
- UniSTS:266542

RAG2 (e-PCR)
- UniSTS:504688

RAG2_770 (e-PCR)
- UniSTS:277657

RAG2_V121 (e-PCR)
- UniSTS:277657

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 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

NG_007573.1 RefSeqGene

Range

4958..11294

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_99

mRNA and Protein(s)

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
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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

36590996..36598236 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

A8K9E9, P55895, Q8TBL4
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

NC_060935.1 Alternate T2T-CHM13v2.0

Range

36734171..36741410 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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.