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RAG1 recombination activating 1 [ Homo sapiens (human) ]

Gene ID: 5896, updated on 3-Apr-2024

Summary

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Official Symbol
RAG1provided by HGNC
Official Full Name
recombination activating 1provided by HGNC
Primary source
HGNC:HGNC:9831
See related
Ensembl:ENSG00000166349 MIM:179615; AllianceGenome:HGNC:9831
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-1; RNF74
Summary
The protein encoded by this gene is involved in activation of immunoglobulin V-D-J recombination. The encoded protein is involved in recognition of the DNA substrate, but stable binding and cleavage activity also requires RAG2. Defects in this gene can be the cause of several diseases. [provided by RefSeq, Jul 2008]
Expression
Broad expression in thyroid (RPKM 2.3), bone marrow (RPKM 1.9) and 20 other tissues See more
Orthologs
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Genomic context

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Location:
11p12
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (36510353..36579762)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (36653524..36722938)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (36531903..36601312)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene proline rich 5 like Neighboring gene Sharpr-MPRA regulatory region 5372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:36398745-36399316 Neighboring gene Sharpr-MPRA regulatory region 14138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:36476801-36477325 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:36522348-36523547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4633 Neighboring gene TNF receptor associated factor 6 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 recombination activating 2 Neighboring gene uncharacterized LOC107984325

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. Expression and clinical significance of RAG1 in myelodysplastic syndromes. Huang X, et al. Hematology, 2022 Dec. PMID 36166051
  2. RAG1 co-expression signature identifies ETV6-RUNX1-like B-cell precursor acute lymphoblastic leukemia in children. Chen D, et al. Cancer Med, 2021 Jun. PMID 33987955, Free PMC Article
  3. Znc2 module of RAG1 contributes towards structure-specific nuclease activity of RAGs. Nilavar NM, et al. Biochem J, 2020 Sep 30. PMID 32886094
  4. Multipotent RAG1+ progenitors emerge directly from haemogenic endothelium in human pluripotent stem cell-derived haematopoietic organoids. Motazedian A, et al. Nat Cell Biol, 2020 Jan. PMID 31907413
  5. [Characteristics and Clinical Significance of RAG1 Expression in Adult B-Cell Acute Lymphoblastic Leukemia]. Han Q, et al. Zhongguo Shi Yan Xue Ye Xue Za Zhi, 2019 Jun. PMID 31204924

See all (153) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  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. First Report of FARSA in the Regulation of Cell Cycle and Survival in Mantle Cell Lymphoma Cells via PI3K-AKT and FOXO1-RAG1 Axes.
    Title: First Report of FARSA in the Regulation of Cell Cycle and Survival in Mantle Cell Lymphoma Cells via PI3K-AKT and FOXO1-RAG1 Axes.
  4. Expression and clinical significance of RAG1 in myelodysplastic syndromes.
    Title: Expression and clinical significance of RAG1 in myelodysplastic syndromes.
  5. 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.
  6. RAG2 abolishes RAG1 aggregation to facilitate V(D)J recombination.
    Title: RAG2 abolishes RAG1 aggregation to facilitate V(D)J recombination.
  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. RAG1 co-expression signature identifies ETV6-RUNX1-like B-cell precursor acute lymphoblastic leukemia in children.
    Title: RAG1 co-expression signature identifies ETV6-RUNX1-like B-cell precursor acute lymphoblastic leukemia in children.
  9. 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.
  10. Co-evolution of mutagenic genome editors and vertebrate adaptive immunity.
    Title: Co-evolution of mutagenic genome editors and vertebrate adaptive immunity.
Submit: New GeneRIF Correction See all GeneRIFs (99)

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

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

Clone Names

  • MGC43321

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding TAS
Traceable Author Statement
more info
 PubMed 
contributes_to double-stranded DNA endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables endonuclease activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables histone binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables metal ion binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin-protein transferase activity ISS
Inferred from Sequence or Structural Similarity
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 DNA recombination TAS
Traceable Author Statement
more info
 PubMed 
involved_in T cell differentiation in thymus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in T cell homeostasis 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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in V(D)J recombination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in adaptive immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in immune response TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of thymocyte apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of T cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in pre-B cell allelic exclusion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in pre-B cell allelic exclusion ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein autoubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of behavioral fear response IEA
Inferred from Electronic Annotation
more info
  
involved_in thymus development IEA
Inferred from Electronic Annotation
more info
  
involved_in visual learning IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of DNA recombinase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of endodeoxyribonuclease complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
V(D)J recombination-activating protein 1
Names
RING finger protein 74
recombination activating gene 1
recombination activating protein 1
NP_000439.2
NP_001364206.1
NP_001364207.1
NP_001364208.1
NP_001364209.1
XP_047283340.1
XP_054225565.1

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_007528.1 RefSeqGene

    Range
    5001..16750
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_98

mRNA and Protein(s)

  1. NM_000448.3 → NP_000439.2  V(D)J recombination-activating protein 1

    Status: REVIEWED

    Description
    Transcript Variant: Variants 1 through 5 encode the same protein.
    Source sequence(s)
    AC139427, M29474
    Consensus CDS
    CCDS7902.1
    UniProtKB/Swiss-Prot
    E9PPC4, P15918, Q8IY72, Q8NER2
    UniProtKB/TrEMBL
    A0A6F7R719, A0A6F7R8J6
    Related
    ENSP00000299440.5, ENST00000299440.6
    Conserved Domains (4) summary
    pfam10426
    Location:354 → 383
    zf-RAG1; Recombination-activating protein 1 zinc-finger domain
    pfam12940
    Location:386 → 1021
    RAG1; Recombination-activation protein 1 (RAG1), recombinase
    cd16530
    Location:289 → 334
    RING-HC_RAG1; RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar proteins
    pfam12560
    Location:12 → 290
    RAG1_imp_bd; RAG1 importin binding

  2. NM_001377277.1 → NP_001364206.1  V(D)J recombination-activating protein 1

    Status: REVIEWED

    Description
    Transcript Variant: Variants 1 through 5 encode the same protein.
    Source sequence(s)
    AC061999, AC139427
    Consensus CDS
    CCDS7902.1
    UniProtKB/Swiss-Prot
    E9PPC4, P15918, Q8IY72, Q8NER2
    UniProtKB/TrEMBL
    A0A6F7R719, A0A6F7R8J6
    Related
    ENSP00000513413.1, ENST00000697715.1
    Conserved Domains (4) summary
    pfam10426
    Location:354 → 383
    zf-RAG1; Recombination-activating protein 1 zinc-finger domain
    pfam12940
    Location:386 → 1021
    RAG1; Recombination-activation protein 1 (RAG1), recombinase
    cd16530
    Location:289 → 334
    RING-HC_RAG1; RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar proteins
    pfam12560
    Location:12 → 290
    RAG1_imp_bd; RAG1 importin binding

  3. NM_001377278.1 → NP_001364207.1  V(D)J recombination-activating protein 1

    Status: REVIEWED

    Description
    Transcript Variant: Variants 1 through 5 encode the same protein.
    Source sequence(s)
    AC061999, AC139427
    Consensus CDS
    CCDS7902.1
    UniProtKB/Swiss-Prot
    E9PPC4, P15918, Q8IY72, Q8NER2
    UniProtKB/TrEMBL
    A0A6F7R719, A0A6F7R8J6
    Conserved Domains (4) summary
    pfam10426
    Location:354 → 383
    zf-RAG1; Recombination-activating protein 1 zinc-finger domain
    pfam12940
    Location:386 → 1021
    RAG1; Recombination-activation protein 1 (RAG1), recombinase
    cd16530
    Location:289 → 334
    RING-HC_RAG1; RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar proteins
    pfam12560
    Location:12 → 290
    RAG1_imp_bd; RAG1 importin binding

  4. NM_001377279.1 → NP_001364208.1  V(D)J recombination-activating protein 1

    Status: REVIEWED

    Description
    Transcript Variant: Variants 1 through 5 encode the same protein.
    Source sequence(s)
    AC061999, AC139427
    Consensus CDS
    CCDS7902.1
    UniProtKB/Swiss-Prot
    E9PPC4, P15918, Q8IY72, Q8NER2
    UniProtKB/TrEMBL
    A0A6F7R719, A0A6F7R8J6
    Related
    ENSP00000513411.1, ENST00000697713.1
    Conserved Domains (4) summary
    pfam10426
    Location:354 → 383
    zf-RAG1; Recombination-activating protein 1 zinc-finger domain
    pfam12940
    Location:386 → 1021
    RAG1; Recombination-activation protein 1 (RAG1), recombinase
    cd16530
    Location:289 → 334
    RING-HC_RAG1; RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar proteins
    pfam12560
    Location:12 → 290
    RAG1_imp_bd; RAG1 importin binding

  5. NM_001377280.1 → NP_001364209.1  V(D)J recombination-activating protein 1

    Status: REVIEWED

    Description
    Transcript Variant: Variants 1 through 5 encode the same protein.
    Source sequence(s)
    AC061999, AC139427
    Consensus CDS
    CCDS7902.1
    UniProtKB/Swiss-Prot
    E9PPC4, P15918, Q8IY72, Q8NER2
    UniProtKB/TrEMBL
    A0A6F7R719, A0A6F7R8J6
    Related
    ENSP00000513412.1, ENST00000697714.1
    Conserved Domains (4) summary
    pfam10426
    Location:354 → 383
    zf-RAG1; Recombination-activating protein 1 zinc-finger domain
    pfam12940
    Location:386 → 1021
    RAG1; Recombination-activation protein 1 (RAG1), recombinase
    cd16530
    Location:289 → 334
    RING-HC_RAG1; RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar proteins
    pfam12560
    Location:12 → 290
    RAG1_imp_bd; RAG1 importin binding

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
    36510353..36579762
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427384.1 → XP_047283340.1  V(D)J recombination-activating protein 1 isoform X1

    UniProtKB/Swiss-Prot
    E9PPC4, P15918, Q8IY72, Q8NER2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    36653524..36722938
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369590.1 → XP_054225565.1  V(D)J recombination-activating protein 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P15918.2 GenPept UniProtKB/Swiss-Prot:P15918

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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