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    RAG1 recombination activating 1 [ Homo sapiens (human) ]

    Gene ID: 5896, updated on 2-Nov-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
    mouse all
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    Genomic context

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    See RAG1 in Genome Data Viewer
    Location:
    11p12
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (36510353..36579762)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (36653524..36722938)
    RS_2024_09 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. A hypomorphic recombination-activating gene 1 (RAG1) mutation resulting in a phenotype resembling common variable immunodeficiency. Abolhassani H, et al. J Allergy Clin Immunol, 2014 Dec. PMID 24996264, Free PMC Article
    2. Mutation c.256_257delAA in RAG1 Gene in Polish Children with Severe Combined Immunodeficiency: Diversity of Clinical Manifestations. Szaflarska A, et al. Arch Immunol Ther Exp (Warsz), 2016 Dec. PMID 28083621, Free PMC Article
    3. Agammaglobulinemia associated to nasal polyposis due to a hypomorphic RAG1 mutation in a 12 years old boy. Cifaldi C, et al. Clin Immunol, 2016 Dec. PMID 27713031
    4. Modeling altered T-cell development with induced pluripotent stem cells from patients with RAG1-dependent immune deficiencies. Brauer PM, et al. Blood, 2016 Aug 11. PMID 27301863, Free PMC Article
    5. Illegitimate RAG-mediated recombination events are involved in IKZF1 Δ3-6 deletion in BCR-ABL1 lymphoblastic leukaemia. Dong Y, et al. Clin Exp Immunol, 2016 Sep. PMID 27198500, Free PMC Article

    See all (157) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Understanding the Role of miR-29a in the Regulation of RAG1, a Gene Associated with the Development of the Immune System.
      Title: Understanding the Role of miR-29a in the Regulation of RAG1, a Gene Associated with the Development of the Immune System.
    2. miR-3202 inhibits bronchopulmonary dysplasia-mediated apoptosis and oxidative stress in bronchial epithelial cells via targeting RAG1.
      Title: miR-3202 inhibits bronchopulmonary dysplasia-mediated apoptosis and oxidative stress in bronchial epithelial cells via targeting RAG1.
    3. 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.
    4. 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.
    5. 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.
    6. Expression and clinical significance of RAG1 in myelodysplastic syndromes.
      Title: Expression and clinical significance of RAG1 in myelodysplastic syndromes.
    7. 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.
    8. RAG2 abolishes RAG1 aggregation to facilitate V(D)J recombination.
      Title: RAG2 abolishes RAG1 aggregation to facilitate V(D)J recombination.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (101)

    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)

    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_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
      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

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