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Aliases for RAG1 Gene

Aliases for RAG1 Gene

  • Recombination Activating Gene 1 2 3
  • RING Finger Protein 74 2 3 4
  • Recombination Activating Protein 1 2 3
  • RAG-1 3 4
  • RNF74 3 4
  • V(D)J Recombination-Activating Protein 1 2

External Ids for RAG1 Gene

Previous GeneCards Identifiers for RAG1 Gene

  • GC11P038146
  • GC11P037266
  • GC11P036628
  • GC11P036553
  • GC11P036292

Summaries for RAG1 Gene

Entrez Gene Summary for RAG1 Gene

  • 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]

GeneCards Summary for RAG1 Gene

RAG1 (Recombination Activating Gene 1) is a Protein Coding gene. Diseases associated with RAG1 include omenn syndrome and combined immunodeficiency t+ b+ due to partial rag1 deficiency. Among its related pathways are Signaling by GPCR and Interleukin receptor SHC signaling. GO annotations related to this gene include protein homodimerization activity and ubiquitin-protein transferase activity.

UniProtKB/Swiss-Prot for RAG1 Gene

  • Catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell receptor genes in developing B and T-lymphocytes through rearrangement of different V (variable), in some cases D (diversity), and J (joining) gene segments. In the RAG complex, RAG1 mediates the DNA-binding to the conserved recombination signal sequences (RSS) and catalyzes the DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. RAG2 is not a catalytic component but is required for all known catalytic activities. DNA cleavage occurs in 2 steps: a first nick is introduced in the top strand immediately upstream of the heptamer, generating a 3-hydroxyl group that can attack the phosphodiester bond on the opposite strand in a direct transesterification reaction, thereby creating 4 DNA ends: 2 hairpin coding ends and 2 blunt, 5-phosphorylated ends. The chromatin structure plays an essential role in the V(D)J recombination reactions and the presence of histone H3 trimethylated at Lys-4 (H3K4me3) stimulates both the nicking and haipinning steps. The RAG complex also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and monospecific recognition by the B-cell antigen receptor (BCR) expressed on individual B-lymphocytes. The introduction of DNA breaks by the RAG complex on one immunoglobulin allele induces ATM-dependent repositioning of the other allele to pericentromeric heterochromatin, preventing accessibility to the RAG complex and recombination of the second allele. In addition to its endonuclease activity, RAG1 also acts as a E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3. Histone H3 monoubiquitination is required for the joining step of V(D)J recombination. Mediates polyubiquitination of KPNA1 (By similarity).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RAG1 Gene

Genomics for RAG1 Gene

Regulatory Elements for RAG1 Gene

Genomic Location for RAG1 Gene

Chromosome:
11
Start:
36,510,400 bp from pter
End:
36,593,156 bp from pter
Size:
82,757 bases
Orientation:
Plus strand

Genomic View for RAG1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for RAG1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAG1 Gene

Proteins for RAG1 Gene

  • Protein details for RAG1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P15918-RAG1_HUMAN
    Recommended name:
    V(D)J recombination-activating protein 1
    Protein Accession:
    P15918
    Secondary Accessions:
    • E9PPC4
    • Q8IY72
    • Q8NER2

    Protein attributes for RAG1 Gene

    Size:
    1043 amino acids
    Molecular mass:
    119097 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Note=Binds 1 divalent metal cation per subunit. Mg(2+) or Mn(2+).;
    Quaternary structure:
    • Homodimer. Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2. Interacts with VPRBP, leading to recruitment of the CUL4A-RBX1-DDB1-DCAF1/VPRBP complex to ubiquitinate proteins and limit error-prone repair during V(D)J recombination (By similarity).
    SequenceCaution:
    • Sequence=AAM77798.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for RAG1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RAG1 Gene

Proteomics data for RAG1 Gene at MOPED

Post-translational modifications for RAG1 Gene

Other Protein References for RAG1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for RAG1 (RAG1)

No data available for DME Specific Peptides for RAG1 Gene

Domains & Families for RAG1 Gene

Gene Families for RAG1 Gene

Suggested Antigen Peptide Sequences for RAG1 Gene

Graphical View of Domain Structure for InterPro Entry

P15918

UniProtKB/Swiss-Prot:

RAG1_HUMAN :
  • The RING-type zinc finger mediates the E3 ubiquitin-protein ligase activity.
  • Belongs to the RAG1 family.
  • Contains 1 RAG1-type zinc finger.
Domain:
  • The RING-type zinc finger mediates the E3 ubiquitin-protein ligase activity.
  • The NBD (nonamer binding) DNA-binding domain mediates the specific binding to the nonamer RSS motif by forming a tightly interwoven homodimer that binds and synapses 2 nonamer elements, with each NBD making contact with both DNA molecules. Each RSS is composed of well-conserved heptamer (consensus 5-CACAGTG-3) and nonamer (consensus 5-ACAAAAACC-3) sequences separated by a spacer of either 12 bp or 23 bp.
  • Contains 1 NBD (nonamer binding) DNA-binding domain.
Family:
  • Belongs to the RAG1 family.
Similarity:
  • Contains 1 RAG1-type zinc finger.
  • Contains 1 RING-type zinc finger.
genes like me logo Genes that share domains with RAG1: view

Function for RAG1 Gene

Molecular function for RAG1 Gene

GENATLAS Biochemistry:
recombination V(D)J activating gene 1,acting,in conjuction with RAG2,at a pair of recombination signal sequences and making double strand breaks,next to these signals,located 8kb apart from RAG2,convergently oriented
UniProtKB/Swiss-Prot Function:
Catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell receptor genes in developing B and T-lymphocytes through rearrangement of different V (variable), in some cases D (diversity), and J (joining) gene segments. In the RAG complex, RAG1 mediates the DNA-binding to the conserved recombination signal sequences (RSS) and catalyzes the DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. RAG2 is not a catalytic component but is required for all known catalytic activities. DNA cleavage occurs in 2 steps: a first nick is introduced in the top strand immediately upstream of the heptamer, generating a 3-hydroxyl group that can attack the phosphodiester bond on the opposite strand in a direct transesterification reaction, thereby creating 4 DNA ends: 2 hairpin coding ends and 2 blunt, 5-phosphorylated ends. The chromatin structure plays an essential role in the V(D)J recombination reactions and the presence of histone H3 trimethylated at Lys-4 (H3K4me3) stimulates both the nicking and haipinning steps. The RAG complex also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and monospecific recognition by the B-cell antigen receptor (BCR) expressed on individual B-lymphocytes. The introduction of DNA breaks by the RAG complex on one immunoglobulin allele induces ATM-dependent repositioning of the other allele to pericentromeric heterochromatin, preventing accessibility to the RAG complex and recombination of the second allele. In addition to its endonuclease activity, RAG1 also acts as a E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3. Histone H3 monoubiquitination is required for the joining step of V(D)J recombination. Mediates polyubiquitination of KPNA1 (By similarity).

Gene Ontology (GO) - Molecular Function for RAG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding TAS 9630231
GO:0004519 endonuclease activity ISS --
GO:0004842 ubiquitin-protein transferase activity ISS --
GO:0005515 protein binding IPI 17474147
GO:0008270 zinc ion binding ISS --
genes like me logo Genes that share ontologies with RAG1: view
genes like me logo Genes that share phenotypes with RAG1: view

Animal Models for RAG1 Gene

MGI Knock Outs for RAG1:

Animal Model Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for RAG1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for RAG1 Gene

Localization for RAG1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAG1 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RAG1 Gene COMPARTMENTS Subcellular localization image for RAG1 gene
Compartment Confidence
nucleus 4
extracellular 2
mitochondrion 2
plasma membrane 2
cytosol 1

Gene Ontology (GO) - Cellular Components for RAG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with RAG1: view

Pathways & Interactions for RAG1 Gene

genes like me logo Genes that share pathways with RAG1: view

Pathways by source for RAG1 Gene

1 Cell Signaling Technology pathway for RAG1 Gene
2 KEGG pathways for RAG1 Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

SIGNOR curated interactions for RAG1 Gene

Activates:

Gene Ontology (GO) - Biological Process for RAG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002250 adaptive immune response IEA --
GO:0002331 pre-B cell allelic exclusion ISS --
GO:0006310 DNA recombination TAS 9630231
GO:0006955 immune response TAS 9630231
GO:0010390 histone monoubiquitination ISS --
genes like me logo Genes that share ontologies with RAG1: view

Drugs & Compounds for RAG1 Gene

(11) Drugs for RAG1 Gene - From: NovoSeek and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Dexamethasone Approved, Investigational Pharma Agonist 1806
Probenecid Approved Pharma Activator 27
Zinc Approved Pharma 1404
Caffeine Approved Nutra Activator 317
Cytidine Experimental Pharma 0

(4) Additional Compounds for RAG1 Gene - From: NovoSeek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
12-O-Tetradecanoylphorbol 13-acetate
aspartate
IONOMYCIN
TCDD
genes like me logo Genes that share compounds with RAG1: view

Transcripts for RAG1 Gene

mRNA/cDNA for RAG1 Gene

Unigene Clusters for RAG1 Gene

Recombination activating gene 1:
Representative Sequences:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for RAG1

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for RAG1 Gene

No ASD Table

Relevant External Links for RAG1 Gene

GeneLoc Exon Structure for
RAG1
ECgene alternative splicing isoforms for
RAG1

Expression for RAG1 Gene

mRNA expression in normal human tissues for RAG1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RAG1 Gene

This gene is overexpressed in Spleen (x6.5).

Protein differential expression in normal tissues from HIPED for RAG1 Gene

This gene is overexpressed in Plasma (68.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for RAG1 Gene



SOURCE GeneReport for Unigene cluster for RAG1 Gene Hs.73958

mRNA Expression by UniProt/SwissProt for RAG1 Gene

P15918-RAG1_HUMAN
Tissue specificity: Maturing lymphoid cells
genes like me logo Genes that share expression patterns with RAG1: view

Protein tissue co-expression partners for RAG1 Gene

Primer Products

In Situ Assay Products

Orthologs for RAG1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RAG1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia RAG1 35
  • 88.18 (n)
  • 91.28 (a)
RAG1 36
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RAG1 35
  • 81.02 (n)
  • 83.6 (a)
RAG1 36
  • 84 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rag1 35
  • 86.09 (n)
  • 89.81 (a)
Rag1 16
Rag1 36
  • 90 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RAG1 35
  • 99.71 (n)
  • 99.71 (a)
RAG1 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rag1 35
  • 86.35 (n)
  • 90.1 (a)
oppossum
(Monodelphis domestica)
Mammalia RAG-1 36
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RAG1 36
  • 95 (a)
OneToOne
chicken
(Gallus gallus)
Aves RAG1 35
  • 73.03 (n)
  • 76.8 (a)
lizard
(Anolis carolinensis)
Reptilia RAG1 36
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rag1 35
  • 69.54 (n)
  • 73.13 (a)
zebrafish
(Danio rerio)
Actinopterygii rag1 35
  • 63.18 (n)
  • 62.95 (a)
rag1 36
  • 58 (a)
OneToOne
Species with no ortholog for RAG1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RAG1 Gene

ENSEMBL:
Gene Tree for RAG1 (if available)
TreeFam:
Gene Tree for RAG1 (if available)

Paralogs for RAG1 Gene

(1) SIMAP similar genes for RAG1 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with RAG1: view

No data available for Paralogs for RAG1 Gene

Variants for RAG1 Gene

Sequence variations from dbSNP and Humsavar for RAG1 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs331440 -- 36,526,684(+) ctaat(C/T)tacac intron-variant
rs331441 -- 36,525,613(+) tgttt(A/C/T)gtacg intron-variant
rs331442 -- 36,523,845(+) gtaac(A/G)tcatg intron-variant
rs331443 -- 36,523,120(+) atttt(C/G)aaatg intron-variant
rs331444 -- 36,521,754(+) ttgac(C/T)aaaat intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RAG1 Gene

Variant ID Type Subtype PubMed ID
esv2422305 CNV Duplication 17116639
nsv467791 CNV Gain 19166990
nsv832123 CNV Gain 17160897

Variation tolerance for RAG1 Gene

Residual Variation Intolerance Score: 16.02% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.76; 86.71% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RAG1 Gene

HapMap Linkage Disequilibrium report
RAG1
Human Gene Mutation Database (HGMD)
RAG1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RAG1 Gene

Disorders for RAG1 Gene

MalaCards: The human disease database

(22) MalaCards diseases for RAG1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, NovoSeek, and GeneCards

Disorder Aliases PubMed IDs
omenn syndrome
  • reticuloendotheliosis familial with eosinophilia
combined immunodeficiency t+ b+ due to partial rag1 deficiency
  • cid t+ b+ due to partial rag1 deficiency
alpha/beta t-cell lymphopenia with gamma/delta t-cell expansion, severe cytomegalovirus infection, and autoimmunity
  • alpha/beta t-cell lymphopenia, with gamma/delta t-cell expansion, severe cytomegalovirus infection and autoimmunity
combined cellular and humoral immune defects with granulomas
  • chidg
combined immunodeficiency with skin granulomas
  • cid due to rag 1/2 deficiency
- elite association
Search RAG1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RAG1_HUMAN
  • Alpha/beta T-cell lymphopenia, with gamma/delta T-cell expansion, severe cytomegalovirus infection and autoimmunity (T-CMVA) [MIM:609889]: An immunological disorder characterized by oligoclonal expansion of TCR gamma/delta T-cells, TCR alpha/beta T-cell lymphopenia, severe, disseminated cytomegalovirus infection and autoimmune cytopenia. {ECO:0000269 PubMed:16276422}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Combined cellular and humoral immune defects with granulomas (CHIDG) [MIM:233650]: Immunodeficiency disease with granulomas in the skin, mucous membranes, and internal organs. Other characteristics include hypogammaglobulinemia, a diminished number of T and B-cells, and sparse thymic tissue on ultrasonography. {ECO:0000269 PubMed:18463379}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Omenn syndrome (OS) [MIM:603554]: Severe immunodeficiency characterized by the presence of activated, anergic, oligoclonal T-cells, hypereosinophilia, and high IgE levels. {ECO:0000269 PubMed:10606976, ECO:0000269 PubMed:11133745, ECO:0000269 PubMed:19912631, ECO:0000269 PubMed:21624848, ECO:0000269 PubMed:21771083, ECO:0000269 PubMed:9630231}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-negative/NK-cell-positive (T(-)B(-)NK(+) SCID) [MIM:601457]: A form of severe combined immunodeficiency (SCID), a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients present in infancy recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. {ECO:0000269 PubMed:19912631, ECO:0000269 PubMed:8810255}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for RAG1

Genetic Association Database (GAD)
RAG1
Human Genome Epidemiology (HuGE) Navigator
RAG1
Tumor Gene Database (TGDB):
RAG1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RAG1
genes like me logo Genes that share disorders with RAG1: view

No data available for Genatlas for RAG1 Gene

Publications for RAG1 Gene

  1. Requirement for ubiquitin conjugation and 26S proteasome activity at an early stage in V(D)J recombination. (PMID: 20116856) Bhattacharyya A. … Jones J.M. (Mol. Immunol. 2010) 23 67
  2. The RING domain of RAG1 ubiquitylates histone H3: a novel activity in chromatin-mediated regulation of V(D)J joining. (PMID: 20122409) Grazini U. … McBlane F. (Mol. Cell 2010) 23 67
  3. The in vivo pattern of binding of RAG1 and RAG2 to antigen receptor loci. (PMID: 20398922) Ji Y. … Schatz D.G. (Cell 2010) 23 67
  4. Striking decrease in the total precursor B-cell compartment during early childhood as evidenced by flow cytometry and gene expression changes. (PMID: 20121553) Jensen K. … Osnes L.T. (Pediatr Hematol Oncol 2010) 23 67
  5. Karyopherin alpha 1 is a putative substrate of the RAG1 ubiquitin ligase. (PMID: 19118899) Simkus C. … Jones J.M. (Mol. Immunol. 2009) 23 67

Products for RAG1 Gene

Sources for RAG1 Gene

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