RAG1 recombination activating 1 [Homo sapiens (human)] - Gene

Summary

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

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_000011.10 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?

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.
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.
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.
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.
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.
Expression and clinical significance of RAG1 in myelodysplastic syndromes.
Title: Expression and clinical significance of RAG1 in myelodysplastic syndromes.
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.
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.
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

Associated conditions

Description	Tests
Combined immunodeficiency due to partial RAG1 deficiency MedGen: C1835931 OMIM: 609889 GeneReviews: Not available	not available
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

GDB:197902 (e-PCR)
- UniSTS:155995

PMC164518P1 (e-PCR)
- UniSTS:271491

GDB:624547 (e-PCR)
- UniSTS:158347

RAG1_1421 (e-PCR)
- UniSTS:277656

RAG1_v468 (e-PCR)
- UniSTS:277656

SGC44589 (e-PCR)
- UniSTS:22426

GDB:316201 (e-PCR)
- UniSTS:156575

SHGC-6028 (e-PCR)
- UniSTS:58283

SHGC-44589 (e-PCR)
- UniSTS:43218

RAG1 (e-PCR)
- UniSTS:8930

STS-M29474 (e-PCR)
- UniSTS:8954

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

EC 2.3.2.27

NP_001364206.1

EC 2.3.2.27

NP_001364207.1

EC 2.3.2.27

NP_001364208.1

EC 2.3.2.27

NP_001364209.1

EC 2.3.2.27

XP_047283340.1

EC 2.3.2.27

XP_054225565.1

EC 2.3.2.27

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_007528.1 RefSeqGene

Range

5001..16750

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_98

mRNA and Protein(s)

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
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
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
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
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

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

36510353..36579762

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

E9PPC4, P15918, Q8IY72, Q8NER2

UniProtKB/TrEMBL

A0A6F7R719, A0A6F7R8J6