Rag1 recombination activating 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rag1provided by MGI
Official Full Name: recombination activating 1provided by MGI
Primary source: MGI:MGI:97848
See related: Ensembl:ENSMUSG00000061311 AllianceGenome:MGI:97848
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Rag-1
Summary: Enables several functions, including protein homodimerization activity; ubiquitin protein ligase activity; and zinc ion binding activity. Involved in immune system development; positive regulation of T cell differentiation; and protein ubiquitination. Acts upstream of or within several processes, including T cell homeostasis; hematopoietic or lymphoid organ development; and negative regulation of apoptotic process. Located in nucleus. Is expressed in several structures, including arterial system; early conceptus; genitourinary system; gut; and hemolymphoid system. Human ortholog(s) of this gene implicated in Omenn syndrome; combined cellular and humoral immune defects with granulomas; severe combined immunodeficiency; and severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, Nk cell-positive. Orthologous to human RAG1 (recombination activating 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Restricted expression toward thymus adult (RPKM 117.3) See more
Orthologs: human all
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Genomic context

Location:: 2 E2; 2 53.88 cM

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (101468597..101479877, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (101638252..101649532, complement)

Chromosome 2 - NC_000068.8 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The thymocyte-specific RNA-binding protein Arpp21 provides TCR repertoire diversity by binding to the 3'-UTR and promoting Rag1 mRNA expression.
Title: The thymocyte-specific RNA-binding protein Arpp21 provides TCR repertoire diversity by binding to the 3'-UTR and promoting Rag1 mRNA expression.
Exonic knockout and knockin gene editing in hematopoietic stem and progenitor cells rescues RAG1 immunodeficiency.
Title: Exonic knockout and knockin gene editing in hematopoietic stem and progenitor cells rescues RAG1 immunodeficiency.
Rag1 Deficiency Impairs Arteriogenesis in Mice.
Title: Rag1 Deficiency Impairs Arteriogenesis in Mice.
Spi-C and PU.1 Counterregulate Rag1 and Igkappa Transcription to Effect Vkappa-Jkappa Recombination in Small Pre-B Cells.
Title: Spi-C and PU.1 Counterregulate Rag1 and Igκ Transcription to Effect Vκ-Jκ Recombination in Small Pre-B Cells.
The RAG1 Ubiquitin Ligase Domain Stimulates Recombination of TCRbeta and TCRalpha Genes and Influences Development of alphabeta T Cell Lineages.
Title: The RAG1 Ubiquitin Ligase Domain Stimulates Recombination of TCRβ and TCRα Genes and Influences Development of αβ T Cell Lineages.
Zika virus vertical transmission in interferon receptor1-antagonized Rag1(-/-) mice results in postnatal brain abnormalities and clinical disease.
Title: Zika virus vertical transmission in interferon receptor1-antagonized Rag1(-/-) mice results in postnatal brain abnormalities and clinical disease.
MicroRNA miR-29c regulates RAG1 expression and modulates V(D)J recombination during B cell development.
Title: MicroRNA miR-29c regulates RAG1 expression and modulates V(D)J recombination during B cell development.
Healing of sub-critical femoral osteotomies in mice is unaffected by tacrolimus and deletion of recombination activating gene 1.
Title: Healing of sub-critical femoral osteotomies in mice is unaffected by tacrolimus and deletion of recombination activating gene 1.
The RAG1 N-terminal region regulates the efficiency and pathways of synapsis for V(D)J recombination.
Title: The RAG1 N-terminal region regulates the efficiency and pathways of synapsis for V(D)J recombination.
ADAM9 enhances Th17 cell differentiation and autoimmunity by activating TGF-beta1.
Title: ADAM9 enhances Th17 cell differentiation and autoimmunity by activating TGF-β1.

Submit: New GeneRIF Correction See all GeneRIFs (107)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (11) 1 citation
Chemically induced (ENU) (6) 1 citation
Endonuclease-mediated (18) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Rag1 (e-PCR), detects polymorphism
- UniSTS:261910

M29475 (e-PCR)
- UniSTS:124951

Rag1 (e-PCR), detects polymorphism
- UniSTS:516123

PMC133542P3 (e-PCR)
- UniSTS:270627

Rag1 (e-PCR), detects polymorphism
- UniSTS:259400

PMC209472P1 (e-PCR)
- UniSTS:271996

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

Rag1 (e-PCR), detects polymorphism
- UniSTS:256450

PMC155324P1 (e-PCR)
- UniSTS:271337

PMC102110P1 (e-PCR)
- UniSTS:270074

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables catalytic activity	IEA Inferred from Electronic Annotation more info
contributes_to double-stranded DNA endonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables endonuclease activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone binding	IDA Inferred from Direct Assay more info	PubMed
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables nuclease activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within B cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in B cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within DNA recombination	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within T cell differentiation in thymus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in T cell differentiation in thymus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within T cell homeostasis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in V(D)J recombination	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within V(D)J recombination	IGI Inferred from Genetic Interaction more info	PubMed
involved_in V(D)J recombination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in V(D)J recombination	ISO Inferred from Sequence Orthology more info
involved_in adaptive immune response	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within adaptive immune response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of T cell apoptotic process	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of cysteine-type endopeptidase activity involved in apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of thymocyte apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of T cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in pre-B cell allelic exclusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in pre-B cell allelic exclusion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein autoubiquitination	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of T cell differentiation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of behavioral fear response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within thymus development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in visual learning	ISO Inferred from Sequence Orthology 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	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: V(D)J recombination-activating protein 1

Names: recombinase activating gene 1; recombination activating gene 1; recombination activating protein 1

NP_033045.2

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.

mRNA and Protein(s)

NM_009019.2 → NP_033045.2 V(D)J recombination-activating protein 1

See identical proteins and their annotated locations for NP_033045.2

Status: VALIDATED

Source sequence(s)

AK162974, AL929569

Consensus CDS

CCDS16463.1

UniProtKB/Swiss-Prot

A2AVN8, P15919

UniProtKB/TrEMBL

Q78NA6

Related

ENSMUSP00000077584.6, ENSMUST00000078494.6

Conserved Domains (4) summary

pfam00097
Location:290 → 328

zf-C3HC4; Zinc finger, C3HC4 type (RING finger)

pfam10426
Location:351 → 380

zf-RAG1; Recombination-activating protein 1 zinc-finger domain

pfam12560
Location:12 → 288

RAG1_imp_bd; RAG1 importin binding

pfam12940
Location:386 → 1024

RAG1; Recombination-activation protein 1 (RAG1)