MOUSE:RAG1

Species (Taxon ID)	Mus musculus (Mouse). (10090)
Gene Name(s)	Rag1
Protein Name(s)	V(D)J recombination-activating protein 1 RAG-1 Endonuclease RAG1 E3 ubiquitin-protein ligase RAG1
External Links
UniProt	P15919
EMBL	M29475 AL929569 CH466519 BC138342
CCDS	CCDS16463.1
PIR	B33754
RefSeq	NP_033045.2 XP_006499075.1
UniGene	Mm.828
PDB	1RMD 3GNA 3GNB
PDBsum	1RMD 3GNA 3GNB
ProteinModelPortal	P15919
SMR	P15919
BioGrid	202574
DIP	DIP-48518N
IntAct	P15919
MINT	MINT-4131682
PhosphoSite	P15919
PaxDb	P15919
PRIDE	P15919
Ensembl	ENSMUST00000078494
GeneID	19373
KEGG	mmu:19373
UCSC	uc008lhk.2
CTD	5896
MGI	MGI:97848
eggNOG	NOG45367
GeneTree	ENSGT00390000008679
HOGENOM	HOG000232009
HOVERGEN	HBG003861
InParanoid	P15919
KO	K10628
OMA	IAKRFRY
OrthoDB	EOG76MK7J
TreeFam	TF331926
EvolutionaryTrace	P15919
NextBio	296463
PRO	PR:P15919
Proteomes	UP000000589
Bgee	P15919
CleanEx	MM_RAG1
ExpressionAtlas	P15919
Genevestigator	P15919
GO	GO:0005634 GO:0016881 GO:0004519 GO:0042393 GO:0046872 GO:0042803 GO:0043565 GO:0061630 GO:0004842 GO:0008270 GO:0002250 GO:0030183 GO:0016265 GO:0006310 GO:0010390 GO:0043154 GO:0070233 GO:0070244 GO:0090305 GO:0002331 GO:0051865 GO:0045580 GO:0033077 GO:0043029 GO:0048538 GO:0033151
Gene3D	3.30.160.60 3.30.40.10
InterPro	IPR024627 IPR023336 IPR015880 IPR013087 IPR018957 IPR001841 IPR013083 IPR017907 IPR019485
PANTHER	PTHR11539
Pfam	PF12940 PF00097 PF10426
SMART	SM00184 SM00355
PROSITE	PS51487 PS00518 PS50089

Annotations

Qualifier	GO ID	GO term name	Reference	ECO ID	ECO term name	with/from	Aspect	Extension	Notes	Status
	GO:0045582	positive regulation of T cell differentiation	PMID:1547488^[1]	ECO:0000315			P		Figures 3 and 4: in particular the lack of anti-IgM and -IgD staining indicates that there are no mature B cells in the spleen or bone marrow	complete CACAO 2852
involved_in	GO:0045582	positive regulation of T cell differentiation	PMID:1547488^[1]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:0051865	protein autoubiquitination	PMID:14671314^[2]	ECO:0000314	direct assay evidence used in manual assertion		P		Seeded From UniProt	complete
enables	GO:0046872	metal ion binding	PMID:10601033^[3]	ECO:0000315	mutant phenotype evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0043565	sequence-specific DNA binding	PMID:10601033^[3]	ECO:0000315	mutant phenotype evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0043565	sequence-specific DNA binding	PMID:19396172^[4]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0042803	protein homodimerization activity	PMID:9228952^[5]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0042803	protein homodimerization activity	PMID:19396172^[4]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0042393	histone binding	PMID:20122409^[6]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
involved_in	GO:0033151	V(D)J recombination	PMID:1547488^[1]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:0033151	V(D)J recombination	PMID:8284210^[7]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:0033151	V(D)J recombination	PMID:10601033^[3]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:0033151	V(D)J recombination	PMID:20122409^[6]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:0033077	T cell differentiation in thymus	PMID:1547488^[1]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:0030183	B cell differentiation	PMID:1547488^[1]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:0010390	histone monoubiquitination	PMID:20122409^[6]	ECO:0000314	direct assay evidence used in manual assertion		P		Seeded From UniProt	complete
enables	GO:0008270	zinc ion binding	PMID:9228952^[5]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
part_of	GO:0005634	nucleus	PMID:8284210^[7]	ECO:0000314	direct assay evidence used in manual assertion		C		Seeded From UniProt	complete
enables	GO:0004842	ubiquitin-protein transferase activity	PMID:12629039^[8]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0004842	ubiquitin-protein transferase activity	PMID:20122409^[6]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0004842	ubiquitin-protein transferase activity	PMID:14671314^[2]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0004519	endonuclease activity	PMID:10601033^[3]	ECO:0000315	mutant phenotype evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0004519	endonuclease activity	PMID:19396172^[4]	ECO:0000315	mutant phenotype evidence used in manual assertion		F		Seeded From UniProt	complete
involved_in	GO:0002331	pre-B cell allelic exclusion	PMID:19448632^[9]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
acts_upstream_of_or_within	GO:2000822	regulation of behavioral fear response	GO_REF:0000096	ECO:0000266	sequence orthology evidence used in manual assertion	RGD:619790	P		Seeded From UniProt	complete
acts_upstream_of_or_within	GO:0070244	negative regulation of thymocyte apoptotic process	PMID:15728238^[10]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
acts_upstream_of_or_within	GO:0070233	negative regulation of T cell apoptotic process	PMID:18684012^[11]	ECO:0000316	genetic interaction evidence used in manual assertion	MGI:MGI:1353616	P		Seeded From UniProt	complete
enables	GO:0061630	ubiquitin protein ligase activity	PMID:20122409^[6]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0061630	ubiquitin protein ligase activity	PMID:14671314^[2]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0061630	ubiquitin protein ligase activity	PMID:12629039^[8]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0061630	ubiquitin protein ligase activity	GO_REF:0000008	ECO:0000266	sequence orthology evidence used in manual assertion	UniProtKB:P21784	F		Seeded From UniProt	complete
acts_upstream_of_or_within	GO:0048538	thymus development	PMID:18684012^[11]	ECO:0000316	genetic interaction evidence used in manual assertion	MGI:MGI:1353616	P		Seeded From UniProt	complete
acts_upstream_of_or_within	GO:0045580	regulation of T cell differentiation	PMID:18684012^[11]	ECO:0000316	genetic interaction evidence used in manual assertion	MGI:MGI:1353616	P		Seeded From UniProt	complete
acts_upstream_of_or_within	GO:0043154	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process	PMID:15728238^[10]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
acts_upstream_of_or_within	GO:0043029	T cell homeostasis	PMID:18684012^[11]	ECO:0000316	genetic interaction evidence used in manual assertion	MGI:MGI:1353616	P		Seeded From UniProt	complete
acts_upstream_of_or_within	GO:0033151	V(D)J recombination	PMID:2360047^[12]	ECO:0000316	genetic interaction evidence used in manual assertion	MGI:MGI:97849	P	occurs_in:(CL:0000057)	Seeded From UniProt	complete
acts_upstream_of_or_within	GO:0033151	V(D)J recombination	GO_REF:0000096	ECO:0000266	sequence orthology evidence used in manual assertion	UniProtKB:P15918	P		Seeded From UniProt	complete
acts_upstream_of_or_within	GO:0033077	T cell differentiation in thymus	PMID:9215624^[13]	ECO:0000315	mutant phenotype evidence used in manual assertion	MGI:MGI:2448994	P	occurs_in:(EMAPA:18768)	Seeded From UniProt	complete
acts_upstream_of_or_within	GO:0030183	B cell differentiation	PMID:11976687^[14]	ECO:0000314	direct assay evidence used in manual assertion		P		Seeded From UniProt	complete
acts_upstream_of_or_within	GO:0008542	visual learning	GO_REF:0000096	ECO:0000266	sequence orthology evidence used in manual assertion	RGD:619790	P		Seeded From UniProt	complete
acts_upstream_of_or_within	GO:0002250	adaptive immune response	PMID:22801499^[15]	ECO:0000315	mutant phenotype evidence used in manual assertion	MGI:MGI:1857241	P		Seeded From UniProt	complete
enables	GO:0042802	identical protein binding	PMID:21149691^[16]	ECO:0000353	physical interaction evidence used in manual assertion	UniProtKB:P15919	F		Seeded From UniProt	complete
enables	GO:0042802	identical protein binding	PMID:19396172^[4]	ECO:0000353	physical interaction evidence used in manual assertion	UniProtKB:P15919	F		Seeded From UniProt	complete
involved_in	GO:0090305	nucleic acid phosphodiester bond hydrolysis	GO_REF:0000108	ECO:0000366	evidence based on logical inference from automatic annotation used in automatic assertion	GO:0004519	P		Seeded From UniProt	complete
involved_in	GO:0090305	nucleic acid phosphodiester bond hydrolysis	GO_REF:0000108	ECO:0000364	evidence based on logical inference from manual annotation used in automatic assertion	GO:0004519	P		Seeded From UniProt	complete
involved_in	GO:0090305	nucleic acid phosphodiester bond hydrolysis	GO_REF:0000108	ECO:0000364	evidence based on logical inference from manual annotation used in automatic assertion	GO:0004519	P		Seeded From UniProt	complete
involved_in	GO:0090305	nucleic acid phosphodiester bond hydrolysis	GO_REF:0000108	ECO:0000366	evidence based on logical inference from automatic annotation used in automatic assertion	GO:0004519	P		Seeded From UniProt	complete
involved_in	GO:0090305	nucleic acid phosphodiester bond hydrolysis	GO_REF:0000108	ECO:0000366	evidence based on logical inference from automatic annotation used in automatic assertion	GO:0004518	P		Seeded From UniProt	complete
involved_in	GO:2000822	regulation of behavioral fear response	GO_REF:0000107	ECO:0000265	sequence orthology evidence used in automatic assertion	UniProtKB:G3V6K9 ensembl:ENSRNOP00000006115	P		Seeded From UniProt	complete
involved_in	GO:0008542	visual learning	GO_REF:0000107	ECO:0000265	sequence orthology evidence used in automatic assertion	UniProtKB:G3V6K9 ensembl:ENSRNOP00000006115	P		Seeded From UniProt	complete
involved_in	GO:0033151	V(D)J recombination	GO_REF:0000107	ECO:0000265	sequence orthology evidence used in automatic assertion	UniProtKB:P15918 ensembl:ENSP00000299440	P		Seeded From UniProt	complete
enables	GO:0004519	endonuclease activity	GO_REF:0000002	ECO:0000256	match to sequence model evidence used in automatic assertion	InterPro:IPR024627	F		Seeded From UniProt	complete
involved_in	GO:0033151	V(D)J recombination	GO_REF:0000002	ECO:0000256	match to sequence model evidence used in automatic assertion	InterPro:IPR024627	P		Seeded From UniProt	complete
enables	GO:0043565	sequence-specific DNA binding	GO_REF:0000002	ECO:0000256	match to sequence model evidence used in automatic assertion	InterPro:IPR024627	F		Seeded From UniProt	complete
enables	GO:0046872	metal ion binding	GO_REF:0000002	ECO:0000256	match to sequence model evidence used in automatic assertion	InterPro:IPR018957	F		Seeded From UniProt	complete
enables	GO:0061630	ubiquitin protein ligase activity	GO_REF:0000002	ECO:0000256	match to sequence model evidence used in automatic assertion	InterPro:IPR024627	F		Seeded From UniProt	complete
part_of	GO:0005654	nucleoplasm	Reactome:R-MMU-8865728	ECO:0000304	author statement supported by traceable reference used in manual assertion		C		Seeded From UniProt	complete
acts_upstream_of_or_within	GO:0006310	DNA recombination	PMID:12606021^[17]	ECO:0000304	author statement supported by traceable reference used in manual assertion		P		Seeded From UniProt	complete
enables	GO:0016740	transferase activity	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0808	F		Seeded From UniProt	complete
enables	GO:0004519	endonuclease activity	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0255	F		Seeded From UniProt	complete
enables	GO:0004518	nuclease activity	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0540	F		Seeded From UniProt	complete
enables	GO:0003677	DNA binding	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0238	F		Seeded From UniProt	complete
part_of	GO:0005634	nucleus	GO_REF:0000037 GO_REF:0000039	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0539 UniProtKB-SubCell:SL-0191	C		Seeded From UniProt	complete
involved_in	GO:0008152	metabolic process	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0511	P		Seeded From UniProt	complete
enables	GO:0003824	catalytic activity	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0511	F		Seeded From UniProt	complete
enables	GO:0046872	metal ion binding	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0479	F		Seeded From UniProt	complete
involved_in	GO:0006325	chromatin organization	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0156	P		Seeded From UniProt	complete
enables	GO:0016787	hydrolase activity	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0378	F		Seeded From UniProt	complete
involved_in	GO:0006310	DNA recombination	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0233	P		Seeded From UniProt	complete
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Notes

References

See Help:References for how to manage references in GONUTS.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 Mombaerts, P et al. (1992) RAG-1-deficient mice have no mature B and T lymphocytes. Cell 68 869-77 PubMed GONUTS page
↑ ^2.0 ^2.1 ^2.2 Jones, JM & Gellert, M (2003) Autoubiquitylation of the V(D)J recombinase protein RAG1. Proc. Natl. Acad. Sci. U.S.A. 100 15446-51 PubMed GONUTS page
↑ ^3.0 ^3.1 ^3.2 ^3.3 Kim, DR et al. (1999) Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase. Genes Dev. 13 3070-80 PubMed GONUTS page
↑ ^4.0 ^4.1 ^4.2 ^4.3 Yin, FF et al. (2009) Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis. Nat. Struct. Mol. Biol. 16 499-508 PubMed GONUTS page
↑ ^5.0 ^5.1 Bellon, SF et al. (1997) Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster. Nat. Struct. Biol. 4 586-91 PubMed GONUTS page
↑ ^6.0 ^6.1 ^6.2 ^6.3 ^6.4 Grazini, U et al. (2010) The RING domain of RAG1 ubiquitylates histone H3: a novel activity in chromatin-mediated regulation of V(D)J joining. Mol. Cell 37 282-93 PubMed GONUTS page
↑ ^7.0 ^7.1 Sadofsky, MJ et al. (1993) Expression and V(D)J recombination activity of mutated RAG-1 proteins. Nucleic Acids Res. 21 5644-50 PubMed GONUTS page
↑ ^8.0 ^8.1 Yurchenko, V et al. (2003) The RAG1 N-terminal domain is an E3 ubiquitin ligase. Genes Dev. 17 581-5 PubMed GONUTS page
↑ Hewitt, SL et al. (2009) RAG-1 and ATM coordinate monoallelic recombination and nuclear positioning of immunoglobulin loci. Nat. Immunol. 10 655-64 PubMed GONUTS page
↑ ^10.0 ^10.1 Mandal, M et al. (2005) The BCL2A1 gene as a pre-T cell receptor-induced regulator of thymocyte survival. J. Exp. Med. 201 603-14 PubMed GONUTS page
↑ ^11.0 ^11.1 ^11.2 ^11.3 Ahn, S et al. (2008) TSCOT+ thymic epithelial cell-mediated sensitive CD4 tolerance by direct presentation. PLoS Biol. 6 e191 PubMed GONUTS page
↑ Oettinger, MA et al. (1990) RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248 1517-23 PubMed GONUTS page
↑ Maraskovsky, E et al. (1997) Bcl-2 can rescue T lymphocyte development in interleukin-7 receptor-deficient mice but not in mutant rag-1-/- mice. Cell 89 1011-9 PubMed GONUTS page
↑ Miyamoto, A et al. (2002) Increased proliferation of B cells and auto-immunity in mice lacking protein kinase Cdelta. Nature 416 865-9 PubMed GONUTS page
↑ Shui, JW et al. (2012) HVEM signalling at mucosal barriers provides host defence against pathogenic bacteria. Nature 488 222-5 PubMed GONUTS page
↑ Grundy, GJ et al. (2010) Autoinhibition of DNA cleavage mediated by RAG1 and RAG2 is overcome by an epigenetic signal in V(D)J recombination. Proc. Natl. Acad. Sci. U.S.A. 107 22487-92 PubMed GONUTS page
↑ Ohinata, Y et al. (2003) A novel testis-specific RAG2-like protein, Peas: its expression in pachytene spermatocyte cytoplasm and meiotic chromatin. FEBS Lett. 537 1-5 PubMed GONUTS page

[PMID:1547488-1] 1.0 ^1.1 ^1.2 ^1.3 ^1.4 Mombaerts, P et al. (1992) RAG-1-deficient mice have no mature B and T lymphocytes. Cell 68 869-77 PubMed GONUTS page

[PMID:14671314-2] 2.0 ^2.1 ^2.2 Jones, JM & Gellert, M (2003) Autoubiquitylation of the V(D)J recombinase protein RAG1. Proc. Natl. Acad. Sci. U.S.A. 100 15446-51 PubMed GONUTS page

[PMID:10601033-3] 3.0 ^3.1 ^3.2 ^3.3 Kim, DR et al. (1999) Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase. Genes Dev. 13 3070-80 PubMed GONUTS page

[PMID:19396172-4] 4.0 ^4.1 ^4.2 ^4.3 Yin, FF et al. (2009) Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis. Nat. Struct. Mol. Biol. 16 499-508 PubMed GONUTS page

[PMID:9228952-5] 5.0 ^5.1 Bellon, SF et al. (1997) Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster. Nat. Struct. Biol. 4 586-91 PubMed GONUTS page

[PMID:20122409-6] 6.0 ^6.1 ^6.2 ^6.3 ^6.4 Grazini, U et al. (2010) The RING domain of RAG1 ubiquitylates histone H3: a novel activity in chromatin-mediated regulation of V(D)J joining. Mol. Cell 37 282-93 PubMed GONUTS page

[PMID:8284210-7] 7.0 ^7.1 Sadofsky, MJ et al. (1993) Expression and V(D)J recombination activity of mutated RAG-1 proteins. Nucleic Acids Res. 21 5644-50 PubMed GONUTS page

[PMID:12629039-8] 8.0 ^8.1 Yurchenko, V et al. (2003) The RAG1 N-terminal domain is an E3 ubiquitin ligase. Genes Dev. 17 581-5 PubMed GONUTS page

[PMID:19448632-9] Hewitt, SL et al. (2009) RAG-1 and ATM coordinate monoallelic recombination and nuclear positioning of immunoglobulin loci. Nat. Immunol. 10 655-64 PubMed GONUTS page

[PMID:15728238-10] 10.0 ^10.1 Mandal, M et al. (2005) The BCL2A1 gene as a pre-T cell receptor-induced regulator of thymocyte survival. J. Exp. Med. 201 603-14 PubMed GONUTS page

[PMID:18684012-11] 11.0 ^11.1 ^11.2 ^11.3 Ahn, S et al. (2008) TSCOT+ thymic epithelial cell-mediated sensitive CD4 tolerance by direct presentation. PLoS Biol. 6 e191 PubMed GONUTS page

[PMID:2360047-12] Oettinger, MA et al. (1990) RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248 1517-23 PubMed GONUTS page

[PMID:9215624-13] Maraskovsky, E et al. (1997) Bcl-2 can rescue T lymphocyte development in interleukin-7 receptor-deficient mice but not in mutant rag-1-/- mice. Cell 89 1011-9 PubMed GONUTS page

[PMID:11976687-14] Miyamoto, A et al. (2002) Increased proliferation of B cells and auto-immunity in mice lacking protein kinase Cdelta. Nature 416 865-9 PubMed GONUTS page

[PMID:22801499-15] Shui, JW et al. (2012) HVEM signalling at mucosal barriers provides host defence against pathogenic bacteria. Nature 488 222-5 PubMed GONUTS page

[PMID:21149691-16] Grundy, GJ et al. (2010) Autoinhibition of DNA cleavage mediated by RAG1 and RAG2 is overcome by an epigenetic signal in V(D)J recombination. Proc. Natl. Acad. Sci. U.S.A. 107 22487-92 PubMed GONUTS page

[PMID:12606021-17] Ohinata, Y et al. (2003) A novel testis-specific RAG2-like protein, Peas: its expression in pachytene spermatocyte cytoplasm and meiotic chromatin. FEBS Lett. 537 1-5 PubMed GONUTS page

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MOUSE:RAG1

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