Rag2 (recombination activating 2)

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Gene: Rag2 (recombination activating 2) Rattus norvegicus

Analyze

Symbol:

Rag2

Name:

recombination activating 2

RGD ID:

1305588

Description:

Predicted to enable several functions, including phosphatidylinositol phosphate binding activity; phosphatidylinositol-3,4-bisphosphate binding activity; and zinc ion binding activity. Involved in mature B cell differentiation involved in immune response and negative regulation of T cell differentiation in thymus. Predicted to be located in nucleus. Predicted to be part of DNA recombinase complex. Used to study severe combined immunodeficiency. 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 RAG2 (recombination activating 2); PARTICIPATES IN histone modification pathway; primary immunodeficiency pathway; INTERACTS WITH ammonium chloride; copper atom; copper(0).

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC295953; recombination activating gene 2; recombination activating protein 2; V(D)J recombination-activating protein 2

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	RAG2 (recombination activating 2)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Rag2 (recombination activating gene 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Rag2 (recombination activating 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	RAG2 (recombination activating 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	RAG2 (recombination activating 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Rag2 (recombination activating 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	RAG2 (recombination activating 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	RAG2 (recombination activating 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Rag2 (recombination activating 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	RAG2 (recombination activating 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Rag2 (recombination activating gene 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	rag2 (recombination activating gene 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	rag2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Allele / Splice:

Rag2^em2Mcwi Rag2^em3Mcwi Rag2^em1Mcwi Rag2^em1Sage Rag2^em1Iexas

Genetic Models:

SD-Rag2^em2Mcwi SS-Rag2^em1Mcwi SD-Rag2^em3Mcwi SD-Rag2^em3McwiIl2rg^em2Mcwi SD-Rag2^em1Sage F344-Rag2^em1Sage F344-Il2rg^em1IexasRag2^em1Iexas F344-Rag2^em1Iexas

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	87,902,373 - 87,910,227 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	87,902,238 - 87,911,066 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	91,393,248 - 91,401,103 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	3	99,992,269 - 100,000,128 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	3	97,824,520 - 97,832,368 (+)	NCBI	Rnor_WKY
Rnor_6.0	3	91,191,837 - 91,200,134 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	91,191,837 - 91,200,134 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	97,851,318 - 97,859,615 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	86,764,810 - 86,773,438 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	86,661,236 - 86,668,153 (+)	NCBI
Celera	3	87,008,586 - 87,016,420 (+)	NCBI		Celera
Cytogenetic Map	3	q31	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

combined cellular and humoral immune defects with granulomas (ISO)

common variable immunodeficiency (ISO)

Eosinophilia (ISO)

Experimental Arthritis (ISO)

genetic disease (ISO)

histiocytic sarcoma (ISO)

Immunodeficiency 104 (ISO)

intellectual disability (ISO)

Metaplasia (ISO)

non-alcoholic fatty liver disease (ISO)

Omenn syndrome (ISO)

recombinase activating gene 2 deficiency (ISO)

severe combined immunodeficiency (IMP,ISO)

severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2-butoxyethanol (ISO)

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

bisphenol A (ISO)

bromodichloromethane (ISO)

copper atom (EXP)

copper(0) (EXP)

cypermethrin (ISO)

lead diacetate (ISO)

lipopolysaccharide (ISO)

paracetamol (EXP)

perfluorohexanesulfonic acid (ISO)

perfluorononanoic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

B cell differentiation (ISO)

B cell homeostatic proliferation (ISO)

B cell lineage commitment (ISO)

defense response to bacterium (ISO)

DN2 thymocyte differentiation (ISO)

mature B cell differentiation involved in immune response (IMP)

negative regulation of T cell differentiation in thymus (IMP)

organ growth (ISO)

positive regulation of organ growth (ISO)

pre-B cell allelic exclusion (ISO)

T cell differentiation (ISO)

T cell differentiation in thymus (ISO)

T cell lineage commitment (ISO)

V(D)J recombination (IBA,ISO)

Cellular Component

DNA recombinase complex (IBA)

nucleus (IEA)

Molecular Function

chromatin binding (ISO)

methylated histone binding (ISO)

phosphatidylinositol binding (ISO)

phosphatidylinositol-3,4,5-trisphosphate binding (ISO)

phosphatidylinositol-3,4-bisphosphate binding (ISO)

phosphatidylinositol-3,5-bisphosphate binding (ISO)

phosphatidylinositol-4,5-bisphosphate binding (ISO)

protein binding (ISO)

sequence-specific DNA binding (IBA)

ubiquitin protein ligase activity (IEA)

zinc ion binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

histone modification pathway (ISO)

primary immunodeficiency pathway (IEA)

Phenotype Annotations Click to see Annotation Detail View

Mammalian Phenotype

absent mature B cells (IMP)

decreased double-positive T cell number (IMP)

decreased thymus weight (IMP)

increased incidence of induced tumors (IMP)

increased NK cell number (IMP)

small spleen (IMP)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
3.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
4.	Sprague Dawley Rag2-Null Rats Created from Engineered Spermatogonial Stem Cells Are Immunodeficient and Permissive to Human Xenografts.	Noto FK, etal., Mol Cancer Ther. 2018 Nov;17(11):2481-2489. doi: 10.1158/1535-7163.MCT-18-0156. Epub 2018 Sep 11.
5.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
6.	Readout of epigenetic modifications.	Patel DJ and Wang Z, Annu Rev Biochem. 2013;82:81-118. doi: 10.1146/annurev-biochem-072711-165700.
7.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
8.	GOA pipeline	RGD automated data pipeline
9.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
11.	Comprehensive gene review and curation	RGD comprehensive gene curation
12.	RAG mutations in human B cell-negative SCID.	Schwarz K, etal., Science. 1996 Oct 4;274(5284):97-9.
13.	Partial V(D)J recombination activity leads to Omenn syndrome.	Villa A, etal., Cell. 1998 May 29;93(5):885-96.

Additional References at PubMed

PMID:1547487	PMID:1547488	PMID:2360047	PMID:8788039	PMID:9052834	PMID:9252127	PMID:9875844	PMID:11214319	PMID:11980719	PMID:14530129	PMID:14595002	PMID:14766966
PMID:15964836	PMID:18025461	PMID:18033247	PMID:19448632

Genomics

Comparative Map Data

Rag2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	87,902,373 - 87,910,227 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	87,902,238 - 87,911,066 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	91,393,248 - 91,401,103 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	3	99,992,269 - 100,000,128 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	3	97,824,520 - 97,832,368 (+)	NCBI	Rnor_WKY
Rnor_6.0	3	91,191,837 - 91,200,134 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	91,191,837 - 91,200,134 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	97,851,318 - 97,859,615 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	86,764,810 - 86,773,438 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	86,661,236 - 86,668,153 (+)	NCBI
Celera	3	87,008,586 - 87,016,420 (+)	NCBI		Celera
Cytogenetic Map	3	q31	NCBI

RAG2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	11	36,590,996 - 36,598,236 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	11	36,575,574 - 36,598,279 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	11	36,613,493 - 36,619,786 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	36,570,069 - 36,576,388 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	11	36,765,924 - 36,772,260 (-)	NCBI		Celera
Cytogenetic Map	11	p12	NCBI
HuRef	11	36,316,277 - 36,322,614 (-)	NCBI		HuRef
CHM1_1	11	36,612,179 - 36,618,515 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	11	36,734,171 - 36,741,410 (-)	NCBI		T2T-CHM13v2.0

Rag2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	101,455,057 - 101,462,873 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	101,455,063 - 101,462,874 (+)	Ensembl		GRCm39 Ensembl
GRCm38	2	101,624,712 - 101,632,528 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	101,624,718 - 101,632,529 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	101,464,905 - 101,472,685 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	101,425,587 - 101,433,367 (+)	NCBI		MGSCv36	mm8
Celera	2	102,849,742 - 102,857,519 (+)	NCBI		Celera
Cytogenetic Map	2	E2	NCBI
cM Map	2	53.87	NCBI

Rag2
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955422	9,867,307 - 9,869,732 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955422	9,867,307 - 9,869,732 (+)	NCBI	ChiLan1.0	ChiLan1.0

RAG2
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1	11	38,810,920 - 38,813,448 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	11	36,558,419 - 36,564,997 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	11	36,431,067 - 36,437,390 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	36,431,703 - 36,433,286 (-)	Ensembl	panpan1.1		panPan2

RAG2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	18	31,614,143 - 31,621,489 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	18	31,618,481 - 31,620,064 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	18	31,225,259 - 31,228,771 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	18	32,228,286 - 32,231,796 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	18	32,228,787 - 32,230,370 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	18	31,798,300 - 31,801,806 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	18	31,382,649 - 31,386,158 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	18	32,019,854 - 32,023,367 (+)	NCBI		UU_Cfam_GSD_1.0

Rag2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404947	28,680,736 - 28,683,548 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936533	1,801,391 - 1,807,431 (+)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936533	1,801,207 - 1,807,431 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RAG2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	24,547,644 - 24,558,403 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	24,547,605 - 24,553,944 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	26,716,416 - 26,717,999 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

RAG2
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	1	28,645,175 - 28,653,823 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	1	28,649,930 - 28,651,513 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666038	125,790,092 - 125,792,520 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Rag2
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624767	10,678,359 - 10,680,132 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624767	10,678,547 - 10,680,130 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Rag2
61 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	145
Count of miRNA genes:	99
Interacting mature miRNAs:	121
Transcripts:	ENSRNOT00000006097
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	91609953	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10861912	89878372	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	29463235	118376539	Rat
61419	Cia11	Collagen induced arthritis QTL 11	5.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	3	30356773	98535386	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	31172320	163586636	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	33703347	104104347	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	38192233	133483320	Rat
1331777	Bw24	Body weight QTL 24	3.503		body mass (VT:0001259)	body weight (CMO:0000012)	3	39454637	89115240	Rat
1331795	Rf30	Renal function QTL 30	3.708		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	3	39454637	89115240	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	41874578	104104347	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	41874578	155617519	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	41874578	155617519	Rat
1300178	Hrtrt4	Heart rate QTL 4	3.74		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	43827364	90905114	Rat
1581503	Cm58	Cardiac mass QTL 58	2.7	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	43827364	121056321	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	43827364	169034231	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	47233211	147415807	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	47233430	110362260	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	47233430	110362260	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	50437042	119183768	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	50437504	115638231	Rat
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	115665732	Rat
1582238	Bw68	Body weight QTL 68	3.2	0.0064	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	115665732	Rat
1582239	Epfw1	Epididymal fat weight QTL 1	4.5	0.0006	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	3	53184593	115665732	Rat
61377	Edpm3	Estrogen-dependent pituitary mass QTL 3	7.05	0.038	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	53184692	89878207	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	53781112	91609953	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	53781112	91609953	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	53781112	91609953	Rat
1581568	Rf53	Renal function QTL 53			urine total protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	56395968	161299569	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	59242096	157323038	Rat
1300111	Rf12	Renal function QTL 12	3.78		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	61017749	121056321	Rat
631200	Cm25	Cardiac mass QTL 25	4.8	0.0001	heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	3	61134348	89115068	Rat
1582210	Bw71	Body weight QTL 71	3.3	0.0012	body mass (VT:0001259)	body weight (CMO:0000012)	3	64655305	115665732	Rat
1582221	Kidm30	Kidney mass QTL 30	3.5	0.0008	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	3	64655305	115665732	Rat
12879848	Bw181	Body weght QTL 181		0.015	body mass (VT:0001259)	body weight (CMO:0000012)	3	70348525	121056321	Rat
2301414	Kidm37	Kidney mass QTL 37		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	70653097	121056321	Rat
1600376	Arunc5	Aerobic running capacity QTL 5		0.21	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	73376539	118376539	Rat
1581546	Pur13	Proteinuria QTL 13	2.93	0.0335	urine total protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	3	78196190	146592722	Rat
2302273	Gluco35	Glucose level QTL 35	5.3	0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	80800231	114297550	Rat

Markers in Region

Rag2

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	87,906,536 - 87,907,242 (+)	MAPPER	mRatBN7.2
mRatBN7.2	3	87,906,902 - 87,907,242 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	91,196,367 - 91,197,149	NCBI	Rnor6.0
Rnor_6.0	3	91,196,810 - 91,197,149	NCBI	Rnor6.0
Rnor_5.0	3	97,856,291 - 97,856,630	UniSTS	Rnor5.0
Rnor_5.0	3	97,855,848 - 97,856,630	UniSTS	Rnor5.0
RGSC_v3.4	3	86,770,114 - 86,770,453	UniSTS	RGSC3.4
Celera	3	87,013,090 - 87,013,429	UniSTS
Cytogenetic Map	3	q31	UniSTS

UniSTS:259651

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Celera	3	87,011,896 - 87,013,491	UniSTS
Cytogenetic Map	3	q31	UniSTS

PMC196132P1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	87,906,536 - 87,907,220 (+)	MAPPER	mRatBN7.2
mRatBN7.2	3	87,906,897 - 87,907,220 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	91,196,362 - 91,197,127	NCBI	Rnor6.0
Rnor_6.0	3	91,196,805 - 91,197,127	NCBI	Rnor6.0
Rnor_5.0	3	97,856,286 - 97,856,608	UniSTS	Rnor5.0
Rnor_5.0	3	97,855,843 - 97,856,608	UniSTS	Rnor5.0
RGSC_v3.4	3	86,770,109 - 86,770,431	UniSTS	RGSC3.4
Celera	3	87,013,085 - 87,013,407	UniSTS
Cytogenetic Map	3	q31	UniSTS

Genetic Models

This gene Rag2 is modified in the following models/strains

SD-Rag2^em2Mcwi

SS-Rag2^em1Mcwi

SD-Rag2^em3Mcwi

SD-Rag2^em3McwiIl2rg^em2Mcwi

SD-Rag2^em1Sage

F344-Rag2^em1Sage

F344-Il2rg^em1IexasRag2^em1Iexas

F344-Rag2^em1Iexas

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium			7		7
Low			14	12	11	12			1		3	4
Below cutoff	2	14	27	20	1	20	8	8	8	10	17	6	8

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001100528	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AY011941	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY303209	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000118	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000006097 ⟹ ENSRNOP00000006097

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	87,902,238 - 87,911,066 (+)	Ensembl
Rnor_6.0 Ensembl	3	91,191,837 - 91,200,134 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000103802 ⟹ ENSRNOP00000086217

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	87,902,238 - 87,911,066 (+)	Ensembl

RefSeq Acc Id:

NM_001100528 ⟹ NP_001093998

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	87,902,373 - 87,910,227 (+)	NCBI
Rnor_6.0	3	91,191,837 - 91,200,134 (+)	NCBI
Rnor_5.0	3	97,851,318 - 97,859,615 (+)	NCBI
RGSC_v3.4	3	86,764,810 - 86,773,438 (+)	RGD
Celera	3	87,008,586 - 87,016,420 (+)	RGD

Sequence:

show sequence

CACTCTACCCTTCAGCCTTCAGCTTGCCACAGTCAAACTAAACAGTCAGTGACCCTCCCCAAGT
GCCGAGTTTAATTCCCCGCTTGGCAGCAAGGATTCAGAGAGGGATAAGCAGCCCCTCTGGCCTT
CAGTGCCAAAATAAGAGTACTTCACATCCACAAGCAGGAAGTAGACTTCATACCTCTCTAAGAT
AAAAGACCTACTCACAATCAAAAAATGTCCCTGCAGATGGTTACAGTGGGTCATAACATAGCCT
TAATTCAACCAGGCTTCTCACTGATGAATTTTGATGGTCAAGTTTTTTTCTTTGGCCAAAAAGG
CTGGCCTAAGAGATCCTGCCCTACTGGAGTCTTTCATTTTGATATAAAACAAAATCATCTCAAA
CTGAAGCCTGCAGTTTTCTCTAAAGATTCCTGCTACCTCCCACCTCTTCGTTACCCAGCTACTT
GCTCGTACAAAGGCAGCACAGACTCTGACAAGCATCAATATATCATCCACGGAGGGAAAACGCC
AAACAATGAGCTTTCCGATAAGATTTATATCATGTCTGTCGCTTGCAAGAATAACAAAAAAGTT
ACTTTCCGTTGTACAGAGAAAGACTTAGTAGGAGATGTCCCTGAAGCCAGATATGGCCATTCCA
TTGACGTGGTATATAGCCGAGGAAAAAGTGTTGGTGTTCTCTTTGGAGGACGGTCATACATGCC
TTCTACCCAAAGAACCACAGAAAAATGGAATAGTGTAGCTGATTGCCTACCCCATGTTTTCTTG
GTAGATTTTGAATTTGGGTGTGCAACGTCATATATTCTCCCAGAACTTCAGGACGGGCTGTCTT
TTCATGTTTCTATTGCCAGAAATGATACCATTTATATTTTGGGAGGACACTCACTTGCCAGTAA
CATACGTCCTGCTAACTTGTATAGAATAAGAGTAGATCTTCCCCTGGGTACCCCAGCAGTGAAT
TGCACTGTCTTGCCAGGAGGAATCTCTGTCTCCAGTGCAATTGTCACTCAAACAAATAATGATG
AATTTGTTATTGTTGGTGGTTATCAGCTGGAAAATCAAAAAAGGATGGTGTGTAGCATTGTCTC
TCTAGGGGACAACAGGATTGAAATTAGTGAGATGGAGACCCCAGACTGGACCCCAGATATTAAG
CATAGCAAAATATGGTTTGGAAGCAACATGGGAAACGGGACTGTTTTCCTTGGCATACCAGGAG
ACAACAAGCAGGCTATGTCAGAAGCATTCTATTTCTATATGTTGAGATGCTCTGAAGATAATTC
GAGTGAGGAGCAGAAAATTGTCTCAAACAGTCAGACATCAACTGAAGATGCCGGGGACTCCACT
CCCTTTGAAGACTCGGAAGAATTTTGTTTCAGTGCTGAAGCAATCAGCTTTGATGGTGATGATG
AATTTGACACTTACAATGAAGATGATGAAGATGATGAATCTGTAACCGGCTACTGGATAACGTG
TTCCCCTACTTGTGATGTGGACATCAATACTTGGGTTCCATTCTATTCAACTGAGCTCAATAAA
CCCGCCATGATCTATTGTTCTCATGGGGATGGACACTGGGTGCATGCCCAGTGCATGGATCTGG
AAGAACGCACACTCATCCACTTGTCAGAAGGAAGCAACAAATATTACTGCAATGAGCATGTGCG
GATAGCAAGAGCATTACAAACTCCCAAAAGAAACCTCCCCTTACAAAAGCCCCCAATGAAATCC
CTCCACAAAAAAGGCTCCGGGAAAGTCTTGACTCCTGCCAAGAAATCCTTTCTTAGGAGGTTGT
TTGATTAGTTCAGCAAAAGCCCCTCAGATTCACGTGCGTTGGTTTCTAAATCTACTCTTTAAAT
CATAAACGGAATTTCGATTTTTGTTTACTGAAATCTATATGCTACGTTTTGGTTGTGTGAATTA
AGCGCTGTTTTGATGTGATGTTAAGTACAATTATTCTAACATGTGTGGTTTTTAACATTTTATC
TGTAATTTCTTAAATGAGAAATGTTACACAGTCTTTCATTAAGGATAGCAGTGATAAAGTATAG
AGCTCTTGCATTATTTTGTAACAATCTACATGTTGAATAGTAACTAAATACCAATAAACTAATG
CACAAAAACAATTAAGTTGTTTTGTGTAATAAATAGCCTATAGTTGGTTTAAACAGTTAAAACT
ATATTCCACACTACTGCTGTTTATAAATTTTAAGGTGGCCTCTTGGATTATACCCATGAACAGA
CAGATATAGATATAGATATAGATATAGATATAGATATAGATATAGATATAGATATAGATATAGA
TATAGATATAGATATAGATAGATAGATATAGATAGATATAGATAGACAGACAGACAGACAGACA
GATAGATAGAGATAGAGATAGATATATTGTGTATTCAGCACCATGAAGAAAAAAACTAATCTAT
ATCAAGCCAGGTATAGTGATGGTGATACACGCCTGTAATCCTGGCAAATTTGTGAGTTTGATGC
TCGTTGAGGTATGGTCTCTTGCTATGTGTTGTAATGCTAAGTGCGGGCCCCAAGATCTGCTTGC
TCCAGAGTCAAGAGAGCCCACAAATAGACCCAAGTGATTCTCTGCAACCTTGCCCCCAAGTTAT
TTGTGGTTGAGTGAATAAAGATGCCAACAGCCAATAGCTGAGCAGAAGATACATAGGTGGGGGT
TGATGATGCCCTGGCTTGGGGTAGGAGGAGACCATGAGGAAGGGGGAGAAAAAGGTGAAGTCTC
CTCCTTCACCTAAAAAAGCATAGGTTAGGAGTCAAAAAAACATGGCCCTGAGTGCTGGCCACTG
GGAGTTAAGAGCAGCCCAGATGAAATGTCGCAATAACTTGGGGTATAAGTAGGAAATAGATTTT
AATAGCATATAAGGTAGATATCTACCCAGCCCTAGAGCTAATTAAGGCTTATTGTAAATATAAA
GGTCTTACGTGTCAGGAAAAAAATGGTCAAACAAGGAGTAGAAACTCTGAATTGGGATCAAAAT
TTTCTACAACAGACACCGTCTGGGGCTACATTTTATCTCAAATCCAAAAGCTGATAGAAGACAG
AGCACTGGTGGCATTGTCACGTCCCATGCTCAAAGTCCTGAGTCCAATACTGTGGACATTTTCT
TGAATTACCTACATACGCTTCAGGAGTAAAAAATATATTCCAAACACACGCCTTTGTCCGAATC
ACTCGCTTTGGGGCCTCACATTTAATTCCTTCAAAATCAATGGTTCACCCCCTTTGAAAATGCT
CAATTGTTGTTCCTCTTTTTCCTTAAAGATGGTTGTCATCTCTGGAAATAGTCATATGTCATTC
AAGGCCCGATAGCATGAAGCCCTGAAGTGTTGCCTTACCACTTTAATTGAAAAGTGAAATATGA
CCATAAGCTTAGACAGTGGTTTGGGGCTATTAATCTCATGGCAGGGTTTGGGGGTGCCTAATAC
TGAGTCCTGAACTGTTTTCTAAGTACCTGTTTTCAAACAAGTATGGAAATGTTATCAATAAATA
TGCTATCAATAAAAAGAAAACTTTCATATTCC

hide sequence

Protein Sequences


Protein RefSeqs	NP_001093998	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAG38684	(Get FASTA)	NCBI Sequence Viewer
	AAQ77003	(Get FASTA)	NCBI Sequence Viewer
	EDL79623	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001093998 ⟸ NM_001100528

- UniProtKB:

G3V6K7 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPAVFSK
DSCYLPPLRYPATCSYKGSTDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKVTFRCTEKD
LVGDVPEARYGHSIDVVYSRGKSVGVLFGGRSYMPSTQRTTEKWNSVADCLPHVFLVDFEFGCA
TSYILPELQDGLSFHVSIARNDTIYILGGHSLASNIRPANLYRIRVDLPLGTPAVNCTVLPGGI
SVSSAIVTQTNNDEFVIVGGYQLENQKRMVCSIVSLGDNRIEISEMETPDWTPDIKHSKIWFGS
NMGNGTVFLGIPGDNKQAMSEAFYFYMLRCSEDNSSEEQKIVSNSQTSTEDAGDSTPFEDSEEF
CFSAEAISFDGDDEFDTYNEDDEDDESVTGYWITCSPTCDVDINTWVPFYSTELNKPAMIYCSH
GDGHWVHAQCMDLEERTLIHLSEGSNKYYCNEHVRIARALQTPKRNLPLQKPPMKSLHKKGSGK
VLTPAKKSFLRRLFD

hide sequence

RefSeq Acc Id:

ENSRNOP00000006097 ⟸ ENSRNOT00000006097

RefSeq Acc Id:

ENSRNOP00000086217 ⟸ ENSRNOT00000103802

Protein Domains

Recombination activating protein 2 PHD

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-G3V6K7-F1-model_v2	AlphaFold	G3V6K7	1-527	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13692240

Promoter ID:

EPDNEW_R2764

Type:

initiation region

Name:

Rag2_1

Description:

recombination activating 2

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	91,191,830 - 91,191,890	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305588	AgrOrtholog
BioCyc Gene	G2FUF-48612	BioCyc
Ensembl Genes	ENSRNOG00000004623	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000006097	ENTREZGENE
	ENSRNOP00000006097.4	UniProtKB/TrEMBL
	ENSRNOP00000086217.1	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000006097	ENTREZGENE
	ENSRNOT00000006097.6	UniProtKB/TrEMBL
	ENSRNOT00000103802.1	UniProtKB/TrEMBL
Gene3D-CATH	2.120.10.80	UniProtKB/TrEMBL
	Rag2 PHD finger	UniProtKB/TrEMBL
InterPro	Gal_Oxase/kelch_b-propeller	UniProtKB/TrEMBL
	Kelch-typ_b-propeller	UniProtKB/TrEMBL
	RAG2	UniProtKB/TrEMBL
	RAG2_PHD	UniProtKB/TrEMBL
	Znf_FYVE_PHD	UniProtKB/TrEMBL
KEGG Report	rno:295953	UniProtKB/TrEMBL
NCBI Gene	295953	ENTREZGENE
PANTHER	RAG2	UniProtKB/TrEMBL
	V(D)J RECOMBINATION-ACTIVATING PROTEIN 2	UniProtKB/TrEMBL
Pfam	RAG2	UniProtKB/TrEMBL
	RAG2_PHD	UniProtKB/TrEMBL
PhenoGen	Rag2	PhenoGen
Superfamily-SCOP	Gal_oxid_central	UniProtKB/TrEMBL
	SSF57903	UniProtKB/TrEMBL
UniProt	G3V6K7	ENTREZGENE, UniProtKB/TrEMBL
	Q6W9A2_RAT	UniProtKB/TrEMBL
	Q99NM1_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-08-24	Rag2	recombination activating 2	Rag2	recombination activating gene 2	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Rag2	recombination activating gene 2	Rag2_predicted	recombination activating gene 2 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Rag2_predicted	recombination activating gene 2 (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)

Mammalian Phenotype

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)

Mammalian Phenotype