Rag1 MGI Mouse Gene Detail - MGI:97848 - recombination activating 1

Symbol

Rag1
Name

recombination activating 1
Synonyms

Rag-1

Feature Type

protein coding gene
IDs

MGI:97848
NCBI Gene: 19373
Alliance

gene page
Transcription Start Sites

12 TSS

Sequence Map

Chr2:101468627-101479846 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 53.88 cM
Mapping Data

17 experiments

SNPs within 2kb

411 from dbSNP Build 142
Strain Annotations

18
RFLP

4

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_97848	protein coding gene	Chr2:101468597-101479877 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0026190	protein coding gene	Chr2:103508950-103520166 (-)
A/J	MGP_AJ_G0026151	protein coding gene	Chr2:99236713-99247930 (-)
AKR/J	MGP_AKRJ_G0026132	protein coding gene	Chr2:101939265-101950481 (-)
BALB/cJ	MGP_BALBcJ_G0026160	protein coding gene	Chr2:99540846-99552061 (-)
C3H/HeJ	MGP_C3HHeJ_G0025911	protein coding gene	Chr2:102305886-102317104 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0026611	protein coding gene	Chr2:107014169-107025388 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024002	protein coding gene	Chr2:94942211-94953437 (-)
CAST/EiJ	MGP_CASTEiJ_G0025376	protein coding gene	Chr2:102723021-102734264 (-)
CBA/J	MGP_CBAJ_G0025889	protein coding gene	Chr2:110704403-110715617 (-)
DBA/2J	MGP_DBA2J_G0026025	protein coding gene	Chr2:98820406-98831620 (-)
FVB/NJ	MGP_FVBNJ_G0025988	protein coding gene	Chr2:97822407-97833646 (-)
LP/J	MGP_LPJ_G0026129	protein coding gene	Chr2:103668615-103679860 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0026014	protein coding gene	Chr2:114682783-114694024 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0026665	protein coding gene	Chr2:102156615-102167835 (-)
PWK/PhJ	MGP_PWKPhJ_G0025111	protein coding gene	Chr2:98295783-98307002 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0024912	protein coding gene	Chr2:101366076-101377281 (-)
WSB/EiJ	MGP_WSBEiJ_G0025443	protein coding gene	Chr2:102856430-102867654 (-)

Human Ortholog

RAG1, recombination activating 1

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

RAG1, recombination activating 1
Synonyms

RAG-1, RNF74
Links

HGNC:9831

NCBI Gene ID: 5896

neXtProt AC: NX_P15918

UniProt: P15918
Chr Location

11p12; chr11:36510353-36593156 (+) GRCh38

MGI Vertebrate Homology

Rag1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: RAG1
Gene Tree

Rag1

Diseases

4 with human RAG1 associations

Human Disease

Mouse Models

combined cellular and humoral immune defects with granulomas

IDs

Omenn syndrome

IDs

View 1 "NOT" model

severe combined immunodeficiency

IDs

severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, Nk cell-positive

IDs

Click on a disease name to see all genes associated with that disease.

Mutations/Alleles

2 with disease annotations

References

6 with disease annotations

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Phenotype Summary

77 phenotypes from 15 alleles in 23 genetic backgrounds
200 phenotypes from multigenic genotypes
1 images
2222 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

43
Chemically induced (ENU)

6
Chemically induced (other)

1
Endonuclease-mediated

20
Radiation induced

1
Targeted

15
Genomic Mutations

4 involving Rag1
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

123 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygotes for targeted null mutations exhibit arrested development of T and B cell maturation at the CD4-8- thymocyte or B220+/CD43+pro-B cell stage due to inability to undergo V(D)J recombination.

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All GO Annotations

50
GO References

25

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

892
Tissues

110
cDNA Data

24
Literature Summary

18

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase rag1

ZFIN rag1

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All Sequences

33
RefSeq

2
UniProt

3
CCDS

CCDS16463.1

Ensembl

ENSMUSG00000061311 (Evidence)
NCBI Gene

19373

			Length	Strain/Species	Flank
genomic	ENSMUSG00000061311	Ensembl Gene Model \| MGI Sequence Detail	11220	C57BL/6J	± kb
transcript	ENSMUST00000078494	Ensembl \| MGI Sequence Detail	6608	Not Applicable
polypeptide	ENSMUSP00000077584	Ensembl \| MGI Sequence Detail	1040	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000003457 V(D)J recombination-activating protein 1

(term hierarchy)
PDB

1RMD, 3GNA, 3GNB, 4WWX, 5ZDZ, 5ZE0, 5ZE1, 5ZE2, 6CG0, 6CIJ, 6CIK, 6CIL, 6CIM, 6OEM, 6OEN, 6OEO, 6OEP, 6OEQ, 6OER, 6OES, 6OET, 6V0V, 6XNX, 6XNY, 6XNZ
EC

2.3.2.27, 3.1.-.-
InterPro Domains

IPR035714 RAG1 importin-binding

IPR023336 RAG nonamer-binding domain

IPR024627 V(D)J recombination-activating protein 1

IPR019485 V(D)J recombination-activating protein 1, Zinc finger

IPR036236 Zinc finger C2H2 superfamily

IPR018957 Zinc finger, C3HC4 RING-type

IPR013083 Zinc finger, RING/FYVE/PHD-type

IPR001841 Zinc finger, RING-type

IPR017907 Zinc finger, RING-type, conserved site

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All nucleic 48

Genomic 13

cDNA 26

Primer pair 6

Other 3

Microarray probesets 3

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MGD-MRK-13753, MGD-MRK-13755

Summaries

All 2428

Developmental Gene Expression 18

Diseases 6

Gene Ontology 25

Phenotypes 2222
Earliest

J:109968 Roderick TH, et al., Nineteen paracentric chromosomal inversions in mice. Genetics. 1974 Jan;76(1):109-17
Latest

J:357485 Yomogida K, et al., The transcription factor Aiolos restrains the activation of intestinal intraepithelial lymphocytes. Nat Immunol. 2024 Jan;25(1):77-87

TSS for Rag1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr25375	Chr2:101481021-101481025 (-)	-1,177 bp
Tssr25374	Chr2:101479868-101479884 (-)	-30 bp
Tssr25373	Chr2:101479762-101479767 (-)	81 bp
Tssr25372	Chr2:101475202-101475217 (-)	4,636 bp
Tssr25371	Chr2:101474526-101474537 (-)	5,314 bp
Tssr25370	Chr2:101474257-101474264 (-)	5,585 bp
Tssr25369	Chr2:101474074-101474086 (-)	5,766 bp
Tssr25368	Chr2:101473934-101473943 (-)	5,907 bp
Tssr25367	Chr2:101471908-101471922 (-)	7,931 bp
Tssr25366	Chr2:101471612-101471623 (-)	8,228 bp
Tssr25365	Chr2:101470571-101470581 (-)	9,270 bp
Tssr25364	Chr2:101470447-101470468 (-)	9,388 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/12/2024 MGI 6.24