rag1 recombination activating 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: rag1provided by ZNC
Official Full Name: recombination activating 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-234
See related: Ensembl:ENSDARG00000052122 AllianceGenome:ZFIN:ZDB-GENE-990415-234
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: RAG-1
Summary: Enables magnesium ion binding activity and sequence-specific DNA binding activity. Contributes to double-stranded DNA endonuclease activity. Acts upstream of or within V(D)J recombination and protein-DNA complex assembly. Part of DNA recombinase complex and endodeoxyribonuclease complex. Is expressed in several structures, including gonad; hematopoietic cell; hypophysis; immune system; and ventral wall of dorsal aorta. 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, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 25

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	25	NC_007136.7 (9003355..9009873)
105	previous assembly	GRCz10 (GCF_000002035.5)	25	NC_007136.6 (8926291..8932805)

Chromosome 25 - NC_007136.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Rag1 activity does not seem to be limited to V(D)J recombination but is also involved in senescence and aging.
Title: Rag1 immunodeficiency-induced early aging and senescence in zebrafish are dependent on chronic inflammation and oxidative stress.
Differential gene expression following TLR stimulation in rag1-/- mutant zebrafish tissues and morphological descriptions of lymphocyte-like cell populations
Title: Differential gene expression following TLR stimulation in rag1-/- mutant zebrafish tissues and morphological descriptions of lymphocyte-like cell populations.
first report of any rag1(-/-) mutant vertebrate mounting a protective secondary immune response to a bacterial pathogen
Title: Rag1-/- mutant zebrafish demonstrate specific protection following bacterial re-exposure.
This report describes the leukocyte populations in a unique model, recombination activation gene 1-/- mutant zebrafish (rag1 mutants).
Title: Characterization of rag1 mutant zebrafish leukocytes.
Recombination signal sequences are recognized by rag1 protein.
Title: Analysis of recombination signal sequences in zebrafish.
Rag1 has a role in developing zebrafish cortex-medullary regionalization
Title: Morphologic transformation of the thymus in developing zebrafish.
Rag1 expression is restricted to a subpopulation of zebrafish olfactory neurons projecting to the lateral olfactory bulb; Rag11 catalytic activity is not essential for axon targeting
Title: The recombination activation gene 1 (Rag1) is expressed in a subset of zebrafish olfactory neurons but is not essential for axon targeting or amino acid detection.
by embryonic day 4, rag1 transcripts are seen in the pancreas
Title: B cells develop in the zebrafish pancreas.

Submit: New GeneRIF Correction

General gene information

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Markers

rag1 (e-PCR), detects polymorphism
- UniSTS:205447

Gene Ontology Provided by ZFIN

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
contributes_to double-stranded DNA endonuclease activity	IGI Inferred from Genetic Interaction more info	PubMed
enables endonuclease activity	IEA Inferred from Electronic Annotation more info
enables endonuclease activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone binding	IEA Inferred from Electronic Annotation more info
enables histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity, acting on ester bonds	IEA Inferred from Electronic Annotation more info
enables magnesium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
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	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	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
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	IEA Inferred from Electronic Annotation more info
enables ubiquitin-protein transferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in B cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in B cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within DNA recombination	IEA Inferred from Electronic Annotation more info
involved_in T cell differentiation in thymus	IEA Inferred from Electronic Annotation more info
involved_in T cell differentiation in thymus	ISS Inferred from Sequence or Structural Similarity more info
involved_in V(D)J recombination	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within V(D)J recombination	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within V(D)J recombination	IPI Inferred from Physical Interaction 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
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within protein-DNA complex assembly	IPI Inferred from Physical Interaction more info	PubMed
acts_upstream_of_or_within somatic diversification of immune receptors via germline recombination within a single locus	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of DNA recombinase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of DNA recombinase complex	IPI Inferred from Physical Interaction more info	PubMed
part_of endodeoxyribonuclease complex	IBA Inferred from Biological aspect of Ancestor more info
part_of endodeoxyribonuclease complex	IPI Inferred from Physical Interaction more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation 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: etID309719.25; recombinase; recombination activating gene 1; recombination activating protein 1

NP_571464.1

EC 2.3.2.27

XP_005163033.1

EC 2.3.2.27

XP_009296061.1

EC 2.3.2.27

XP_068073418.1

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.

mRNA and Protein(s)

NM_131389.1 → NP_571464.1 V(D)J recombination-activating protein 1

See identical proteins and their annotated locations for NP_571464.1

Status: PROVISIONAL

Source sequence(s)

U71093

UniProtKB/Swiss-Prot

O13033, Q90258

Related

ENSDARP00000150596.1, ENSDART00000189501.1

Conserved Domains (3) summary

smart00184
Location:296 → 334

RING; Ring finger

pfam12560
Location:13 → 294

RAG1_imp_bd; RAG1 importin binding

pfam12940
Location:400 → 1047

RAG1; Recombination-activation protein 1 (RAG1)

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

NC_007136.7 Reference GRCz11 Primary Assembly

Range

9003355..9009873

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_068217317.1 → XP_068073418.1 V(D)J recombination-activating protein 1 isoform X1

UniProtKB/TrEMBL

A0A8M2BAA4, F1QD74
XM_009297786.4 → XP_009296061.1 V(D)J recombination-activating protein 1 isoform X1

See identical proteins and their annotated locations for XP_009296061.1

UniProtKB/TrEMBL

A0A8M2BAA4, F1QD74

Related

ENSDARP00000120100.1, ENSDART00000142917.3

Conserved Domains (3) summary

smart00184
Location:296 → 334

RING; Ring finger

pfam12560
Location:13 → 294

RAG1_imp_bd; RAG1 importin binding

pfam12940
Location:400 → 1047

RAG1; Recombination-activation protein 1 (RAG1)
XM_005162976.5 → XP_005163033.1 V(D)J recombination-activating protein 1 isoform X1

See identical proteins and their annotated locations for XP_005163033.1

UniProtKB/TrEMBL

A0A8M2BAA4, F1QD74

Related

ENSDARP00000149705.1, ENSDART00000180330.1

Conserved Domains (3) summary

smart00184
Location:296 → 334

RING; Ring finger

pfam12560
Location:13 → 294

RAG1_imp_bd; RAG1 importin binding

pfam12940
Location:400 → 1047

RAG1; Recombination-activation protein 1 (RAG1)