Nbn nibrin [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nbnprovided by RGD
Official Full Name: nibrinprovided by RGD
Primary source: RGD:621420
See related: EnsemblRapid:ENSRNOG00000008580 AllianceGenome:RGD:621420
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Nbs1
Summary: Predicted to enable several functions, including chromatin-protein adaptor activity; phosphorylation-dependent protein binding activity; and protein serine/threonine kinase activator activity. Involved in several processes, including negative regulation of neuron differentiation; negative regulation of viral entry into host cell; and regulation of fibroblast proliferation. Predicted to be located in Golgi apparatus; nucleus; and replication fork. Predicted to be part of BRCA1-C complex and Mre11 complex. Predicted to be active in chromosome, telomeric region and site of double-strand break. Human ortholog(s) of this gene implicated in several diseases, including Nijmegen breakage syndrome; acute lymphoblastic leukemia; aplastic anemia; rectum cancer; and reproductive organ cancer (multiple). Orthologous to human NBN (nibrin). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Heart (RPKM 229.0), Muscle (RPKM 192.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q13

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (34256678..34291163)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (29459574..29494152)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (29622347..29656877)

Chromosome 5 - NC_086023.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Effect of silencing SSB1 gene on the expression of NBS1 in irradiated rat submandibular gland cells.
Title: Effect of silencing SSB1 gene on the expression of NBS1 in irradiated rat submandibular gland cells.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor binding	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin-protein adaptor activity	IEA Inferred from Electronic Annotation more info
enables chromatin-protein adaptor activity	ISO Inferred from Sequence Orthology more info
enables chromatin-protein adaptor activity	ISS Inferred from Sequence or Structural Similarity more info
enables damaged DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables damaged DNA binding	IEA Inferred from Electronic Annotation more info
enables damaged DNA binding	ISO Inferred from Sequence Orthology more info
enables histone binding	IEA Inferred from Electronic Annotation more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables phosphorylation-dependent protein binding	IEA Inferred from Electronic Annotation more info
enables phosphorylation-dependent protein binding	ISO Inferred from Sequence Orthology more info
enables phosphorylation-dependent protein binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein serine/threonine kinase activator activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activator activity	ISO Inferred from Sequence Orthology more info
enables protein serine/threonine kinase activator activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage checkpoint signaling	ISO Inferred from Sequence Orthology more info
involved_in DNA double-strand break processing	IEA Inferred from Electronic Annotation more info
involved_in DNA double-strand break processing	ISO Inferred from Sequence Orthology more info
involved_in DNA double-strand break processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in DNA duplex unwinding	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in DNA duplex unwinding	ISO Inferred from Sequence Orthology more info
involved_in DNA strand resection involved in replication fork processing	IEA Inferred from Electronic Annotation more info
involved_in DNA strand resection involved in replication fork processing	ISO Inferred from Sequence Orthology more info
involved_in R-loop processing	IEA Inferred from Electronic Annotation more info
involved_in R-loop processing	ISO Inferred from Sequence Orthology more info
involved_in R-loop processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in blastocyst growth	IEA Inferred from Electronic Annotation more info
involved_in blastocyst growth	ISO Inferred from Sequence Orthology more info
involved_in blastocyst growth	ISS Inferred from Sequence or Structural Similarity more info
involved_in double-strand break repair	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in double-strand break repair via alternative nonhomologous end joining	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair via alternative nonhomologous end joining	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair via homologous recombination	IBA Inferred from Biological aspect of Ancestor more info
involved_in double-strand break repair via homologous recombination	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair via homologous recombination	ISO Inferred from Sequence Orthology more info
involved_in in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in in utero embryonic development	ISS Inferred from Sequence or Structural Similarity more info
involved_in intrinsic apoptotic signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within intrinsic apoptotic signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in isotype switching	IEA Inferred from Electronic Annotation more info
involved_in isotype switching	ISO Inferred from Sequence Orthology more info
involved_in isotype switching	ISS Inferred from Sequence or Structural Similarity more info
involved_in meiotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in mitotic G2 DNA damage checkpoint signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitotic G2 DNA damage checkpoint signaling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mitotic G2 DNA damage checkpoint signaling	ISO Inferred from Sequence Orthology more info
involved_in mitotic G2 DNA damage checkpoint signaling	ISO Inferred from Sequence Orthology more info
involved_in mitotic G2 DNA damage checkpoint signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of telomere capping	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of telomere capping	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of viral entry into host cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuroblast proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuroblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in neuromuscular process controlling balance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuromuscular process controlling balance	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of kinase activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein autophosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of telomere maintenance	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of telomere maintenance	ISO Inferred from Sequence Orthology more info
involved_in protection from non-homologous end joining at telomere	IEA Inferred from Electronic Annotation more info
involved_in protection from non-homologous end joining at telomere	ISO Inferred from Sequence Orthology more info
involved_in protection from non-homologous end joining at telomere	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to site of double-strand break	IEA Inferred from Electronic Annotation more info
involved_in protein localization to site of double-strand break	ISO Inferred from Sequence Orthology more info
involved_in protein localization to site of double-strand break	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of fibroblast proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in t-circle formation	IEA Inferred from Electronic Annotation more info
involved_in t-circle formation	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance	IEA Inferred from Electronic Annotation more info
involved_in telomere maintenance	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance	ISS Inferred from Sequence or Structural Similarity more info
involved_in telomere maintenance in response to DNA damage	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance in response to DNA damage	ISS Inferred from Sequence or Structural Similarity more info
involved_in telomere maintenance via telomere trimming	ISO Inferred from Sequence Orthology more info
involved_in telomeric 3' overhang formation	IEA Inferred from Electronic Annotation more info
involved_in telomeric 3' overhang formation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of BRCA1-C complex	IEA Inferred from Electronic Annotation more info
part_of BRCA1-C complex	ISO Inferred from Sequence Orthology more info
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
part_of Mre11 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Mre11 complex	IEA Inferred from Electronic Annotation more info
part_of Mre11 complex	ISO Inferred from Sequence Orthology more info
part_of Mre11 complex	ISS Inferred from Sequence or Structural Similarity more info
located_in PML body	IEA Inferred from Electronic Annotation more info
located_in PML body	ISO Inferred from Sequence Orthology more info
located_in chromosome, telomeric region	IEA Inferred from Electronic Annotation more info
is_active_in chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
located_in chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
is_active_in chromosome, telomeric region	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear inclusion body	IEA Inferred from Electronic Annotation more info
located_in nuclear inclusion body	ISO Inferred from Sequence Orthology more info
located_in nuclear inclusion body	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in replication fork	IEA Inferred from Electronic Annotation more info
located_in replication fork	ISO Inferred from Sequence Orthology more info
located_in site of double-strand break	IEA Inferred from Electronic Annotation more info
is_active_in site of double-strand break	ISO Inferred from Sequence Orthology more info
located_in site of double-strand break	ISO Inferred from Sequence Orthology more info
is_active_in site of double-strand break	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: nibrin

Names: nijmegen breakage syndrome protein 1 homolog

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_138873.2 → NP_620228.1 nibrin

See identical proteins and their annotated locations for NP_620228.1

Status: PROVISIONAL

Source sequence(s)

AF218575

UniProtKB/Swiss-Prot

Q5RKL2, Q9JIL9

Related

ENSRNOP00000091774.1, ENSRNOT00000111074.2

Conserved Domains (4) summary

cd00027
Location:114 → 182

BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...

cd00060
Location:1 → 109

FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...

pfam08599
Location:680 → 742

Nbs1_C; DNA damage repair protein Nbs1

pfam16508
Location:217 → 325

NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

34256678..34291163

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006237916.4 → XP_006237978.4 nibrin isoform X1

Related

ENSRNOP00000012377.3, ENSRNOT00000012377.6
XM_039110890.2 → XP_038966818.1 nibrin isoform X2

Conserved Domains (3) summary

pfam08599
Location:529 → 590

Nbs1_C; DNA damage repair protein Nbs1

pfam16508
Location:66 → 174

NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein

cl00038
Location:1 → 33

BRCT; C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains