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Nhej1 nonhomologous end-joining factor 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 363251, updated on 11-Apr-2024

Summary

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Official Symbol
Nhej1provided by RGD
Official Full Name
nonhomologous end-joining factor 1provided by RGD
Primary source
RGD:1359338
See related
Ensembl:ENSRNOG00000018162 AllianceGenome:RGD:1359338
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
Summary
Predicted to enable DNA end binding activity and DNA polymerase binding activity. Predicted to be involved in DNA metabolic process; lymphocyte differentiation; and response to ionizing radiation. Predicted to be located in fibrillar center and nucleoplasm. Predicted to be part of DNA ligase IV complex and nonhomologous end joining complex. Predicted to be active in site of double-strand break. Orthologous to human NHEJ1 (non-homologous end joining factor 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Kidney (RPKM 20.2), Spleen (RPKM 18.8) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
9q33
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (83974995..84071161, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (76526322..76622488, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (82230230..82327923, complement)

Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene cilia and flagella associated protein 65 Neighboring gene uncharacterized LOC102549980 Neighboring gene Indian hedgehog signaling molecule Neighboring gene ATP synthase membrane subunit c locus 2 like 1 Neighboring gene solute carrier family 23, member 3 Neighboring gene cyclin Pas1/PHO80 domain containing 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. Nhej1 Deficiency Causes Abnormal Development of the Cerebral Cortex. El Waly B, et al. Mol Neurobiol, 2015 Aug. PMID 25288157
  2. Calorie restriction (CR) reduces age-dependent decline of non-homologous end joining (NHEJ) activity in rat tissues. Lee JE, et al. Exp Gerontol, 2011 Nov. PMID 21821112
  3. Cernunnos, a novel nonhomologous end-joining factor, is mutated in human immunodeficiency with microcephaly. Buck D, et al. Cell, 2006 Jan 27. PMID 16439204
  4. XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining. Ahnesorg P, et al. Cell, 2006 Jan 27. PMID 16439205
  5. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Lieber MR. Annu Rev Biochem, 2010. PMID 20192759, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. These results indicate that the Nhej1 protein is necessary for proper rat cortical development.
    Title: Nhej1 Deficiency Causes Abnormal Development of the Cerebral Cortex.
  2. Rresults suggest that Caloric Restriction could reduce age-dependent decline of NHEJ activity in various tissues of rats possibly through up-regulation of XRCC4.
    Title: Calorie restriction (CR) reduces age-dependent decline of non-homologous end joining (NHEJ) activity in rat tissues.
Submit: New GeneRIF Correction

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA end binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA end binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA end binding ISO
Inferred from Sequence Orthology
more info
  
enables DNA end binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables DNA polymerase binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA polymerase binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in B cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in B cell differentiation ISO
Inferred from Sequence Orthology
more info
  
involved_in B cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in DNA ligation involved in DNA repair IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA ligation involved in DNA repair ISO
Inferred from Sequence Orthology
more info
  
involved_in T cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in T cell differentiation ISO
Inferred from Sequence Orthology
more info
  
involved_in T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in biological_process ND
No biological Data available
more info
  
involved_in double-strand break repair via nonhomologous end joining IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in double-strand break repair via nonhomologous end joining IEA
Inferred from Electronic Annotation
more info
  
involved_in double-strand break repair via nonhomologous end joining ISO
Inferred from Sequence Orthology
more info
  
involved_in double-strand break repair via nonhomologous end joining ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in immunoglobulin V(D)J recombination IEA
Inferred from Electronic Annotation
more info
  
involved_in immunoglobulin V(D)J recombination ISO
Inferred from Sequence Orthology
more info
  
involved_in immunoglobulin V(D)J recombination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in response to ionizing radiation IEA
Inferred from Electronic Annotation
more info
  
involved_in response to ionizing radiation ISO
Inferred from Sequence Orthology
more info
  
involved_in response to ionizing radiation ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
Component Evidence Code Pubs
part_of DNA ligase IV complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of DNA-dependent protein kinase-DNA ligase 4 complex IEA
Inferred from Electronic Annotation
more info
  
part_of DNA-dependent protein kinase-DNA ligase 4 complex ISO
Inferred from Sequence Orthology
more info
  
part_of DNA-dependent protein kinase-DNA ligase 4 complex ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in fibrillar center IEA
Inferred from Electronic Annotation
more info
  
located_in fibrillar center ISO
Inferred from Sequence Orthology
more info
  
part_of nonhomologous end joining complex ISO
Inferred from Sequence Orthology
more info
  
part_of nonhomologous end joining complex ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
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
  
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
non-homologous end-joining factor 1
Names
XRCC4-like factor
protein cernunnos

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)

  1. NM_001014217.1 → NP_001014239.1  non-homologous end-joining factor 1

    See identical proteins and their annotated locations for NP_001014239.1

    Status: PROVISIONAL

    Source sequence(s)
    BC079033
    UniProtKB/Swiss-Prot
    Q6AYI4
    UniProtKB/TrEMBL
    A0A8L2QD40, A6JVX2
    Related
    ENSRNOP00000024444.5, ENSRNOT00000024444.6
    Conserved Domains (1) summary
    pfam09302
    Location:12 → 179
    XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component

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

  1. NC_086027.1 Reference GRCr8

    Range
    83974995..84071161 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006245240.3 → XP_006245302.1  non-homologous end-joining factor 1 isoform X2

    See identical proteins and their annotated locations for XP_006245302.1

    UniProtKB/Swiss-Prot
    Q6AYI4
    UniProtKB/TrEMBL
    A0A8L2QD40, A6JVX2
    Conserved Domains (1) summary
    pfam09302
    Location:12 → 179
    XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component

  2. XM_039083877.2 → XP_038939805.1  non-homologous end-joining factor 1 isoform X1

    UniProtKB/TrEMBL
    A0A8I5Y7R3, A0A8L2QD40, A6JVX1
    Related
    ENSRNOP00000077416.1
    Conserved Domains (1) summary
    pfam09302
    Location:13 → 181
    XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component

  3. XM_017596524.3 → XP_017452013.1  non-homologous end-joining factor 1 isoform X1

    UniProtKB/TrEMBL
    A0A8I5Y7R3, A0A8L2QD40, A6JVX1
    Conserved Domains (1) summary
    pfam09302
    Location:13 → 181
    XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component

  4. XM_006245242.5 → XP_006245304.1  non-homologous end-joining factor 1 isoform X2

    See identical proteins and their annotated locations for XP_006245304.1

    UniProtKB/Swiss-Prot
    Q6AYI4
    UniProtKB/TrEMBL
    A0A8L2QD40, A6JVX2
    Conserved Domains (1) summary
    pfam09302
    Location:12 → 179
    XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component

  5. XM_006245241.5 → XP_006245303.1  non-homologous end-joining factor 1 isoform X2

    See identical proteins and their annotated locations for XP_006245303.1

    UniProtKB/Swiss-Prot
    Q6AYI4
    UniProtKB/TrEMBL
    A0A8L2QD40, A6JVX2
    Conserved Domains (1) summary
    pfam09302
    Location:12 → 179
    XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component

  6. XM_063267395.1 → XP_063123465.1  non-homologous end-joining factor 1 isoform X7

  7. XM_017596523.3 → XP_017452012.1  non-homologous end-joining factor 1 isoform X1

    UniProtKB/TrEMBL
    A0A8I5Y7R3, A0A8L2QD40, A6JVX1
    Conserved Domains (1) summary
    pfam09302
    Location:13 → 181
    XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component

  8. XM_063267394.1 → XP_063123464.1  non-homologous end-joining factor 1 isoform X6

  9. XM_063267393.1 → XP_063123463.1  non-homologous end-joining factor 1 isoform X5

  10. XM_063267391.1 → XP_063123461.1  non-homologous end-joining factor 1 isoform X3

  11. XM_063267392.1 → XP_063123462.1  non-homologous end-joining factor 1 isoform X4

RNA

  1. XR_005488935.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6AYI4.1 GenPept UniProtKB/Swiss-Prot:Q6AYI4

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