U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 363251, updated on 2-May-2024

    Summary

    Go to the top of the page Help
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Nhej1 in Genome Data Viewer
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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

    Go to the top of the page

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    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

    Go to the top of the page Help
    Preferred Names
    non-homologous end-joining factor 1
    Names
    XRCC4-like factor
    protein cernunnos

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous