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

Summary

Official Symbol: Nhej1provided by RGD
Official Full Name: nonhomologous end-joining factor 1provided by RGD
Primary source: RGD:1359338
See related: EnsemblRapid:ENSRNOG00000018162 AllianceGenome:RGD:1359338
Gene type: protein coding
RefSeq status: VALIDATED
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 DNA-dependent protein kinase-DNA ligase 4 complex. Predicted to be active in site of double-strand break. Human ortholog(s) of this gene implicated in severe combined immunodeficiency. Orthologous to human NHEJ1 (non-homologous end joining factor 1). [provided by Alliance of Genome Resources, Nov 2024]
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

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_086027.1 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?

These results indicate that the Nhej1 protein is necessary for proper rat cortical development.
Title: Nhej1 Deficiency Causes Abnormal Development of the Cerebral Cortex.
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

General gene information

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Markers

D9Mco48 (e-PCR)
- UniSTS:518463

D9Mco50 (e-PCR)
- UniSTS:518559

D9Mco49 (e-PCR)
- UniSTS:518834

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

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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)

NM_001014217.2 → NP_001014239.1 non-homologous end-joining factor 1 isoform 1

See identical proteins and their annotated locations for NP_001014239.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/Swiss-Prot

Q6AYI4

UniProtKB/TrEMBL

A0A8L2QD40, A6JVX2

Conserved Domains (1) summary

pfam09302
Location:12 → 179

XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component
NM_001432765.1 → NP_001419694.1 non-homologous end-joining factor 1 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/Swiss-Prot

Q6AYI4

UniProtKB/TrEMBL

A6JVX2
NM_001432766.1 → NP_001419695.1 non-homologous end-joining factor 1 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/Swiss-Prot

Q6AYI4

UniProtKB/TrEMBL

A6JVX2
NM_001432767.1 → NP_001419696.1 non-homologous end-joining factor 1 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/Swiss-Prot

Q6AYI4

UniProtKB/TrEMBL

A6JVX2
NM_001432768.1 → NP_001419697.1 non-homologous end-joining factor 1 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/Swiss-Prot

Q6AYI4

UniProtKB/TrEMBL

A6JVX2
NM_001432769.1 → NP_001419698.1 non-homologous end-joining factor 1 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/Swiss-Prot

Q6AYI4

UniProtKB/TrEMBL

A6JVX2
NM_001432770.1 → NP_001419699.1 non-homologous end-joining factor 1 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

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_086027.1 Reference GRCr8

Range

83974995..84071161 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (1) summary

pfam09302
Location:12 → 179

XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component
XM_039083877.2 → XP_038939805.1 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
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
XM_006245242.5 → XP_006245304.1 non-homologous end-joining factor 1 isoform X2

Conserved Domains (1) summary

pfam09302
Location:12 → 179

XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component
XM_006245241.5 → XP_006245303.1 non-homologous end-joining factor 1 isoform X2

Conserved Domains (1) summary

pfam09302
Location:12 → 179

XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component
XM_063267395.1 → XP_063123465.1 non-homologous end-joining factor 1 isoform X7
XM_017596523.3 → XP_017452012.1 non-homologous end-joining factor 1 isoform X1

UniProtKB/TrEMBL

A0A8I5Y7R3, A0A8L2QD40, A6JVX1

Related

ENSRNOP00000077416.1, ENSRNOT00000098045.2

Conserved Domains (1) summary

pfam09302
Location:13 → 181

XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component
XM_063267394.1 → XP_063123464.1 non-homologous end-joining factor 1 isoform X6
XM_063267393.1 → XP_063123463.1 non-homologous end-joining factor 1 isoform X5
XM_063267391.1 → XP_063123461.1 non-homologous end-joining factor 1 isoform X3
XM_063267392.1 → XP_063123462.1 non-homologous end-joining factor 1 isoform X4