Xrcc4 X-ray repair cross complementing 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Xrcc4provided by RGD
Official Full Name: X-ray repair cross complementing 4provided by RGD
Primary source: RGD:1359573
See related: Ensembl:ENSRNOG00000029966 AllianceGenome:RGD:1359573
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 FHA domain binding activity; identical protein binding activity; and protein C-terminus binding activity. Predicted to contribute to 3' overhang single-stranded DNA endodeoxyribonuclease activity. Involved in cellular response to lithium ion. Predicted to be located in chromosome, telomeric region; cytosol; and nucleoplasm. Predicted to be part of DNA ligase IV complex; DNA-dependent protein kinase-DNA ligase 4 complex; and ERCC4-ERCC1 complex. Predicted to be active in cytoplasm; nucleus; and site of double-strand break. Human ortholog(s) of this gene implicated in multiple myeloma. Orthologous to human XRCC4 (X-ray repair cross complementing 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 28.4), Heart (RPKM 22.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q12

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (22686506..22932929, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (20948464..21197705, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (18674496..18927463, complement)

Chromosome 2 - NC_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

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Markers

BI303647 (e-PCR)
- UniSTS:248274

D10Ulb1 (e-PCR)
- UniSTS:518612

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
contributes_to 3' overhang single-stranded DNA endodeoxyribonuclease activity	ISO Inferred from Sequence Orthology more info
NOT enables DNA binding	ISO Inferred from Sequence Orthology more info
enables FHA domain binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
NOT enables ligase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DN2 thymocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within DNA ligation	ISO Inferred from Sequence Orthology more info
involved_in DNA ligation involved in DNA repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA ligation involved in DNA repair	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within V(D)J recombination	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lithium ion	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within central nervous system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within double-strand break repair	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair via nonhomologous end joining	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of fibroblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in immunoglobulin V(D)J recombination	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within immunoglobulin V(D)J recombination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within isotype switching	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neuron apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protection from non-homologous end joining at telomere	ISO Inferred from Sequence Orthology more info
acts_upstream_of neurogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of neuron apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of fibroblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of ligase activity	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of neurogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of phosphatidylserine exposure on apoptotic cell surface	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pro-B cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in protein localization to site of double-strand break	ISO Inferred from Sequence Orthology more info
involved_in response to X-ray	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within response to X-ray	ISO Inferred from Sequence Orthology more info
involved_in response to X-ray	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to gamma radiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to ionizing radiation	ISO Inferred from Sequence Orthology more info
involved_in telomeric DNA-containing double minutes formation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of DNA ligase IV complex	IBA Inferred from Biological aspect of Ancestor more info
part_of DNA ligase IV complex	ISO Inferred from Sequence Orthology more info
part_of DNA-dependent protein kinase-DNA ligase 4 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of DNA-dependent protein kinase-DNA ligase 4 complex	ISO Inferred from Sequence Orthology more info
part_of ERCC4-ERCC1 complex	ISO Inferred from Sequence Orthology more info
located_in chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
NOT located_in condensed chromosome	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
part_of nonhomologous end joining complex	ISO Inferred from Sequence Orthology 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
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

General protein information

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Preferred Names: DNA repair protein XRCC4

Names: X-ray repair complementing defective repair in Chinese hamster cells 4; X-ray repair cross complementing protein 4

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_001006999.1 → NP_001007000.1 DNA repair protein XRCC4

See identical proteins and their annotated locations for NP_001007000.1

Status: PROVISIONAL

Source sequence(s)

BC083848

UniProtKB/TrEMBL

A0A8I6A2T0, A6I4N6, F7EEB9, Q5XI44

Related

ENSRNOP00000048754.3, ENSRNOT00000045850.3

Conserved Domains (1) summary

pfam06632
Location:2 → 323

XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4

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_086020.1 Reference GRCr8

Range

22686506..22932929 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_008760636.3 → XP_008758858.1 DNA repair protein XRCC4 isoform X1

See identical proteins and their annotated locations for XP_008758858.1

UniProtKB/TrEMBL

F7EEB9

Conserved Domains (1) summary

pfam06632
Location:2 → 334

XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
XM_006231751.4 → XP_006231813.1 DNA repair protein XRCC4 isoform X2

See identical proteins and their annotated locations for XP_006231813.1

UniProtKB/TrEMBL

A0A8I6A2T0, A6I4N6, F7EEB9, Q5XI44

Related

ENSRNOP00000085204.1

Conserved Domains (1) summary

pfam06632
Location:2 → 323

XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
XM_008760637.4 → XP_008758859.1 DNA repair protein XRCC4 isoform X1

See identical proteins and their annotated locations for XP_008758859.1

UniProtKB/TrEMBL

F7EEB9

Conserved Domains (1) summary

pfam06632
Location:2 → 334

XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
XM_063281711.1 → XP_063137781.1 DNA repair protein XRCC4 isoform X2

UniProtKB/TrEMBL

A0A8I6A2T0, A6I4N6, Q5XI44
XM_039102166.2 → XP_038958094.1 DNA repair protein XRCC4 isoform X1

UniProtKB/TrEMBL

F7EEB9

Conserved Domains (1) summary

pfam06632
Location:2 → 334

XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
XM_063281710.1 → XP_063137780.1 DNA repair protein XRCC4 isoform X2

UniProtKB/TrEMBL

A0A8I6A2T0, A6I4N6, Q5XI44
XM_039102165.2 → XP_038958093.1 DNA repair protein XRCC4 isoform X1

UniProtKB/TrEMBL

F7EEB9

Conserved Domains (1) summary

pfam06632
Location:2 → 334

XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
XM_039102168.2 → XP_038958096.1 DNA repair protein XRCC4 isoform X2

UniProtKB/TrEMBL

A0A8I6A2T0, A6I4N6, F7EEB9, Q5XI44

Conserved Domains (1) summary

pfam06632
Location:2 → 323

XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
XM_063281713.1 → XP_063137783.1 DNA repair protein XRCC4 isoform X4
XM_063281712.1 → XP_063137782.1 DNA repair protein XRCC4 isoform X3
XM_063281714.1 → XP_063137784.1 DNA repair protein XRCC4 isoform X4