Slx4 SLX4 structure-specific endonuclease subunit [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Slx4provided by RGD
Official Full Name: SLX4 structure-specific endonuclease subunitprovided by RGD
Primary source: RGD:1566009
See related: EnsemblRapid:ENSRNOG00000024445 AllianceGenome:RGD:1566009
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
Also known as: Btbd12; RGD1566009
Summary: Predicted to enable enzyme activator activity. Predicted to be involved in DNA metabolic process and regulation of telomere maintenance. Predicted to act upstream of or within response to intra-S DNA damage checkpoint signaling. Predicted to be located in several cellular components, including chromosome; cytosol; and nucleoplasm. Predicted to be part of ERCC4-ERCC1 complex; Holliday junction resolvase complex; and Slx1-Slx4 complex. Human ortholog(s) of this gene implicated in Fanconi anemia complementation group P. Orthologous to human SLX4 (SLX4 structure-specific endonuclease subunit). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Adrenal (RPKM 79.8), Thymus (RPKM 68.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q12

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (12032131..12055685)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (11526623..11549313)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (11787756..11808326)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables enzyme activator activity	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA double-strand break processing involved in repair via single-strand annealing	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in DNA replication	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 negative regulation of telomere maintenance via telomere lengthening	ISO Inferred from Sequence Orthology more info
involved_in nucleotide-excision repair	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of t-circle formation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of telomere maintenance	ISO Inferred from Sequence Orthology more info
involved_in resolution of meiotic recombination intermediates	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within response to intra-S DNA damage checkpoint signaling	ISO Inferred from Sequence Orthology more info
involved_in t-circle formation	ISO Inferred from Sequence Orthology more info
involved_in telomeric D-loop disassembly	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of ERCC4-ERCC1 complex	ISO Inferred from Sequence Orthology more info
part_of Holliday junction resolvase complex	ISO Inferred from Sequence Orthology more info
part_of Slx1-Slx4 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Slx1-Slx4 complex	ISO Inferred from Sequence Orthology more info
located_in cell junction	IEA Inferred from Electronic Annotation more info
located_in cell junction	ISO Inferred from Sequence Orthology more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	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

General protein information

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Preferred Names: structure-specific endonuclease subunit SLX4

Names: BTB (POZ) domain containing 12; SLX4 structure-specific endonuclease subunit 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_001398651.1 → NP_001385580.1 structure-specific endonuclease subunit SLX4

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

F1LU18

Conserved Domains (2) summary

cl38908
Location:599 → 713

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1640 → 1697

Slx4; Slx4 endonuclease

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_086028.1 Reference GRCr8

Range

12032131..12055685

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063268905.1 → XP_063124975.1 structure-specific endonuclease subunit SLX4 isoform X1

UniProtKB/TrEMBL

F1LU18
XM_063268904.1 → XP_063124974.1 structure-specific endonuclease subunit SLX4 isoform X1

UniProtKB/TrEMBL

F1LU18
XM_063268903.1 → XP_063124973.1 structure-specific endonuclease subunit SLX4 isoform X1

UniProtKB/TrEMBL

F1LU18

Related

ENSRNOP00000031220.6, ENSRNOT00000033919.8
XM_063268908.1 → XP_063124978.1 structure-specific endonuclease subunit SLX4 isoform X2
XM_063268907.1 → XP_063124977.1 structure-specific endonuclease subunit SLX4 isoform X1

UniProtKB/TrEMBL

F1LU18
XM_063268906.1 → XP_063124976.1 structure-specific endonuclease subunit SLX4 isoform X1

UniProtKB/TrEMBL

F1LU18
XM_039087052.2 → XP_038942980.1 structure-specific endonuclease subunit SLX4 isoform X3

Conserved Domains (3) summary

PTZ00449
Location:713 → 1027

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

cl38908
Location:239 → 353

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1280 → 1337

Slx4; Slx4 endonuclease
XM_039087053.2 → XP_038942981.1 structure-specific endonuclease subunit SLX4 isoform X4

Conserved Domains (2) summary

PTZ00449
Location:386 → 700

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

pfam09494
Location:953 → 1010

Slx4; Slx4 endonuclease