Slx4 (SLX4 structure-specific endonuclease subunit) - Rat Genome Database

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Gene: Slx4 (SLX4 structure-specific endonuclease subunit) Rattus norvegicus
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Symbol: Slx4
Name: SLX4 structure-specific endonuclease subunit
RGD ID: 1566009
Description: 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 chromatin and chromosome, telomeric region. 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); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BTB (POZ) domain containing 12; Btbd12; LOC302953; RGD1566009; similar to BTB (PO)Z domain containing 12; SLX4 structure-specific endonuclease subunit homolog; SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae); structure-specific endonuclease subunit SLX4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81012,032,131 - 12,055,685 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1012,033,048 - 12,055,650 (+)EnsemblGRCr8
mRatBN7.21011,526,623 - 11,549,313 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1011,528,424 - 11,549,295 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1016,234,089 - 16,256,809 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01015,722,918 - 15,745,639 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01011,392,149 - 11,414,867 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01011,787,756 - 11,808,326 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1011,786,121 - 11,807,928 (+)Ensemblrn6Rnor6.0
Rnor_5.01010,542,217 - 10,563,267 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41011,778,216 - 11,816,839 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1010,485,070 - 10,505,983 (+)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19595721   PMID:19595722   PMID:19596235   PMID:19596236   PMID:22579284   PMID:23361013   PMID:24012755  


Genomics

Comparative Map Data
Slx4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81012,032,131 - 12,055,685 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1012,033,048 - 12,055,650 (+)EnsemblGRCr8
mRatBN7.21011,526,623 - 11,549,313 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1011,528,424 - 11,549,295 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1016,234,089 - 16,256,809 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01015,722,918 - 15,745,639 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01011,392,149 - 11,414,867 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01011,787,756 - 11,808,326 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1011,786,121 - 11,807,928 (+)Ensemblrn6Rnor6.0
Rnor_5.01010,542,217 - 10,563,267 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41011,778,216 - 11,816,839 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1010,485,070 - 10,505,983 (+)NCBICelera
Cytogenetic Map10q12NCBI
SLX4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38163,581,181 - 3,611,606 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl163,581,181 - 3,611,606 (-)Ensemblhg38GRCh38
GRCh37163,631,182 - 3,661,607 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36163,571,183 - 3,601,586 (-)NCBIBuild 36Build 36hg18NCBI36
Celera163,837,948 - 3,868,351 (-)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef163,600,446 - 3,630,802 (-)NCBIHuRef
CHM1_1163,631,183 - 3,661,586 (-)NCBICHM1_1
T2T-CHM13v2.0163,608,449 - 3,638,875 (-)NCBIT2T-CHM13v2.0
Slx4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39163,796,969 - 3,821,708 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl163,796,969 - 3,821,634 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38163,979,105 - 4,003,829 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl163,979,105 - 4,003,770 (-)Ensemblmm10GRCm38
MGSCv37163,979,123 - 4,001,680 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36163,894,351 - 3,918,984 (-)NCBIMGSCv36mm8
Celera164,610,428 - 4,633,144 (-)NCBICelera
Cytogenetic Map16A1NCBI
cM Map162.34NCBI
Slx4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544213,770,340 - 13,791,314 (+)Ensembl
ChiLan1.0NW_00495544213,765,660 - 13,792,106 (+)NCBIChiLan1.0ChiLan1.0
SLX4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2184,106,721 - 4,136,566 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1167,890,349 - 7,920,138 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0162,502,334 - 2,532,172 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1163,678,018 - 3,707,934 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl163,678,018 - 3,707,842 (-)EnsemblpanPan2panpan1.1
SLX4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1637,648,297 - 37,666,584 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl637,647,976 - 37,703,190 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha638,976,853 - 38,995,126 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0637,863,103 - 37,881,377 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl637,860,796 - 37,881,349 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1637,646,259 - 37,664,532 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0637,539,374 - 37,557,647 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0637,950,110 - 37,968,384 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Slx4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344105,964,986 - 105,988,936 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936694722,481 - 744,600 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936694720,585 - 744,477 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLX4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl338,646,938 - 38,670,168 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1338,646,904 - 38,670,173 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2339,968,849 - 39,987,767 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLX4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.153,281,468 - 3,308,296 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606827,507,222 - 27,536,853 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slx4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248241,395,434 - 1,420,622 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248241,398,258 - 1,423,652 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Slx4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1917,846,638 - 17,867,335 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Slx4
287 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:37
Count of miRNA genes:36
Interacting mature miRNAs:37
Transcripts:ENSRNOT00000033919
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10666111835509383Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10117749933Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat

Markers in Region
AI237031  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21011,548,909 - 11,549,121 (+)MAPPERmRatBN7.2
Rnor_6.01011,807,994 - 11,808,205NCBIRnor6.0
Rnor_5.01010,562,930 - 10,563,141UniSTSRnor5.0
RGSC_v3.41011,816,461 - 11,816,672UniSTSRGSC3.4
Celera1010,505,651 - 10,505,862UniSTS
Cytogenetic Map10q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000033919   ⟹   ENSRNOP00000031220
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1012,033,048 - 12,055,650 (+)Ensembl
mRatBN7.2 Ensembl1011,528,424 - 11,549,295 (+)Ensembl
Rnor_6.0 Ensembl1011,786,121 - 11,807,928 (+)Ensembl
RefSeq Acc Id: NM_001398651   ⟹   NP_001385580
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81012,032,996 - 12,055,685 (+)NCBI
mRatBN7.21011,526,623 - 11,549,313 (+)NCBI
RefSeq Acc Id: XM_039087052   ⟹   XP_038942980
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81012,040,690 - 12,055,667 (+)NCBI
mRatBN7.21011,535,135 - 11,549,291 (+)NCBI
RefSeq Acc Id: XM_039087053   ⟹   XP_038942981
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81012,046,894 - 12,055,667 (+)NCBI
mRatBN7.21011,540,523 - 11,549,291 (+)NCBI
RefSeq Acc Id: XM_063268903   ⟹   XP_063124973
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81012,033,011 - 12,055,667 (+)NCBI
RefSeq Acc Id: XM_063268904   ⟹   XP_063124974
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81012,032,992 - 12,055,667 (+)NCBI
RefSeq Acc Id: XM_063268905   ⟹   XP_063124975
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81012,032,131 - 12,055,667 (+)NCBI
RefSeq Acc Id: XM_063268906   ⟹   XP_063124976
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81012,033,086 - 12,055,667 (+)NCBI
RefSeq Acc Id: XM_063268907   ⟹   XP_063124977
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81012,033,058 - 12,055,667 (+)NCBI
RefSeq Acc Id: XM_063268908   ⟹   XP_063124978
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81012,033,021 - 12,055,667 (+)NCBI
Ensembl Acc Id: ENSRNOP00000031220   ⟸   ENSRNOT00000033919
RefSeq Acc Id: XP_038942980   ⟸   XM_039087052
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038942981   ⟸   XM_039087053
- Peptide Label: isoform X4
RefSeq Acc Id: NP_001385580   ⟸   NM_001398651
- UniProtKB: F1LU18 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124975   ⟸   XM_063268905
- Peptide Label: isoform X1
- UniProtKB: F1LU18 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124974   ⟸   XM_063268904
- Peptide Label: isoform X1
- UniProtKB: F1LU18 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124973   ⟸   XM_063268903
- Peptide Label: isoform X1
- UniProtKB: F1LU18 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124978   ⟸   XM_063268908
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063124977   ⟸   XM_063268907
- Peptide Label: isoform X1
- UniProtKB: F1LU18 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124976   ⟸   XM_063268906
- Peptide Label: isoform X1
- UniProtKB: F1LU18 (UniProtKB/TrEMBL)
Protein Domains
BTB   UBZ4-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LU18-F1-model_v2 AlphaFold F1LU18 1-1721 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566009 AgrOrtholog
BioCyc Gene G2FUF-25997 BioCyc
Ensembl Genes ENSRNOG00000024445 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000033919 ENTREZGENE
  ENSRNOT00000033919.8 UniProtKB/TrEMBL
Gene3D-CATH Potassium Channel Kv1.1, Chain A UniProtKB/TrEMBL
InterPro BTB/POZ-like UniProtKB/TrEMBL
  BTB/POZ_fold UniProtKB/TrEMBL
  Rad18_UBZ4 UniProtKB/TrEMBL
  Structure-sp_endonuc_su_Slx4 UniProtKB/TrEMBL
NCBI Gene 302953 ENTREZGENE
PANTHER BTB POZ DOMAIN CONTAINING 12 UniProtKB/TrEMBL
  STRUCTURE-SPECIFIC ENDONUCLEASE SUBUNIT SLX4 UniProtKB/TrEMBL
Pfam BTB UniProtKB/TrEMBL
  Slx4 UniProtKB/TrEMBL
PhenoGen Slx4 PhenoGen
PROSITE BTB UniProtKB/TrEMBL
  ZF_UBZ4 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000024445 RatGTEx
SMART BTB UniProtKB/TrEMBL
Superfamily-SCOP BTB/POZ_fold UniProtKB/TrEMBL
UniProt F1LU18 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-06-14 Slx4  SLX4 structure-specific endonuclease subunit  Slx4  SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-07-28 Slx4  SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)  Btbd12  BTB (POZ) domain containing 12  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Btbd12  BTB (POZ) domain containing 12  RGD1566009_predicted  similar to BTB (PO)Z domain containing 12 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1566009_predicted  similar to BTB (PO)Z domain containing 12 (predicted)  LOC302953  similar to BTB (PO)Z domain containing 12  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302953  similar to BTB (PO)Z domain containing 12      Symbol and Name status set to provisional 70820 PROVISIONAL