Ercc6 (ERCC excision repair 6, chromatin remodeling factor) - Rat Genome Database

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Gene: Ercc6 (ERCC excision repair 6, chromatin remodeling factor) Rattus norvegicus
Analyze
Symbol: Ercc6
Name: ERCC excision repair 6, chromatin remodeling factor
RGD ID: 1311509
Description: Predicted to enable several functions, including ATP binding activity; ATP-dependent chromatin remodeler activity; and protein tyrosine kinase activator activity. Involved in DNA protection; regulation of transcription elongation by RNA polymerase II; and transcription-coupled nucleotide-excision repair. Predicted to be located in nuclear body; nucleolus; and site of DNA damage. Predicted to be part of B-WICH complex and transcription elongation factor complex. Predicted to be active in nucleus. Used to study Cockayne syndrome B. Biomarker of middle cerebral artery infarction and transient cerebral ischemia. Human ortholog(s) of this gene implicated in several diseases, including Cockayne syndrome (multiple); De Sanctis-Cacchione syndrome; UV-sensitive syndrome; gastrointestinal system cancer (multiple); and respiratory system cancer (multiple). Orthologous to human ERCC6 (ERCC excision repair 6, chromatin remodeling factor); PARTICIPATES IN altered nucleotide excision repair pathway; nucleotide excision repair pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; amphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: DNA excision repair protein ERCC-6; excision repair cross-complementation group 6; excision repair cross-complementing rodent repair deficiency, complementation group 6; LOC306274
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Ercc6em1Cgen  
Genetic Models: SD-Ercc6em1Cgen
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2167,764,983 - 7,835,587 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl167,765,013 - 7,835,587 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx167,780,912 - 7,847,534 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0168,925,860 - 8,992,482 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0167,779,882 - 7,846,470 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0168,734,028 - 8,804,610 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl168,734,035 - 8,804,610 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01610,699,983 - 10,770,565 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4168,024,881 - 8,091,587 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1168,024,868 - 8,088,560 (+)NCBI
Celera167,365,531 - 7,432,176 (-)NCBICelera
Cytogenetic Map16p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3-aminobenzamide  (ISO)
3-hydroxybutyric acid  (ISO)
3-methylcholanthrene  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (ISO)
acetyl-CoA  (ISO)
acrolein  (ISO)
adenosine 5'-monophosphate  (ISO)
aflatoxin B1  (ISO)
alpha-pinene  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
ascaridole  (ISO)
ATP  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
caffeine  (ISO)
cannabidiol  (ISO)
carbazoles  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (EXP,ISO)
citric acid  (ISO)
copper(II) sulfate  (ISO)
cypermethrin  (ISO)
diarsenic trioxide  (ISO)
doxorubicin  (ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
genistein  (EXP)
glycidol  (EXP)
gold atom  (ISO)
gold(0)  (ISO)
hydrogen peroxide  (ISO)
Illudin S  (ISO)
irofulven  (ISO)
L-methionine  (ISO)
lovastatin  (EXP)
lutein  (ISO)
methoxychlor  (EXP)
methylisothiazolinone  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-ribosylnicotinamide  (ISO)
NAD zwitterion  (ISO)
NAD(+)  (ISO)
nicotinamide  (ISO)
NMN zwitterion  (ISO)
NU 1025  (ISO)
oxaliplatin  (ISO)
ozone  (ISO)
paracetamol  (EXP)
paraquat  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
permethrin  (EXP)
potassium bromate  (ISO)
potassium dichromate  (ISO)
Pyridostigmine bromide  (EXP)
rac-lactic acid  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
succinic acid  (ISO)
superoxide  (ISO)
urethane  (ISO)
valproic acid  (ISO)
veliparib  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
base-excision repair  (ISO)
chromatin remodeling  (IEA)
DNA damage checkpoint signaling  (ISO)
DNA damage response  (ISO)
DNA protection  (IMP)
DNA repair  (ISO)
double-strand break repair via classical nonhomologous end joining  (ISO)
intrinsic apoptotic signaling pathway in response to DNA damage  (ISO)
JNK cascade  (ISO)
multicellular organism growth  (ISO)
negative regulation of double-strand break repair via nonhomologous end joining  (ISO)
neurogenesis  (ISO)
neuron differentiation  (ISO)
neuron projection development  (ISO)
photoreceptor cell maintenance  (ISO)
positive regulation of defense response to virus by host  (ISO)
positive regulation of DNA repair  (ISO)
positive regulation of DNA-templated transcription, elongation  (ISO)
positive regulation of double-strand break repair via homologous recombination  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of peptidyl-serine phosphorylation of STAT protein  (ISO)
positive regulation of transcription by RNA polymerase III  (ISO)
positive regulation of transcription initiation by RNA polymerase II  (ISO)
pyrimidine dimer repair  (ISO)
regulation of DNA-templated transcription elongation  (ISO)
regulation of transcription elongation by RNA polymerase II  (IMP)
response to gamma radiation  (ISO)
response to oxidative stress  (ISO)
response to superoxide  (ISO)
response to toxic substance  (ISO)
response to UV  (ISO)
response to UV-B  (ISO)
response to X-ray  (ISO)
single strand break repair  (ISO)
transcription elongation by RNA polymerase I  (ISO)
transcription-coupled nucleotide-excision repair  (IBA,IMP,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Laryngeal cancer risk associated with smoking and alcohol consumption is modified by genetic polymorphisms in ERCC5, ERCC6 and RAD23B but not by polymorphisms in five other nucleotide excision repair genes. Abbasi R, etal., Int J Cancer. 2009 Sep 15;125(6):1431-9. doi: 10.1002/ijc.24442.
2. The ERCC6 gene and age-related macular degeneration. Baas DC, etal., PLoS One. 2010 Nov 1;5(11):e13786. doi: 10.1371/journal.pone.0013786.
3. Genetic variation in the nucleotide excision repair pathway and colorectal cancer risk. Berndt SI, etal., Cancer Epidemiol Biomarkers Prev. 2006 Nov;15(11):2263-9. doi: 10.1158/1055-9965.EPI-06-0449.
4. Polymorphisms of cancer-related genes and risk of multipleprimary malignancies involving colorectal cancer Cao P, etal., Turk J Med Sci. 2017 Nov 13;47(5):1549-1554. doi: 10.3906/sag-1612-119.
5. Reduced expression levels of nucleotide excision repair genes in lung cancer: a case-control analysis. Cheng L, etal., Carcinogenesis. 2000 Aug;21(8):1527-30.
6. Cockayne syndrome type II in a Druze isolate in Northern Israel in association with an insertion mutation in ERCC6. Falik-Zaccai TC, etal., Am J Med Genet A. 2008 Jun 1;146A(11):1423-9. doi: 10.1002/ajmg.a.32309.
7. Transcription-coupled nucleotide excision repair in mammalian cells: molecular mechanisms and biological effects. Fousteri M and Mullenders LH, Cell Res. 2008 Jan;18(1):73-84. doi: 10.1038/cr.2008.6.
8. 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.
9. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
10. ERCC6 founder mutation identified in Finnish patients with COFS syndrome. Jaakkola E, etal., Clin Genet. 2010 Dec;78(6):541-7. doi: 10.1111/j.1399-0004.2010.01424.x.
11. Nucleotide excision repair: new tricks with old bricks. Kamileri I, etal., Trends Genet. 2012 Nov;28(11):566-73. doi: 10.1016/j.tig.2012.06.004. Epub 2012 Jul 22.
12. A variant of the Cockayne syndrome B gene ERCC6 confers risk of lung cancer. Lin Z, etal., Hum Mutat. 2008 Jan;29(1):113-22.
13. Neuronal ERCC6 mRNA expression in rat brain induced by a transient focal cerebral ischemia. Ling X, etal., Zhongguo Yao Li Xue Bao. 1999 Jan;20(1):15-20.
14. Polymorphisms of multiple genes involved in NER pathway predict prognosis of gastric cancer. Liu J, etal., Oncotarget. 2016 Jul 26;7(30):48130-48142. doi: 10.18632/oncotarget.10173.
15. Disruption of the Cockayne syndrome B gene impairs spontaneous tumorigenesis in cancer-predisposed Ink4a/ARF knockout mice. Lu Y, etal., Mol Cell Biol. 2001 Mar;21(5):1810-8.
16. Prognostic Value of Excision Repair Cross-Complementing mRNA Expression in Gastric Cancer. Luo SS, etal., Biomed Res Int. 2018 Oct 17;2018:6204684. doi: 10.1155/2018/6204684. eCollection 2018.
17. ERCC6/CSB gene polymorphisms and lung cancer risk. Ma H, etal., Cancer Lett. 2009 Jan 8;273(1):172-6. doi: 10.1016/j.canlet.2008.08.002. Epub 2008 Sep 11.
18. Genetic variation in the DNA repair genes is predictive of outcome in lung cancer. Matakidou A, etal., Hum Mol Genet. 2007 Oct 1;16(19):2333-40.
19. Manitoba aboriginal kindred with original cerebro-oculo- facio-skeletal syndrome has a mutation in the Cockayne syndrome group B (CSB) gene. Meira LB, etal., Am J Hum Genet. 2000 Apr;66(4):1221-8. Epub 2000 Mar 15.
20. Cockayne syndrome group B (Csb) and group a (Csa) deficiencies predispose to hearing loss and cochlear hair cell degeneration in mice. Nagtegaal AP, etal., J Neurosci. 2015 Mar 11;35(10):4280-6. doi: 10.1523/JNEUROSCI.5063-14.2015.
21. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
22. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
23. GOA pipeline RGD automated data pipeline
24. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
25. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
26. Comprehensive gene review and curation RGD comprehensive gene curation
27. Functional, genetic, and epigenetic aspects of base and nucleotide excision repair in colorectal carcinomas. Slyskova J, etal., Clin Cancer Res. 2012 Nov 1;18(21):5878-87. doi: 10.1158/1078-0432.CCR-12-1380. Epub 2012 Sep 10.
28. Single nucleotide polymorphisms of nucleotide excision repair pathway are significantly associated with outcomes of platinum-based chemotherapy in lung cancer. Song X, etal., Sci Rep. 2017 Sep 18;7(1):11785. doi: 10.1038/s41598-017-08257-7.
29. Defective transcription-coupled repair in Cockayne syndrome B mice is associated with skin cancer predisposition. van der Horst GT, etal., Cell. 1997 May 2;89(3):425-35.
30. Role for Nucleotide Excision Repair Gene Variants in Oxaliplatin-Induced Peripheral Neuropathy. West H, etal., JCO Precis Oncol. 2018 Nov;2:1-18. doi: 10.1200/PO.18.00090.
31. Identification of Two Novel ERCC6 Mutations in Old Order Amish with Cockayne Syndrome. Xin B and Wang H, Mol Syndromol. 2013 Jan;3(6):288-90. doi: 10.1159/000345924. Epub 2012 Dec 21.
32. Rat Model of Cockayne Syndrome Neurological Disease. Xu Y, etal., Cell Rep. 2019 Oct 22;29(4):800-809.e5. doi: 10.1016/j.celrep.2019.09.028.
33. CSB affected on the sensitivity of lung cancer cells to platinum-based drugs through the global decrease of let-7 and miR-29. Yang Z, etal., BMC Cancer. 2019 Oct 15;19(1):948. doi: 10.1186/s12885-019-6194-z.
34. Effect of dextromethorphan, a NMDA antagonist, on DNA repair in rat photochemical thrombotic cerebral ischemia. Yin KJ and Sun FY, Brain Res. 1999 Jan 2;815(1):29-35.
35. DNA repair pathway profiling and microsatellite instability in colorectal cancer. Yu J, etal., Clin Cancer Res. 2006 Sep 1;12(17):5104-11. doi: 10.1158/1078-0432.CCR-06-0547.
36. Identification of two missense mutations of ERCC6 in three Chinese sisters with Cockayne syndrome by whole exome sequencing. Yu S, etal., PLoS One. 2014 Dec 2;9(12):e113914. doi: 10.1371/journal.pone.0113914. eCollection 2014.
37. Gender and cell-type-specific effects of the transcription-coupled repair protein, ERCC6/CSB, on repeat expansion in a mouse model of the fragile X-related disorders. Zhao XN and Usdin K, Hum Mutat. 2014 Mar;35(3):341-9.
38. Elevated Expression of ERCC6 Confers Resistance to 5-Fluorouracil and Is Associated with Poor Patient Survival in Colorectal Cancer. Zhao Z, etal., DNA Cell Biol. 2017 Sep;36(9):781-786. doi: 10.1089/dna.2017.3768. Epub 2017 Jun 30.
Additional References at PubMed
PMID:7664335   PMID:8999876   PMID:9326587   PMID:9973627   PMID:10564257   PMID:10806208   PMID:10843671   PMID:10850428   PMID:11005836   PMID:11408355   PMID:12447686   PMID:12509265  
PMID:12560492   PMID:15340056   PMID:15979950   PMID:16107709   PMID:16246722   PMID:16319174   PMID:17145777   PMID:17213818   PMID:17626041   PMID:22323595   PMID:22483866   PMID:23562818  
PMID:24874740   PMID:25820262   PMID:26218421   PMID:26620705   PMID:28292928   PMID:29203878   PMID:29545921  


Genomics

Comparative Map Data
Ercc6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2167,764,983 - 7,835,587 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl167,765,013 - 7,835,587 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx167,780,912 - 7,847,534 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0168,925,860 - 8,992,482 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0167,779,882 - 7,846,470 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0168,734,028 - 8,804,610 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl168,734,035 - 8,804,610 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01610,699,983 - 10,770,565 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4168,024,881 - 8,091,587 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1168,024,868 - 8,088,560 (+)NCBI
Celera167,365,531 - 7,432,176 (-)NCBICelera
Cytogenetic Map16p16NCBI
ERCC6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381049,434,881 - 49,539,538 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1049,454,168 - 49,539,538 (-)EnsemblGRCh38hg38GRCh38
GRCh371050,642,927 - 50,747,584 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361050,336,715 - 50,417,078 (-)NCBINCBI36Build 36hg18NCBI36
Build 341050,336,714 - 50,417,078NCBI
Celera1044,250,656 - 44,333,241 (-)NCBICelera
Cytogenetic Map10q11.23NCBI
HuRef1044,927,342 - 45,011,950 (-)NCBIHuRef
CHM1_11050,944,706 - 51,029,274 (-)NCBICHM1_1
T2T-CHM13v2.01050,283,667 - 50,388,257 (-)NCBIT2T-CHM13v2.0
Ercc6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391432,235,248 - 32,302,947 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1432,235,478 - 32,302,947 (+)EnsemblGRCm39 Ensembl
GRCm381432,513,291 - 32,580,990 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1432,513,521 - 32,580,990 (+)EnsemblGRCm38mm10GRCm38
MGSCv371433,326,707 - 33,394,175 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361431,342,530 - 31,409,998 (+)NCBIMGSCv36mm8
Celera1428,771,098 - 28,837,767 (+)NCBICelera
Cytogenetic Map14BNCBI
cM Map1419.4NCBI
Ercc6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955556748,231 - 813,133 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955556745,175 - 812,215 (+)NCBIChiLan1.0ChiLan1.0
ERCC6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan11061,721,084 - 61,812,606 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01044,703,720 - 44,784,948 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
ERCC6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1281,358,383 - 1,432,276 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl281,361,107 - 1,427,162 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha281,593,582 - 1,667,457 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0281,534,813 - 1,608,719 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl281,534,813 - 1,608,641 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1281,333,055 - 1,406,921 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0281,370,132 - 1,444,015 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0281,502,030 - 1,575,915 (-)NCBIUU_Cfam_GSD_1.0
Ercc6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721379,558,979 - 79,640,918 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936728761,804 - 844,690 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936728706,499 - 843,447 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ERCC6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1490,002,024 - 90,075,898 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11489,998,125 - 90,075,911 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21497,907,746 - 97,985,104 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Ercc6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624928463,279 - 530,115 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624928458,651 - 532,201 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ercc6
240 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:341
Count of miRNA genes:191
Interacting mature miRNAs:249
Transcripts:ENSRNOT00000064255
Prediction methods:Miranda, Targetscan
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1619639137Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16285170915884239Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760916039848Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16422773017696785Rat

Markers in Region
RH143983  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2167,833,969 - 7,834,082 (+)MAPPERmRatBN7.2
Rnor_6.0168,802,993 - 8,803,105NCBIRnor6.0
Rnor_5.01610,768,948 - 10,769,060UniSTSRnor5.0
RGSC_v3.4168,089,970 - 8,090,082UniSTSRGSC3.4
Celera167,367,036 - 7,367,148UniSTS
RH 3.4 Map1672.2UniSTS
Cytogenetic Map16p16UniSTS
RH131315  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2167,833,488 - 7,833,695 (+)MAPPERmRatBN7.2
Rnor_6.0168,802,512 - 8,802,718NCBIRnor6.0
Rnor_5.01610,768,467 - 10,768,673UniSTSRnor5.0
RGSC_v3.4168,089,489 - 8,089,695UniSTSRGSC3.4
Celera167,367,423 - 7,367,629UniSTS
RH 3.4 Map1670.8UniSTS
Cytogenetic Map16p16UniSTS
AW531214  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2167,828,045 - 7,828,245 (+)MAPPERmRatBN7.2
Rnor_6.0168,797,069 - 8,797,268NCBIRnor6.0
Rnor_5.01610,763,024 - 10,763,223UniSTSRnor5.0
RGSC_v3.4168,084,046 - 8,084,245UniSTSRGSC3.4
Celera167,372,873 - 7,373,072UniSTS
RH 3.4 Map1672.2UniSTS
Cytogenetic Map16p16UniSTS


Genetic Models
This gene Ercc6 is modified in the following models/strains:
SD-Ercc6em1Cgen    


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 6 16 4 15 4 67 19 35
Low 3 37 41 37 4 37 8 11 7 16 6 11 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000064255   ⟹   ENSRNOP00000063005
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl167,765,013 - 7,835,587 (+)Ensembl
Rnor_6.0 Ensembl168,737,974 - 8,804,610 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088529   ⟹   ENSRNOP00000068845
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl167,765,052 - 7,833,708 (+)Ensembl
Rnor_6.0 Ensembl168,734,035 - 8,803,182 (+)Ensembl
RefSeq Acc Id: NM_001107296   ⟹   NP_001100766
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2167,768,947 - 7,835,587 (+)NCBI
Rnor_6.0168,737,974 - 8,804,610 (+)NCBI
Rnor_5.01610,699,983 - 10,770,565 (+)NCBI
RGSC_v3.4168,024,881 - 8,091,587 (+)RGD
Celera167,365,531 - 7,432,176 (-)RGD
Sequence:
RefSeq Acc Id: XM_006252734   ⟹   XP_006252796
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2167,764,983 - 7,834,182 (+)NCBI
Rnor_6.0168,734,028 - 8,803,205 (+)NCBI
Rnor_5.01610,699,983 - 10,770,565 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252735   ⟹   XP_006252797
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2167,768,648 - 7,834,182 (+)NCBI
Rnor_6.0168,737,757 - 8,803,205 (+)NCBI
Rnor_5.01610,699,983 - 10,770,565 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252736   ⟹   XP_006252798
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2167,765,234 - 7,834,182 (+)NCBI
Rnor_6.0168,734,146 - 8,803,205 (+)NCBI
Rnor_5.01610,699,983 - 10,770,565 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252737   ⟹   XP_006252799
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2167,764,983 - 7,834,182 (+)NCBI
Rnor_6.0168,734,028 - 8,803,205 (+)NCBI
Rnor_5.01610,699,983 - 10,770,565 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252738   ⟹   XP_006252800
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2167,771,007 - 7,834,182 (+)NCBI
Rnor_6.0168,740,066 - 8,803,205 (+)NCBI
Rnor_5.01610,699,983 - 10,770,565 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001100766   ⟸   NM_001107296
- UniProtKB: D3ZS47 (UniProtKB/TrEMBL),   A6KFV6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252796   ⟸   XM_006252734
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JTU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252799   ⟸   XM_006252737
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006252798   ⟸   XM_006252736
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JTU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252797   ⟸   XM_006252735
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JTU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252800   ⟸   XM_006252738
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000063005   ⟸   ENSRNOT00000064255
RefSeq Acc Id: ENSRNOP00000068845   ⟸   ENSRNOT00000088529
Protein Domains
Helicase ATP-binding   Helicase C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JTU1-F1-model_v2 AlphaFold A0A0G2JTU1 1-1474 view protein structure

Transcriptome

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

Promoters
RGD ID:13699948
Promoter ID:EPDNEW_R10466
Type:multiple initiation site
Name:Ercc6_1
Description:ERCC excision repair 6, chromatin remodeling factor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0168,734,072 - 8,734,132EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311509 AgrOrtholog
BioCyc Gene G2FUF-12104 BioCyc
Ensembl Genes ENSRNOG00000030017 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064255 ENTREZGENE
  ENSRNOT00000064255.2 UniProtKB/TrEMBL
  ENSRNOT00000088529 ENTREZGENE
  ENSRNOT00000088529.2 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.10810 UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
InterPro Helicase_ATP-bd UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  SNF2-like_sf UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
KEGG Report rno:306274 UniProtKB/TrEMBL
NCBI Gene 306274 ENTREZGENE
PANTHER DNA EXCISION REPAIR PROTEIN ERCC-6-RELATED UniProtKB/TrEMBL
  SNF2/RAD54 FAMILY MEMBER UniProtKB/TrEMBL
Pfam Helicase_C UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
PharmGKB ERCC6 RGD
PhenoGen Ercc6 PhenoGen
PROSITE HELICASE_ATP_BIND_1 UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/TrEMBL
RatGTEx ENSRNOG00000030017 RatGTEx
SMART DEXDc UniProtKB/TrEMBL
  HELICc UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A0A0G2JTU1 ENTREZGENE, UniProtKB/TrEMBL
  A6KFV6 ENTREZGENE, UniProtKB/TrEMBL
  D3ZS47 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Ercc6  ERCC excision repair 6, chromatin remodeling factor  Ercc6  excision repair cross-complementation group 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-03-12 Ercc6  excision repair cross-complementation group 6  Ercc6  excision repair cross-complementing rodent repair deficiency, complementation group 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Ercc6  excision repair cross-complementing rodent repair deficiency, complementation group 6   Ercc6_predicted  excision repair cross-complementing rodent repair deficiency, complementation group 6 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ercc6_predicted  excision repair cross-complementing rodent repair deficiency, complementation group 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED