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 have several functions, including ATP binding activity; protein C-terminus binding activity; and protein tyrosine kinase activator activity. Predicted to be involved in several processes, including DNA repair; negative regulation of double-strand break repair via nonhomologous end joining; and positive regulation of nitrogen compound metabolic process. Predicted to localize to nuclear lumen and site of DNA damage. Biomarker of middle cerebral artery infarction and transient cerebral ischemia. Human ortholog(s) of this gene implicated in Cockayne syndrome; UV-sensitive syndrome; age related macular degeneration 5; lung cancer; and premature ovarian failure. 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
Also 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 ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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
1,2-dimethylhydrazine  (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)
adenosine 5'-monophosphate  (ISO)
aflatoxin B1  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
ascaridole  (ISO)
ATP  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
cadmium dichloride  (EXP)
carbazoles  (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)
hydrogen peroxide  (ISO)
Illudin S  (ISO)
irofulven  (ISO)
L-methionine  (ISO)
lovastatin  (EXP)
lutein  (ISO)
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)
paraquat  (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
activation of JNKK activity  (ISO)
activation of JUN kinase activity  (ISO)
ATP-dependent chromatin remodeling  (ISO)
base-excision repair  (ISO)
biological_process  (ND)
cellular response to DNA damage stimulus  (ISO)
DNA damage checkpoint  (ISO)
DNA duplex unwinding  (IEA)
DNA repair  (ISO)
double-strand break repair via classical nonhomologous end joining  (ISO)
intrinsic apoptotic signaling pathway in response to DNA damage  (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 protein tyrosine kinase activity  (IEA)
positive regulation of transcription initiation from RNA polymerase II promoter  (ISO)
pyrimidine dimer repair  (ISO)
regulation of DNA-templated transcription, elongation  (ISO)
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 from RNA polymerase I promoter  (ISO)
transcription-coupled nucleotide-excision repair  (IBA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Baas DC, etal., PLoS One. 2010 Nov 1;5(11):e13786. doi: 10.1371/journal.pone.0013786.
2. Falik-Zaccai TC, etal., Am J Med Genet A. 2008 Jun 1;146A(11):1423-9. doi: 10.1002/ajmg.a.32309.
3. Fousteri M and Mullenders LH, Cell Res. 2008 Jan;18(1):73-84. doi: 10.1038/cr.2008.6.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Jaakkola E, etal., Clin Genet. 2010 Dec;78(6):541-7. doi: 10.1111/j.1399-0004.2010.01424.x.
7. Kamileri I, etal., Trends Genet. 2012 Nov;28(11):566-73. doi: 10.1016/j.tig.2012.06.004. Epub 2012 Jul 22.
8. Lin Z, etal., Hum Mutat. 2008 Jan;29(1):113-22.
9. Ling X, etal., Zhongguo Yao Li Xue Bao. 1999 Jan;20(1):15-20.
10. Lu Y, etal., Mol Cell Biol. 2001 Mar;21(5):1810-8.
11. Ma H, etal., Cancer Lett. 2009 Jan 8;273(1):172-6. doi: 10.1016/j.canlet.2008.08.002. Epub 2008 Sep 11.
12. Matakidou A, etal., Hum Mol Genet. 2007 Oct 1;16(19):2333-40.
13. Meira LB, etal., Am J Hum Genet. 2000 Apr;66(4):1221-8. Epub 2000 Mar 15.
14. Nagtegaal AP, etal., J Neurosci. 2015 Mar 11;35(10):4280-6. doi: 10.1523/JNEUROSCI.5063-14.2015.
15. OMIM Disease Annotation Pipeline
16. Pipeline to import KEGG annotations from KEGG into RGD
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. RGD comprehensive gene curation
21. van der Horst GT, etal., Cell. 1997 May 2;89(3):425-35.
22. Xin B and Wang H, Mol Syndromol. 2013 Jan;3(6):288-90. doi: 10.1159/000345924. Epub 2012 Dec 21.
23. Yin KJ and Sun FY, Brain Res. 1999 Jan 2;815(1):29-35.
24. Yu S, etal., PLoS One. 2014 Dec 2;9(12):e113914. doi: 10.1371/journal.pone.0113914. eCollection 2014.
25. Zhao XN and Usdin K, Hum Mutat. 2014 Mar;35(3):341-9.
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:16916636   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   PMID:31644904  


Genomics

Comparative Map Data
Ercc6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl1049,454,470 - 49,539,538 (-)EnsemblGRCh38hg38GRCh38
GRCh381049,434,881 - 49,539,538 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371050,662,526 - 50,747,169 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361050,336,715 - 50,417,078 (-)NCBINCBI36hg18NCBI36
Build 341050,336,714 - 50,417,078NCBI
Celera1044,250,656 - 44,333,241 (-)NCBI
Cytogenetic Map10q11.23NCBI
HuRef1044,927,342 - 45,011,950 (-)NCBIHuRef
CHM1_11050,944,706 - 51,029,689 (-)NCBICHM1_1
Ercc6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391432,235,248 - 32,302,947 (+)NCBIGRCm39mm39
GRCm381432,513,291 - 32,580,990 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1432,513,521 - 32,580,990 (+)EnsemblGRCm38mm10GRCm38
MGSCv371433,326,707 - 33,394,175 (+)NCBIGRCm37mm9NCBIm37
MGSCv361431,342,530 - 31,409,998 (+)NCBImm8
Celera1428,771,098 - 28,837,767 (+)NCBICelera
Cytogenetic Map14BNCBI
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
Mhudiblu_PPA_v01044,703,720 - 44,784,948 (+)NCBIMhudiblu_PPA_v0panPan3
ERCC6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl281,361,107 - 1,427,162 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1281,358,383 - 1,432,276 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ercc6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624928458,651 - 532,201 (+)NCBI

Position Markers
RH143983  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map16p16UniSTS
RH 3.4 Map1672.2UniSTS
RH131315  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map16p16UniSTS
RH 3.4 Map1670.8UniSTS
AW531214  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map16p16UniSTS
RH 3.4 Map1672.2UniSTS


QTLs in Region (Rnor_6.0)
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)16110660736Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16124228366Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16127556253Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16127556253Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16127556253Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16131816439Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16133160624Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16134465490Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16141240937Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16141240937Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16141240957Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)1624459345244593Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16134074146340741Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)16155018749247447Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)16155018763210301Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16155018763210301Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)16155018763210301Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)16155018763210301Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16172829746728297Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16329668817464293Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16413635523105837Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16413635545905331Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380218360147Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16501380245905331Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380250013802Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16501380250169318Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16501380252144919Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380264012784Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16509870419398181Rat

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.


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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl168,737,974 - 8,804,610 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088529   ⟹   ENSRNOP00000068845
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0168,740,066 - 8,803,205 (+)NCBI
Rnor_5.01610,699,983 - 10,770,565 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001100766   ⟸   NM_001107296
- UniProtKB: D3ZS47 (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

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 10704198 10704199 G C snv DOB/Oda (KyushuU)
16 10765438 10765439 A G snv DOB/Oda (KyushuU)
16 10765543 10765544 G A snv SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), SHR/NHsd (KNAW), SHR/NCrlPrin (KNAW), WKY/Gcrc (KNAW)


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 8799588 8799589 G A snv WKY/N (MCW), SHR/NHsd (RGD), WKY/NHsd (RGD), WKY/Gcrc (RGD), WKY/NCrl (RGD)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 8024943 8024944 G C snv LE/Stm (KNAW)
16 8086565 8086566 G A snv WKY/N (KNAW), SHR/OlaIpcv (KNAW), WKY/NCrl (ICL), SHR/NHsd (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), SHR/OlaIpcv (ICL), SHR/OlaIpcv (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311509 AgrOrtholog
Ensembl Genes ENSRNOG00000030017 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063005 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068845 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064255 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000088529 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.10810 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
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
SMART DEXDc UniProtKB/TrEMBL
  HELICc UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniGene Rn.19370 ENTREZGENE
UniProt A0A0G2JTU1 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