Chd6 (chromodomain helicase DNA binding protein 6) - Rat Genome Database

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Gene: Chd6 (chromodomain helicase DNA binding protein 6) Rattus norvegicus
Analyze
Symbol: Chd6
Name: chromodomain helicase DNA binding protein 6
RGD ID: 1310465
Description: Predicted to enable several functions, including ATP hydrolysis activity; ATP-dependent chromatin remodeler activity; and transcription coregulator binding activity. Predicted to be involved in cell redox homeostasis; chromatin remodeling; and positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of chromatin. Predicted to be active in nucleus. Orthologous to human CHD6 (chromodomain helicase DNA binding protein 6); PARTICIPATES IN nuclear factor, erythroid 2 like 2 signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; amphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ATP-dependent helicase CHD6; CHD-6; chromodomain-helicase-DNA-binding protein 6; LOC311607
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83170,016,204 - 170,177,480 (-)NCBIGRCr8
mRatBN7.23149,596,509 - 149,757,765 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3149,596,509 - 149,757,755 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3153,409,455 - 153,571,162 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03161,908,858 - 162,070,560 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03159,648,665 - 159,809,906 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03156,937,746 - 157,099,328 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3156,937,733 - 157,099,306 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03163,164,938 - 163,324,764 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43151,741,389 - 151,924,668 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13151,647,823 - 151,830,771 (-)NCBI
Celera3148,269,027 - 148,429,163 (-)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromatin  (IBA)
nucleoplasm  (IEA,ISO,ISS)
nucleus  (IBA,IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. The Nrf2 regulatory network provides an interface between redox and intermediary metabolism. Hayes JD and Dinkova-Kostova AT, Trends Biochem Sci. 2014 Apr;39(4):199-218. doi: 10.1016/j.tibs.2014.02.002. Epub 2014 Mar 16.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16314513   PMID:17027977  


Genomics

Comparative Map Data
Chd6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83170,016,204 - 170,177,480 (-)NCBIGRCr8
mRatBN7.23149,596,509 - 149,757,765 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3149,596,509 - 149,757,755 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3153,409,455 - 153,571,162 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03161,908,858 - 162,070,560 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03159,648,665 - 159,809,906 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03156,937,746 - 157,099,328 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3156,937,733 - 157,099,306 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03163,164,938 - 163,324,764 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43151,741,389 - 151,924,668 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13151,647,823 - 151,830,771 (-)NCBI
Celera3148,269,027 - 148,429,163 (-)NCBICelera
Cytogenetic Map3q42NCBI
CHD6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382041,402,083 - 41,618,377 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2041,402,083 - 41,618,384 (-)EnsemblGRCh38hg38GRCh38
GRCh372040,030,723 - 40,247,016 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362039,464,584 - 39,680,547 (-)NCBINCBI36Build 36hg18NCBI36
Build 342039,464,583 - 39,680,547NCBI
Celera2036,741,838 - 36,957,790 (-)NCBICelera
Cytogenetic Map20q12NCBI
HuRef2036,768,458 - 36,984,731 (-)NCBIHuRef
CHM1_12039,935,021 - 40,151,300 (-)NCBICHM1_1
T2T-CHM13v2.02043,133,884 - 43,350,249 (-)NCBIT2T-CHM13v2.0
Chd6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392160,788,898 - 160,951,006 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2160,788,898 - 160,950,995 (-)EnsemblGRCm39 Ensembl
GRCm382160,946,978 - 161,109,086 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2160,946,978 - 161,109,075 (-)EnsemblGRCm38mm10GRCm38
MGSCv372160,772,714 - 160,934,792 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362160,638,419 - 160,800,497 (-)NCBIMGSCv36mm8
Celera2166,877,653 - 167,040,009 (-)NCBICelera
Cytogenetic Map2H2NCBI
cM Map280.98NCBI
Chd6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544515,360,025 - 15,560,988 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544515,360,074 - 15,576,410 (+)NCBIChiLan1.0ChiLan1.0
CHD6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22147,144,211 - 47,354,354 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12047,137,310 - 47,347,383 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02037,744,012 - 37,953,593 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12038,839,685 - 38,988,719 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2038,839,685 - 38,999,501 (-)Ensemblpanpan1.1panPan2
CHD6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12429,397,320 - 29,601,206 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2429,397,306 - 29,601,350 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2429,042,568 - 29,246,480 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02430,102,193 - 30,305,887 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2430,102,811 - 30,306,032 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12429,370,977 - 29,574,934 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02429,474,474 - 29,678,500 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02429,971,008 - 30,174,849 (-)NCBIUU_Cfam_GSD_1.0
Chd6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640178,354,920 - 178,570,711 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936561178,700 - 394,842 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936561238,307 - 394,082 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHD6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1744,048,098 - 44,265,431 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11744,048,056 - 44,265,472 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21749,502,246 - 49,555,890 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CHD6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1222,163,836 - 22,373,098 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl222,223,919 - 22,373,275 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605070,981,245 - 71,189,656 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chd6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479012,610,254 - 12,858,368 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462479012,610,418 - 12,858,062 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Chd6
546 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:777
Count of miRNA genes:295
Interacting mature miRNAs:389
Transcripts:ENSRNOT00000022861
Prediction methods:Microtar, Miranda, Rnahybrid, 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
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141339013162184794Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141339236155617360Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3145925360166177555Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3145925360166177555Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3145925360166177555Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3145925360166177555Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3145925360166177555Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3145925360166177555Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145925360166177555Rat
1300113Bp176Blood pressure QTL 1763.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145956084157309487Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)3145956084161299569Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3149040888168026850Rat

Markers in Region
D3Mco22  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23149,662,152 - 149,662,411 (+)MAPPERmRatBN7.2
Rnor_6.03157,002,896 - 157,003,152NCBIRnor6.0
Rnor_5.03163,230,270 - 163,230,526UniSTSRnor5.0
RGSC_v3.43151,807,483 - 151,807,737RGDRGSC3.4
RGSC_v3.43151,807,481 - 151,807,737UniSTSRGSC3.4
RGSC_v3.13151,713,519 - 151,713,773RGD
Celera3148,334,584 - 148,334,840UniSTS
Cytogenetic Map3q42UniSTS
RH143820  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23149,598,826 - 149,598,947 (+)MAPPERmRatBN7.2
Rnor_6.03156,940,064 - 156,940,184NCBIRnor6.0
Rnor_5.03163,167,256 - 163,167,376UniSTSRnor5.0
RGSC_v3.43151,743,707 - 151,743,827UniSTSRGSC3.4
Celera3148,271,345 - 148,271,465UniSTS
RH 3.4 Map31366.6UniSTS
Cytogenetic Map3q42UniSTS
RH144348  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23149,674,946 - 149,675,180 (+)MAPPERmRatBN7.2
Rnor_6.03157,015,687 - 157,015,920NCBIRnor6.0
Rnor_5.03163,243,061 - 163,243,294UniSTSRnor5.0
RGSC_v3.43151,820,272 - 151,820,505UniSTSRGSC3.4
Celera3148,347,375 - 148,347,608UniSTS
RH 3.4 Map31364.7UniSTS
Cytogenetic Map3q42UniSTS
AW522475  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23149,614,786 - 149,614,929 (+)MAPPERmRatBN7.2
Rnor_6.03156,955,991 - 156,956,133NCBIRnor6.0
Rnor_5.03163,183,211 - 163,183,353UniSTSRnor5.0
RGSC_v3.43151,759,971 - 151,760,113UniSTSRGSC3.4
Celera3148,287,265 - 148,287,407UniSTS
RH 3.4 Map31369.5UniSTS
Cytogenetic Map3q42UniSTS


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 2 29 21 5 19 5 1 1 74 35 37 11 1
Low 1 14 36 36 36 7 10 4 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001107797 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006235482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006235483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006235484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762345 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762346 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591790 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591791 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105104 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105105 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105106 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105107 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105108 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105111 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105112 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105113 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105114 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105116 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283862 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283863 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283864 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283865 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283866 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283867 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005501896 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005501897 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH474005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211572 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230879 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000022861   ⟹   ENSRNOP00000022861
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3149,596,509 - 149,757,755 (-)Ensembl
Rnor_6.0 Ensembl3156,937,746 - 157,099,306 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089958   ⟹   ENSRNOP00000071893
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3149,596,509 - 149,708,435 (-)Ensembl
Rnor_6.0 Ensembl3156,937,733 - 157,049,666 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106235   ⟹   ENSRNOP00000093958
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3149,596,509 - 149,757,755 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107966   ⟹   ENSRNOP00000094454
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3149,596,509 - 149,757,755 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114568   ⟹   ENSRNOP00000086889
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3149,596,509 - 149,682,505 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119650   ⟹   ENSRNOP00000076519
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3149,596,509 - 149,700,434 (-)Ensembl
RefSeq Acc Id: NM_001107797   ⟹   NP_001101267
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,204 - 170,177,435 (-)NCBI
mRatBN7.23149,596,509 - 149,757,755 (-)NCBI
Rnor_6.03156,937,746 - 157,099,306 (-)NCBI
Rnor_5.03163,164,938 - 163,324,764 (-)NCBI
RGSC_v3.43151,741,389 - 151,924,668 (-)RGD
Celera3148,269,027 - 148,429,163 (-)RGD
Sequence:
RefSeq Acc Id: XM_006235484   ⟹   XP_006235546
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,177,480 (-)NCBI
mRatBN7.23149,596,511 - 149,757,765 (-)NCBI
Rnor_6.03156,937,746 - 157,050,230 (-)NCBI
Rnor_5.03163,164,938 - 163,324,764 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762345   ⟹   XP_008760567
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,177,480 (-)NCBI
mRatBN7.23149,596,511 - 149,757,765 (-)NCBI
Rnor_6.03156,937,746 - 157,099,328 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762346   ⟹   XP_008760568
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,177,369 (-)NCBI
mRatBN7.23149,596,511 - 149,757,758 (-)NCBI
Rnor_6.03156,937,746 - 157,099,328 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591790   ⟹   XP_017447279
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,177,480 (-)NCBI
mRatBN7.23149,596,511 - 149,757,765 (-)NCBI
Rnor_6.03156,937,746 - 157,050,230 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039105104   ⟹   XP_038961032
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,155,998 (-)NCBI
mRatBN7.23149,596,511 - 149,728,465 (-)NCBI
RefSeq Acc Id: XM_039105105   ⟹   XP_038961033
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,177,480 (-)NCBI
mRatBN7.23149,596,511 - 149,757,765 (-)NCBI
RefSeq Acc Id: XM_039105106   ⟹   XP_038961034
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,177,480 (-)NCBI
mRatBN7.23149,596,511 - 149,757,765 (-)NCBI
RefSeq Acc Id: XM_039105107   ⟹   XP_038961035
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,177,480 (-)NCBI
mRatBN7.23149,596,511 - 149,757,765 (-)NCBI
RefSeq Acc Id: XM_039105108   ⟹   XP_038961036
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,107,341 (-)NCBI
mRatBN7.23149,596,511 - 149,682,473 (-)NCBI
RefSeq Acc Id: XM_039105109   ⟹   XP_038961037
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,030,279 - 170,177,480 (-)NCBI
mRatBN7.23149,610,586 - 149,757,765 (-)NCBI
RefSeq Acc Id: XM_039105111   ⟹   XP_038961039
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,080,195 (-)NCBI
mRatBN7.23149,596,511 - 149,660,495 (-)NCBI
RefSeq Acc Id: XM_039105112   ⟹   XP_038961040
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,059,555 (-)NCBI
mRatBN7.23149,596,511 - 149,639,856 (-)NCBI
RefSeq Acc Id: XM_039105113   ⟹   XP_038961041
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,052,073 (-)NCBI
mRatBN7.23149,596,511 - 149,632,382 (-)NCBI
RefSeq Acc Id: XM_039105114   ⟹   XP_038961042
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,038,069 - 170,177,480 (-)NCBI
mRatBN7.23149,618,377 - 149,757,765 (-)NCBI
RefSeq Acc Id: XM_039105115   ⟹   XP_038961043
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,038,069 - 170,177,480 (-)NCBI
mRatBN7.23149,618,377 - 149,757,765 (-)NCBI
RefSeq Acc Id: XM_039105116   ⟹   XP_038961044
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,049,047 (-)NCBI
mRatBN7.23149,596,511 - 149,629,356 (-)NCBI
RefSeq Acc Id: XM_063283862   ⟹   XP_063139932
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,177,435 (-)NCBI
RefSeq Acc Id: XM_063283863   ⟹   XP_063139933
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,176,644 (-)NCBI
RefSeq Acc Id: XM_063283864   ⟹   XP_063139934
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,177,421 (-)NCBI
RefSeq Acc Id: XM_063283865   ⟹   XP_063139935
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,016,302 - 170,107,341 (-)NCBI
RefSeq Acc Id: XM_063283866   ⟹   XP_063139936
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,030,811 - 170,177,480 (-)NCBI
RefSeq Acc Id: XM_063283867   ⟹   XP_063139937
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,030,811 - 170,177,480 (-)NCBI
RefSeq Acc Id: XR_005501896
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,036,414 - 170,177,480 (-)NCBI
mRatBN7.23149,616,722 - 149,757,765 (-)NCBI
RefSeq Acc Id: XR_005501897
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83170,036,414 - 170,177,480 (-)NCBI
mRatBN7.23149,616,722 - 149,757,765 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001101267 (Get FASTA)   NCBI Sequence Viewer  
  XP_006235546 (Get FASTA)   NCBI Sequence Viewer  
  XP_008760567 (Get FASTA)   NCBI Sequence Viewer  
  XP_008760568 (Get FASTA)   NCBI Sequence Viewer  
  XP_017447279 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961032 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961033 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961034 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961035 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961036 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961037 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961039 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961040 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961041 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961042 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961043 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961044 (Get FASTA)   NCBI Sequence Viewer  
  XP_063139932 (Get FASTA)   NCBI Sequence Viewer  
  XP_063139933 (Get FASTA)   NCBI Sequence Viewer  
  XP_063139934 (Get FASTA)   NCBI Sequence Viewer  
  XP_063139935 (Get FASTA)   NCBI Sequence Viewer  
  XP_063139936 (Get FASTA)   NCBI Sequence Viewer  
  XP_063139937 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D3ZA12 (Get FASTA)   NCBI Sequence Viewer  
  EDL96607 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000022861
  ENSRNOP00000022861.7
  ENSRNOP00000071893.1
  ENSRNOP00000076519
  ENSRNOP00000076519.1
  ENSRNOP00000086889
  ENSRNOP00000086889.1
  ENSRNOP00000093958
  ENSRNOP00000093958.1
  ENSRNOP00000094454
  ENSRNOP00000094454.1
Reference Protein Sequences
RefSeq Acc Id: NP_001101267   ⟸   NM_001107797
- UniProtKB: D3ZA12 (UniProtKB/Swiss-Prot),   A0A8I5Y6Q9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006235546   ⟸   XM_006235484
- Peptide Label: isoform X6
- UniProtKB: A0A8I6AKM1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760568   ⟸   XM_008762346
- Peptide Label: isoform X5
- UniProtKB: A0A8I6AKM1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760567   ⟸   XM_008762345
- Peptide Label: isoform X1
- UniProtKB: A0A8L2QC41 (UniProtKB/TrEMBL),   A0A8I5Y6Q9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447279   ⟸   XM_017591790
- Peptide Label: isoform X4
- UniProtKB: A0A8I6ARM3 (UniProtKB/TrEMBL),   A0A8I6AKM1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071893   ⟸   ENSRNOT00000089958
RefSeq Acc Id: ENSRNOP00000022861   ⟸   ENSRNOT00000022861
RefSeq Acc Id: XP_038961033   ⟸   XM_039105105
- Peptide Label: isoform X3
- UniProtKB: A0A8I5Y6Q9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038961035   ⟸   XM_039105107
- Peptide Label: isoform X8
- UniProtKB: A0A8I5Y6Q9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038961034   ⟸   XM_039105106
- Peptide Label: isoform X7
- UniProtKB: A0A8I5Y6Q9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038961032   ⟸   XM_039105104
- Peptide Label: isoform X1
- UniProtKB: A0A8L2QC41 (UniProtKB/TrEMBL),   A0A8I5Y6Q9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038961036   ⟸   XM_039105108
- Peptide Label: isoform X9
- UniProtKB: A0A8I6A6R3 (UniProtKB/TrEMBL),   A0A8I6AKM1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038961039   ⟸   XM_039105111
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038961040   ⟸   XM_039105112
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038961041   ⟸   XM_039105113
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038961044   ⟸   XM_039105116
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038961037   ⟸   XM_039105109
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038961043   ⟸   XM_039105115
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038961042   ⟸   XM_039105114
- Peptide Label: isoform X18
RefSeq Acc Id: ENSRNOP00000094454   ⟸   ENSRNOT00000107966
RefSeq Acc Id: ENSRNOP00000093958   ⟸   ENSRNOT00000106235
RefSeq Acc Id: ENSRNOP00000086889   ⟸   ENSRNOT00000114568
RefSeq Acc Id: ENSRNOP00000076519   ⟸   ENSRNOT00000119650
RefSeq Acc Id: XP_063139932   ⟸   XM_063283862
- Peptide Label: isoform X1
- UniProtKB: A0A8L2QC41 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139934   ⟸   XM_063283864
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K1L7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139933   ⟸   XM_063283863
- Peptide Label: isoform X1
- UniProtKB: A0A8L2QC41 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139935   ⟸   XM_063283865
- Peptide Label: isoform X10
RefSeq Acc Id: XP_063139937   ⟸   XM_063283867
- Peptide Label: isoform X13
RefSeq Acc Id: XP_063139936   ⟸   XM_063283866
- Peptide Label: isoform X11
Protein Domains
Chromo   Helicase ATP-binding   Helicase C-terminal   Myb-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZA12-F1-model_v2 AlphaFold D3ZA12 1-2698 view protein structure

Transcriptome

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

Promoters
RGD ID:13692629
Promoter ID:EPDNEW_R3152
Type:multiple initiation site
Name:Chd6_1
Description:chromodomain helicase DNA binding protein 6
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_6.03157,099,252 - 157,099,312EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310465 AgrOrtholog
BioCyc Gene G2FUF-46962 BioCyc
Ensembl Genes ENSRNOG00000016744 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022861.7 UniProtKB/TrEMBL
  ENSRNOT00000089958.2 UniProtKB/TrEMBL
  ENSRNOT00000106235.1 UniProtKB/TrEMBL
  ENSRNOT00000107966.1 UniProtKB/TrEMBL
  ENSRNOT00000114568.1 UniProtKB/TrEMBL
  ENSRNOT00000119650.1 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.10810 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro BRK_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromo-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromo/chromo_shadow_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromo_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA/RNA_helicase_DEAH_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_ATP-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2/RAD54-like_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:311607 UniProtKB/Swiss-Prot
NCBI Gene 311607 ENTREZGENE
PANTHER CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 9 UniProtKB/Swiss-Prot
  CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 9 UniProtKB/Swiss-Prot
  CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 9 UniProtKB/TrEMBL
  CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 9 UniProtKB/TrEMBL
Pfam Chromo UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Chd6 PhenoGen
PROSITE CHROMO_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DEAH_ATP_HELICASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HELICASE_ATP_BIND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016744 RatGTEx
SMART BRK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CHROMO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DEXDc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HELICc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54160 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K1L7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5Y6Q9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A6R3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AKM1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6ARM3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8L2QC41 ENTREZGENE, UniProtKB/TrEMBL
  CHD6_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Chd6  chromodomain helicase DNA binding protein 6   Chd6_predicted  chromodomain helicase DNA binding protein 6 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Chd6_predicted  chromodomain helicase DNA binding protein 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED