Chd4 (chromodomain helicase DNA binding protein 4) - Rat Genome Database

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Gene: Chd4 (chromodomain helicase DNA binding protein 4) Rattus norvegicus
Analyze
Symbol: Chd4
Name: chromodomain helicase DNA binding protein 4
RGD ID: 620064
Description: Predicted to enable several functions, including ATP hydrolysis activity; histone deacetylase binding activity; and transcription corepressor activity. Involved in negative regulation of transcription by RNA polymerase II; regulation of synapse assembly; and terminal button organization. Is active in cerebellar granule cell to Purkinje cell synapse. Human ortholog(s) of this gene implicated in Sifrim-Hitz-Weiss syndrome; colorectal cancer (multiple); lung cancer (multiple); and lymphoma. Orthologous to human CHD4 (chromodomain helicase DNA binding protein 4); PARTICIPATES IN CHD family mediated chromatin remodeling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: chromodomain-helicase-DNA-binding protein 4; LOC312712; Mi-2; Mi-2 autoantigen
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
GRCr84159,584,623 - 159,617,867 (+)NCBIGRCr8
mRatBN7.24157,898,503 - 157,931,632 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4157,899,391 - 157,931,541 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.04157,612,531 - 157,645,660 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4157,612,536 - 157,645,659 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04224,629,754 - 224,662,856 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44161,217,964 - 161,251,018 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14161,480,832 - 161,480,988 (+)NCBI
Celera4146,635,417 - 146,668,476 (+)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
acrolein  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzatropine  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP,ISO)
butyric acid  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
cefaloridine  (EXP)
chlorpyrifos  (ISO)
clofibrate  (ISO)
clozapine  (ISO)
coumarin  (ISO)
dexamethasone  (ISO)
diazinon  (ISO)
dicrotophos  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
fipronil  (EXP)
flutamide  (EXP)
FR900359  (ISO)
harmine  (ISO)
hemin  (ISO)
hydrogen peroxide  (ISO)
hypochlorous acid  (ISO)
indometacin  (ISO)
inulin  (ISO)
ivermectin  (ISO)
lead(0)  (ISO)
methamphetamine  (ISO)
methylmercury chloride  (ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
propiconazole  (ISO)
radon atom  (ISO)
radon(0)  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
selumetinib  (ISO)
succimer  (ISO)
testosterone enanthate  (ISO)
thapsigargin  (ISO)
thimerosal  (ISO)
torcetrapib  (ISO)
Tributyltin oxide  (ISO)
trichloroethene  (EXP,ISO)
tungsten  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. The nucleosome remodeling and deacetylase complex in development and disease. Basta J and Rauchman M, Transl Res. 2014 May 10. pii: S1931-5244(14)00166-2. doi: 10.1016/j.trsl.2014.05.003.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Anisoosmotic regulation of the Mi-2 autoantigen mRNA in H4IIE rat hepatoma cells and primary hepatocytes. Hammermann R, etal., FEBS Lett 1998 Sep 11;435(1):21-4.
5. CHD4-mediated loss of E-cadherin determines metastatic ability in triple-negative breast cancer cells. Luo CW, etal., Exp Cell Res. 2018 Feb 1;363(1):65-72. doi: 10.1016/j.yexcr.2017.12.032. Epub 2018 Jan 3.
6. Characteristics of genomic alterations of lung adenocarcinoma in young never-smokers. Luo W, etal., Int J Cancer. 2018 Oct 1;143(7):1696-1705. doi: 10.1002/ijc.31542. Epub 2018 May 7.
7. Active gene repression by the Egr2.NAB complex during peripheral nerve myelination. Mager GM, etal., J Biol Chem. 2008 Jun 27;283(26):18187-97. doi: 10.1074/jbc.M803330200. Epub 2008 May 2.
8. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
9. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
10. Defeating EpCAM(+) liver cancer stem cells by targeting chromatin remodeling enzyme CHD4 in human hepatocellular carcinoma. Nio K, etal., J Hepatol. 2015 Nov;63(5):1164-72. doi: 10.1016/j.jhep.2015.06.009. Epub 2015 Jun 18.
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Comprehensive gene review and curation RGD comprehensive gene curation
15. Prognostic significance of Cytokeratin 20-positive lymph node vascular endothelial growth factor A mRNA and chromodomain helicase DNA binding protein 4 in pN0 colorectal cancer patients. Wong SCC, etal., Oncotarget. 2017 Dec 19;9(6):6737-6751. doi: 10.18632/oncotarget.23424. eCollection 2018 Jan 23.
16. CHD4 Has Oncogenic Functions in Initiating and Maintaining Epigenetic Suppression of Multiple Tumor Suppressor Genes. Xia L, etal., Cancer Cell. 2017 May 8;31(5):653-668.e7. doi: 10.1016/j.ccell.2017.04.005.
17. CHD4 mediates proliferation and migration of non-small cell lung cancer via the RhoA/ROCK pathway by regulating PHF5A. Xu N, etal., BMC Cancer. 2020 Mar 30;20(1):262. doi: 10.1186/s12885-020-06762-z.
18. Association of the chromodomain helicase DNA-binding protein 4 (CHD4) missense variation p.D140E with cancer: potential interaction with smoking. Yamada M, etal., Genes Chromosomes Cancer. 2015 Feb;54(2):122-8. doi: 10.1002/gcc.22227. Epub 2014 Nov 19.
19. Promoter decommissioning by the NuRD chromatin remodeling complex triggers synaptic connectivity in the mammalian brain. Yamada T, etal., Neuron. 2014 Jul 2;83(1):122-34. doi: 10.1016/j.neuron.2014.05.039.
Additional References at PubMed
PMID:15767674   PMID:16217013   PMID:17626165   PMID:19644445   PMID:19796622   PMID:19946888   PMID:20720167   PMID:21245044   PMID:22075476   PMID:22720776   PMID:22926524   PMID:27616479  
PMID:31505169  


Genomics

Comparative Map Data
Chd4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84159,584,623 - 159,617,867 (+)NCBIGRCr8
mRatBN7.24157,898,503 - 157,931,632 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4157,899,391 - 157,931,541 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.04157,612,531 - 157,645,660 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4157,612,536 - 157,645,659 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04224,629,754 - 224,662,856 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44161,217,964 - 161,251,018 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14161,480,832 - 161,480,988 (+)NCBI
Celera4146,635,417 - 146,668,476 (+)NCBICelera
Cytogenetic Map4q42NCBI
CHD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38126,570,082 - 6,607,379 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl126,570,082 - 6,614,524 (-)EnsemblGRCh38hg38GRCh38
GRCh37126,679,248 - 6,716,545 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36126,549,509 - 6,586,812 (-)NCBINCBI36Build 36hg18NCBI36
Build 34126,549,509 - 6,586,812NCBI
Celera128,296,110 - 8,333,413 (-)NCBICelera
Cytogenetic Map12p13.31NCBI
HuRef126,533,326 - 6,569,829 (-)NCBIHuRef
CHM1_1126,678,251 - 6,715,556 (-)NCBICHM1_1
T2T-CHM13v2.0126,580,442 - 6,617,741 (-)NCBIT2T-CHM13v2.0
Chd4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396125,073,144 - 125,107,554 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6125,072,944 - 125,107,554 (+)EnsemblGRCm39 Ensembl
GRCm386125,095,980 - 125,130,591 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6125,095,981 - 125,130,591 (+)EnsemblGRCm38mm10GRCm38
MGSCv376125,046,181 - 125,080,532 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366125,061,782 - 125,096,133 (+)NCBIMGSCv36mm8
Celera6126,765,839 - 126,800,494 (+)NCBICelera
Cytogenetic Map6F2NCBI
cM Map659.28NCBI
Chd4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554134,191,619 - 4,228,225 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554134,191,619 - 4,228,225 (-)NCBIChiLan1.0ChiLan1.0
CHD4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21012,131,970 - 12,176,548 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11212,128,732 - 12,166,445 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0126,701,004 - 6,738,621 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1126,619,001 - 6,656,076 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl126,619,089 - 6,656,076 (-)Ensemblpanpan1.1panPan2
CHD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12738,411,009 - 38,440,367 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2738,411,075 - 38,439,958 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha278,175,956 - 8,205,662 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02738,765,554 - 38,795,264 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2738,765,644 - 38,794,990 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12738,637,593 - 38,667,294 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02738,679,124 - 38,708,819 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0277,654,654 - 7,684,346 (-)NCBIUU_Cfam_GSD_1.0
Chd4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945102,515,698 - 102,546,548 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367091,183,254 - 1,214,149 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367091,183,243 - 1,214,144 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHD4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl564,065,992 - 64,105,173 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1564,071,627 - 64,105,212 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2566,473,994 - 66,506,408 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CHD4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1116,603,820 - 6,641,278 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl116,602,694 - 6,640,351 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660631,578,243 - 1,621,184 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chd4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248603,283,837 - 3,318,985 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248603,285,086 - 3,318,939 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Chd4
95 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:99
Count of miRNA genes:73
Interacting mature miRNAs:93
Transcripts:ENSRNOT00000055970
Prediction methods: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
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
1581566Eae21Experimental allergic encephalomyelitis QTL 216.2body mass (VT:0001259)maximum body weight loss to initial body weight ratio (CMO:0001400)4157680158158841762Rat
1581574Eae20Experimental allergic encephalomyelitis QTL 207.8nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)4153031106158841762Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4147278504167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat

Markers in Region
D6Ertd380e  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24157,931,232 - 157,931,427 (+)MAPPERmRatBN7.2
Rnor_6.04157,645,261 - 157,645,455NCBIRnor6.0
Rnor_5.04224,662,457 - 224,662,651UniSTSRnor5.0
RGSC_v3.44161,250,619 - 161,250,813UniSTSRGSC3.4
Celera4146,668,077 - 146,668,271UniSTS
Cytogenetic Map4q42UniSTS
RH64827  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24157,931,463 - 157,931,602 (+)MAPPERmRatBN7.2
Rnor_6.04157,645,492 - 157,645,630NCBIRnor6.0
Rnor_5.04224,662,688 - 224,662,826UniSTSRnor5.0
RGSC_v3.44161,250,850 - 161,250,988UniSTSRGSC3.4
Celera4146,668,308 - 146,668,446UniSTS
Cytogenetic Map4q42UniSTS
RH143540  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24157,929,005 - 157,929,225 (+)MAPPERmRatBN7.2
Rnor_6.04157,643,034 - 157,643,253NCBIRnor6.0
Rnor_5.04224,660,230 - 224,660,449UniSTSRnor5.0
RGSC_v3.44161,248,391 - 161,248,610UniSTSRGSC3.4
Celera4146,665,850 - 146,666,069UniSTS
RH 3.4 Map41001.5UniSTS
Cytogenetic Map4q42UniSTS
AA963793  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24157,931,325 - 157,931,507 (+)MAPPERmRatBN7.2
Rnor_6.04157,645,354 - 157,645,535NCBIRnor6.0
Rnor_5.04224,662,550 - 224,662,731UniSTSRnor5.0
RGSC_v3.44161,250,712 - 161,250,893UniSTSRGSC3.4
Celera4146,668,170 - 146,668,351UniSTS
RH 3.4 Map41005.8UniSTS
Cytogenetic Map4q42UniSTS
MARC_34374-34375:1062687298:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24157,931,029 - 157,931,486 (+)MAPPERmRatBN7.2
Rnor_6.04157,645,058 - 157,645,514NCBIRnor6.0
Rnor_5.04224,662,254 - 224,662,710UniSTSRnor5.0
RGSC_v3.44161,250,416 - 161,250,872UniSTSRGSC3.4
Celera4146,667,874 - 146,668,330UniSTS
Cytogenetic Map4q42UniSTS


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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001427174 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_001063352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237395 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237396 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237397 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237398 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237399 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237400 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237401 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285425 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285426 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285427 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285428 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285429 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063285430 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC115415 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ010024 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232290 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000004 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000055970   ⟹   ENSRNOP00000052823
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4157,899,391 - 157,931,541 (+)Ensembl
Rnor_6.0 Ensembl4157,612,536 - 157,645,659 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107359   ⟹   ENSRNOP00000091626
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4157,899,391 - 157,931,541 (+)Ensembl
RefSeq Acc Id: NM_001427174   ⟹   NP_001414103
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,584,818 - 159,617,867 (+)NCBI
RefSeq Acc Id: XM_006237396   ⟹   XP_006237458
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,584,623 - 159,617,867 (+)NCBI
mRatBN7.24157,898,503 - 157,931,632 (+)NCBI
Rnor_6.04157,612,531 - 157,645,660 (+)NCBI
Rnor_5.04224,629,754 - 224,662,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237397   ⟹   XP_006237459
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,584,623 - 159,617,867 (+)NCBI
mRatBN7.24157,898,503 - 157,931,632 (+)NCBI
Rnor_6.04157,612,532 - 157,645,660 (+)NCBI
Rnor_5.04224,629,754 - 224,662,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237398   ⟹   XP_006237460
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,584,700 - 159,617,867 (+)NCBI
mRatBN7.24157,898,503 - 157,931,632 (+)NCBI
Rnor_6.04157,612,531 - 157,645,660 (+)NCBI
Rnor_5.04224,629,754 - 224,662,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237399   ⟹   XP_006237461
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,584,623 - 159,617,867 (+)NCBI
mRatBN7.24157,898,503 - 157,931,632 (+)NCBI
Rnor_6.04157,612,532 - 157,645,660 (+)NCBI
Rnor_5.04224,629,754 - 224,662,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237400   ⟹   XP_006237462
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,584,700 - 159,617,867 (+)NCBI
mRatBN7.24157,898,503 - 157,931,632 (+)NCBI
Rnor_6.04157,612,531 - 157,645,660 (+)NCBI
Rnor_5.04224,629,754 - 224,662,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237401   ⟹   XP_006237463
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,584,700 - 159,617,867 (+)NCBI
mRatBN7.24157,898,503 - 157,931,632 (+)NCBI
Rnor_6.04157,612,532 - 157,645,660 (+)NCBI
Rnor_5.04224,629,754 - 224,662,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063285425   ⟹   XP_063141495
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,584,700 - 159,617,867 (+)NCBI
RefSeq Acc Id: XM_063285426   ⟹   XP_063141496
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,584,700 - 159,617,867 (+)NCBI
RefSeq Acc Id: XM_063285427   ⟹   XP_063141497
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,584,700 - 159,617,867 (+)NCBI
RefSeq Acc Id: XM_063285428   ⟹   XP_063141498
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,584,700 - 159,617,867 (+)NCBI
RefSeq Acc Id: XM_063285429   ⟹   XP_063141499
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,584,623 - 159,617,867 (+)NCBI
RefSeq Acc Id: XM_063285430   ⟹   XP_063141500
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,584,700 - 159,617,867 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_006237460   ⟸   XM_006237398
- Peptide Label: isoform X4
- UniProtKB: A0A8I6ACF8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237458   ⟸   XM_006237396
- Peptide Label: isoform X1
- UniProtKB: A0A8I6ACF8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237459   ⟸   XM_006237397
- Peptide Label: isoform X2
- UniProtKB: A0A8I6ACF8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237462   ⟸   XM_006237400
- Peptide Label: isoform X8
- UniProtKB: A0A8I6ACF8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237461   ⟸   XM_006237399
- Peptide Label: isoform X6
- UniProtKB: A0A8I6ACF8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237463   ⟸   XM_006237401
- Peptide Label: isoform X3
- UniProtKB: E9PU01 (UniProtKB/TrEMBL),   A0A8I6ACF8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000052823   ⟸   ENSRNOT00000055970
RefSeq Acc Id: ENSRNOP00000091626   ⟸   ENSRNOT00000107359
RefSeq Acc Id: XP_063141499   ⟸   XM_063285429
- Peptide Label: isoform X11
RefSeq Acc Id: XP_063141495   ⟸   XM_063285425
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063141497   ⟸   XM_063285427
- Peptide Label: isoform X9
RefSeq Acc Id: XP_063141498   ⟸   XM_063285428
- Peptide Label: isoform X10
RefSeq Acc Id: XP_063141496   ⟸   XM_063285426
- Peptide Label: isoform X7
RefSeq Acc Id: XP_063141500   ⟸   XM_063285430
- Peptide Label: isoform X12
RefSeq Acc Id: NP_001414103   ⟸   NM_001427174
- UniProtKB: A0A8I6ACF8 (UniProtKB/TrEMBL)
Protein Domains
Chromo   Helicase ATP-binding   Helicase C-terminal   PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-E9PU01-F1-model_v2 AlphaFold E9PU01 1-1921 view protein structure

Transcriptome

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

Promoters
RGD ID:13693421
Promoter ID:EPDNEW_R3928
Type:initiation region
Name:Chd4_1
Description:chromodomain helicase DNA binding protein 4
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_6.04157,612,605 - 157,612,665EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620064 AgrOrtholog
BioCyc Gene G2FUF-43015 BioCyc
Ensembl Genes ENSRNOG00000018309 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055970.5 UniProtKB/TrEMBL
  ENSRNOT00000107359.1 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.40 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
  3.40.50.10810 UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
InterPro CHD_C2 UniProtKB/TrEMBL
  CHD_N UniProtKB/TrEMBL
  Chromo_domain UniProtKB/TrEMBL
  Chromo_domain/shadow UniProtKB/TrEMBL
  Chromodomain-like UniProtKB/TrEMBL
  DNA/RNA_helicase_DEAH_CS UniProtKB/TrEMBL
  DUF1086 UniProtKB/TrEMBL
  DUF1087 UniProtKB/TrEMBL
  Helicase_ATP-bd UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  SNF2-like_sf UniProtKB/TrEMBL
  SNF2/RAD54-like_C UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
NCBI Gene 117535 ENTREZGENE
PANTHER CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 3-RELATED-RELATED UniProtKB/TrEMBL
  CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 4 UniProtKB/TrEMBL
Pfam CHDCT2 UniProtKB/TrEMBL
  CHDNT UniProtKB/TrEMBL
  Chromo UniProtKB/TrEMBL
  DUF1086 UniProtKB/TrEMBL
  DUF1087 UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
PhenoGen Chd4 PhenoGen
PROSITE CHROMO_2 UniProtKB/TrEMBL
  DEAH_ATP_HELICASE UniProtKB/TrEMBL
  HELICASE_ATP_BIND_1 UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000018309 RatGTEx
SMART CHROMO UniProtKB/TrEMBL
  DEXDc UniProtKB/TrEMBL
  DUF1086 UniProtKB/TrEMBL
  DUF1087 UniProtKB/TrEMBL
  HELICc UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
Superfamily-SCOP Chromodomain-like UniProtKB/TrEMBL
  FYVE_PHD_ZnF UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt A0A8I6ACF8 ENTREZGENE, UniProtKB/TrEMBL
  A6ILR2_RAT UniProtKB/TrEMBL
  A6ILR3_RAT UniProtKB/TrEMBL
  A6ILR4_RAT UniProtKB/TrEMBL
  A6ILR5_RAT UniProtKB/TrEMBL
  A6ILR7_RAT UniProtKB/TrEMBL
  E9PU01 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-04-27 Chd4  chromodomain helicase DNA binding protein 4  Chd4_predicted  chromodomain helicase DNA binding protein 4 (predicted)  Data merged from RGD:1311301 737654 APPROVED
2005-01-20 Chd4  chromodomain helicase DNA binding protein 4      Symbol and Name status set to approved 1299863 APPROVED
2005-01-12 Chd4_predicted  chromodomain helicase DNA binding protein 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED
2002-08-07 Chd4  chromodomain helicase DNA binding protein 4      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_homology protein aa sequence is 100% homologous to human CHD4 632444
gene_regulation transcription is downregulated after hypoosmotic exposure 632444