Chd3 (chromodomain helicase DNA binding protein 3) - Rat Genome Database

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Gene: Chd3 (chromodomain helicase DNA binding protein 3) Rattus norvegicus
Analyze
Symbol: Chd3
Name: chromodomain helicase DNA binding protein 3
RGD ID: 1311923
Description: Predicted to enable several functions, including ATP hydrolysis activity; ATP-dependent chromatin remodeler activity; and histone binding activity. Predicted to be involved in chromatin remodeling; microtubule cytoskeleton organization; and negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within chromatin organization. Predicted to be located in several cellular components, including centriolar satellite; chromatin; and nuclear lumen. Predicted to be part of NuRD complex. Predicted to be active in nucleus. Biomarker of pancreatic carcinoma. Orthologous to human CHD3 (chromodomain helicase DNA binding protein 3); PARTICIPATES IN CHD family mediated chromatin remodeling pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: chromodomain-helicase-DNA-binding protein 3; LOC303241
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81054,562,437 - 54,588,842 (-)NCBIGRCr8
mRatBN7.21054,063,629 - 54,090,030 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1054,063,629 - 54,090,047 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01055,943,467 - 55,970,417 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1055,943,446 - 55,965,216 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01055,685,542 - 55,716,144 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41056,135,930 - 56,166,645 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11056,150,272 - 56,175,839 (-)NCBI
Celera1053,220,188 - 53,247,010 (-)NCBICelera
Cytogenetic Map10q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-tribromophenol  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chlordecone  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
cobalt dichloride  (EXP)
copper(II) chloride  (ISO)
coumarin  (ISO)
decabromodiphenyl ether  (ISO)
Dibutyl phosphate  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
elemental selenium  (ISO)
ethanol  (ISO)
folic acid  (ISO)
FR900359  (ISO)
gentamycin  (EXP)
heptanal  (ISO)
hexadecanoic acid  (ISO)
hexanal  (ISO)
hypochlorous acid  (ISO)
ivermectin  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
mercury dichloride  (ISO)
nonanal  (ISO)
octanal  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
pentanal  (ISO)
perfluorohexanesulfonic acid  (ISO)
pirinixic acid  (ISO)
propanal  (ISO)
quercetin  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
Soman  (EXP)
sunitinib  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
toluene  (ISO)
triphenyl phosphate  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
centriolar satellite  (IEA,ISO)
centrosome  (ISO)
chromatin  (IBA)
cytoplasm  (ISO)
nucleolus  (IEA,ISO)
nucleoplasm  (ISO)
nucleus  (IBA,ISO)
NuRD complex  (IBA,ISO)
PML body  (ISO)

Molecular Function

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. Proteomic analysis of pancreatic intraepithelial neoplasia and pancreatic carcinoma in rat models. Wang L, etal., World J Gastroenterol. 2011 Mar 21;17(11):1434-41. doi: 10.3748/wjg.v17.i11.1434.
Additional References at PubMed
PMID:10204490   PMID:12477932   PMID:17626165   PMID:17827154   PMID:19710508   PMID:22082260   PMID:22658674   PMID:22720776   PMID:30397230  


Genomics

Comparative Map Data
Chd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81054,562,437 - 54,588,842 (-)NCBIGRCr8
mRatBN7.21054,063,629 - 54,090,030 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1054,063,629 - 54,090,047 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01055,943,467 - 55,970,417 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1055,943,446 - 55,965,216 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01055,685,542 - 55,716,144 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41056,135,930 - 56,166,645 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11056,150,272 - 56,175,839 (-)NCBI
Celera1053,220,188 - 53,247,010 (-)NCBICelera
Cytogenetic Map10q24NCBI
CHD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38177,884,796 - 7,912,755 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl177,884,796 - 7,912,760 (+)EnsemblGRCh38hg38GRCh38
GRCh37177,788,114 - 7,816,073 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36177,728,849 - 7,756,246 (+)NCBINCBI36Build 36hg18NCBI36
Build 34177,732,833 - 7,756,246NCBI
Celera177,815,816 - 7,843,619 (+)NCBICelera
Cytogenetic Map17p13.1NCBI
HuRef177,683,207 - 7,710,664 (+)NCBIHuRef
CHM1_1177,797,025 - 7,824,854 (+)NCBICHM1_1
T2T-CHM13v2.0177,790,128 - 7,818,165 (+)NCBIT2T-CHM13v2.0
Chd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391169,234,099 - 69,260,325 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1169,234,099 - 69,260,232 (-)EnsemblGRCm39 Ensembl
GRCm381169,343,273 - 69,369,499 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1169,343,273 - 69,369,406 (-)EnsemblGRCm38mm10GRCm38
MGSCv371169,156,775 - 69,182,928 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361169,159,466 - 69,192,513 (-)NCBIMGSCv36mm8
Celera1176,297,125 - 76,352,461 (-)NCBICelera
Cytogenetic Map11B3NCBI
cM Map1142.53NCBI
Chd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554679,029,265 - 9,050,718 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554679,024,112 - 9,050,062 (-)NCBIChiLan1.0ChiLan1.0
CHD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21915,482,883 - 15,510,860 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11717,448,900 - 17,476,879 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0177,919,803 - 7,947,787 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1177,910,644 - 7,934,285 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl177,910,644 - 7,933,115 (+)Ensemblpanpan1.1panPan2
CHD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1532,747,341 - 32,768,114 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl532,747,397 - 32,766,965 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha532,880,210 - 32,905,018 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0532,846,037 - 32,870,843 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl532,846,060 - 32,870,843 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1532,813,756 - 32,838,554 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0532,769,803 - 32,794,593 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0532,948,914 - 32,973,715 (+)NCBIUU_Cfam_GSD_1.0
Chd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560247,629,303 - 47,680,427 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365951,130,078 - 1,157,822 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365951,131,198 - 1,154,615 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1253,139,366 - 53,163,243 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11253,135,767 - 53,163,244 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21255,505,273 - 55,529,558 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CHD3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1167,274,634 - 7,300,831 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl167,276,850 - 7,300,832 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605914,106,880 - 14,135,184 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Chd3
26 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:134
Count of miRNA genes:88
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000057058
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)104944455181709989Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
1578762Toxo1Toxoplasma gondii resistance QTL 1brain integrity trait (VT:0010579)percentage of study population displaying Toxoplasma gondii brain cysts at a point in time (CMO:0002028)105220003059378278Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
2306787Ean3Experimental allergic neuritis QTL 33.1nervous system integrity trait (VT:0010566)body weight loss (CMO:0001399)105379738566979128Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
1354585Eae18aExperimental allergic encephalomyelitis QTL 18a7.50.0004nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)105379738558445852Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104194452678307017Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)104944455181709989Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104944455181709989Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)104287676679813922Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat

Markers in Region
Chd3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21054,063,744 - 54,064,546 (+)MAPPERmRatBN7.2
Rnor_6.01055,943,583 - 55,944,384NCBIRnor6.0
Rnor_5.01055,685,658 - 55,686,459UniSTSRnor5.0
RGSC_v3.41056,136,115 - 56,136,916UniSTSRGSC3.4
Celera1053,220,304 - 53,221,105UniSTS
Cytogenetic Map10q24UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001419921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597794 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017603958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087613 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087623 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063269028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063269029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063269030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AY724529 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY903245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY903246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY903247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY903248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY903249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY903250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY903251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY903252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC090033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF532397 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF532398 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF532399 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF532400 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF532401 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000057058   ⟹   ENSRNOP00000053890
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1054,063,629 - 54,085,358 (-)Ensembl
Rnor_6.0 Ensembl1055,943,446 - 55,965,216 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000099449   ⟹   ENSRNOP00000091170
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1054,064,487 - 54,090,047 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000101172   ⟹   ENSRNOP00000084279
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1054,064,487 - 54,082,586 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000114886   ⟹   ENSRNOP00000090517
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1054,064,487 - 54,090,047 (-)Ensembl
RefSeq Acc Id: NM_001419921   ⟹   NP_001406850
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,810 (-)NCBI
mRatBN7.21054,063,629 - 54,090,003 (-)NCBI
RefSeq Acc Id: XM_039087613   ⟹   XP_038943541
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,842 (-)NCBI
mRatBN7.21054,063,629 - 54,090,029 (-)NCBI
RefSeq Acc Id: XM_039087614   ⟹   XP_038943542
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,842 (-)NCBI
mRatBN7.21054,063,629 - 54,090,029 (-)NCBI
RefSeq Acc Id: XM_039087615   ⟹   XP_038943543
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,842 (-)NCBI
mRatBN7.21054,063,629 - 54,090,029 (-)NCBI
RefSeq Acc Id: XM_039087616   ⟹   XP_038943544
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,841 (-)NCBI
mRatBN7.21054,063,629 - 54,090,029 (-)NCBI
RefSeq Acc Id: XM_039087617   ⟹   XP_038943545
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,842 (-)NCBI
mRatBN7.21054,063,629 - 54,090,029 (-)NCBI
RefSeq Acc Id: XM_039087618   ⟹   XP_038943546
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,842 (-)NCBI
mRatBN7.21054,063,629 - 54,090,029 (-)NCBI
RefSeq Acc Id: XM_039087619   ⟹   XP_038943547
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,841 (-)NCBI
mRatBN7.21054,063,629 - 54,090,029 (-)NCBI
RefSeq Acc Id: XM_039087620   ⟹   XP_038943548
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,841 (-)NCBI
mRatBN7.21054,063,629 - 54,090,029 (-)NCBI
RefSeq Acc Id: XM_039087623   ⟹   XP_038943551
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,840 (-)NCBI
mRatBN7.21054,063,629 - 54,090,029 (-)NCBI
RefSeq Acc Id: XM_039087626   ⟹   XP_038943554
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,841 (-)NCBI
mRatBN7.21054,063,629 - 54,090,029 (-)NCBI
RefSeq Acc Id: XM_063269028   ⟹   XP_063125098
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,840 (-)NCBI
RefSeq Acc Id: XM_063269029   ⟹   XP_063125099
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,841 (-)NCBI
RefSeq Acc Id: XM_063269030   ⟹   XP_063125100
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,562,437 - 54,588,108 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001406850 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943541 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943542 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943543 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943544 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943545 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943546 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943547 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943548 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943551 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943554 (Get FASTA)   NCBI Sequence Viewer  
  XP_063125098 (Get FASTA)   NCBI Sequence Viewer  
  XP_063125099 (Get FASTA)   NCBI Sequence Viewer  
  XP_063125100 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAX85375 (Get FASTA)   NCBI Sequence Viewer  
  AAX85376 (Get FASTA)   NCBI Sequence Viewer  
  AAX85377 (Get FASTA)   NCBI Sequence Viewer  
  AAX85378 (Get FASTA)   NCBI Sequence Viewer  
  AAX85379 (Get FASTA)   NCBI Sequence Viewer  
  AAX85380 (Get FASTA)   NCBI Sequence Viewer  
  AAX85381 (Get FASTA)   NCBI Sequence Viewer  
  AAX85382 (Get FASTA)   NCBI Sequence Viewer  
  ABU49324 (Get FASTA)   NCBI Sequence Viewer  
  ABU49325 (Get FASTA)   NCBI Sequence Viewer  
  ABU49326 (Get FASTA)   NCBI Sequence Viewer  
  ABU49327 (Get FASTA)   NCBI Sequence Viewer  
  ABU49328 (Get FASTA)   NCBI Sequence Viewer  
  EDM04858 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000053890.5
  ENSRNOP00000084279.1
  ENSRNOP00000090517.1
  ENSRNOP00000091170.1
Ensembl Acc Id: ENSRNOP00000053890   ⟸   ENSRNOT00000057058
RefSeq Acc Id: XP_038943554   ⟸   XM_039087626
- Peptide Label: isoform X13
- UniProtKB: Q2KMK7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038943543   ⟸   XM_039087615
- Peptide Label: isoform X3
- UniProtKB: A0A8I6GIY0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038943545   ⟸   XM_039087617
- Peptide Label: isoform X5
- UniProtKB: A0A8I6GIY0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038943551   ⟸   XM_039087623
- Peptide Label: isoform X11
- UniProtKB: A0A8I6AF31 (UniProtKB/TrEMBL),   Q2KMK9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038943544   ⟸   XM_039087616
- Peptide Label: isoform X4
- UniProtKB: A0A8I6GIY0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038943546   ⟸   XM_039087618
- Peptide Label: isoform X6
- UniProtKB: A0A8I6GIY0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038943548   ⟸   XM_039087620
- Peptide Label: isoform X8
- UniProtKB: Q2KMK7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038943542   ⟸   XM_039087614
- Peptide Label: isoform X2
- UniProtKB: A0A8I6GIY0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038943547   ⟸   XM_039087619
- Peptide Label: isoform X7
- UniProtKB: Q2KMK7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038943541   ⟸   XM_039087613
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GIY0 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000091170   ⟸   ENSRNOT00000099449
Ensembl Acc Id: ENSRNOP00000090517   ⟸   ENSRNOT00000114886
Ensembl Acc Id: ENSRNOP00000084279   ⟸   ENSRNOT00000101172
RefSeq Acc Id: NP_001406850   ⟸   NM_001419921
- UniProtKB: Q2KMK7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063125099   ⟸   XM_063269029
- Peptide Label: isoform X10
- UniProtKB: Q2KMK9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063125098   ⟸   XM_063269028
- Peptide Label: isoform X9
- UniProtKB: Q2KMK7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063125100   ⟸   XM_063269030
- Peptide Label: isoform X12
- UniProtKB: F1LPP8 (UniProtKB/TrEMBL)
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LPP8-F1-model_v2 AlphaFold F1LPP8 1-1835 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311923 AgrOrtholog
BioCyc Gene G2FUF-24560 BioCyc
Ensembl Genes ENSRNOG00000009722 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000057058.5 UniProtKB/TrEMBL
  ENSRNOT00000099449.1 UniProtKB/TrEMBL
  ENSRNOT00000101172.1 UniProtKB/TrEMBL
  ENSRNOT00000114886.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
  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
  HMG_box_dom_sf 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 303241 ENTREZGENE
PANTHER CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 3 UniProtKB/TrEMBL
  CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 3-RELATED-RELATED 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 Chd3 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 ENSRNOG00000009722 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
  SSF47095 UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt A0A8I5ZZ60_RAT UniProtKB/TrEMBL
  A0A8I6AF31 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GIY0 ENTREZGENE, UniProtKB/TrEMBL
  A6HFQ3_RAT UniProtKB/TrEMBL
  B2BL43_RAT UniProtKB/TrEMBL
  F1LPP8 ENTREZGENE, UniProtKB/TrEMBL
  Q2KMK7 ENTREZGENE, UniProtKB/TrEMBL
  Q2KMK9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Chd3  chromodomain helicase DNA binding protein 3  Chd3_predicted  chromodomain helicase DNA binding protein 3 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Chd3_predicted  chromodomain helicase DNA binding protein 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED