Chd2 (chromodomain helicase DNA binding protein 2) - Rat Genome Database
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Gene: Chd2 (chromodomain helicase DNA binding protein 2) Rattus norvegicus
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Symbol: Chd2
Name: chromodomain helicase DNA binding protein 2
RGD ID: 1310056
Description: Predicted to have RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and histone binding activity. Predicted to be involved in cellular response to DNA damage stimulus; hematopoietic stem cell differentiation; and muscle organ development. Predicted to localize to nucleolus and nucleoplasm. Human ortholog(s) of this gene implicated in childhood onset epileptic encephalopathy. Orthologous to human CHD2 (chromodomain helicase DNA binding protein 2); INTERACTS WITH 4-amino-2,6-dinitrotoluene; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: chromodomain-helicase-DNA-binding protein 2; LOC308738
Orthologs:
Homo sapiens (human) : CHD2 (chromodomain helicase DNA binding protein 2)  HGNC  Alliance
Mus musculus (house mouse) : Chd2 (chromodomain helicase DNA binding protein 2)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Chd2 (chromodomain helicase DNA binding protein 2)
Pan paniscus (bonobo/pygmy chimpanzee) : CHD2 (chromodomain helicase DNA binding protein 2)
Canis lupus familiaris (dog) : CHD2 (chromodomain helicase DNA binding protein 2)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Chd2 (chromodomain helicase DNA binding protein 2)
Sus scrofa (pig) : CHD2 (chromodomain helicase DNA binding protein 2)
Chlorocebus sabaeus (African green monkey) : CHD2 (chromodomain helicase DNA binding protein 2)
Heterocephalus glaber (naked mole-rat) : Chd2 (chromodomain helicase DNA binding protein 2)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01134,757,934 - 134,873,053 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1134,757,934 - 134,871,167 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01135,782,462 - 135,897,354 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41128,609,727 - 128,720,325 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11128,688,083 - 128,798,804 (-)NCBI
Celera1119,322,047 - 119,431,932 (-)NCBICelera
Cytogenetic Map1q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
acetylsalicylic acid  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bortezomib  (ISO)
cadmium dichloride  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
chrysene  (ISO)
clobetasol  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibenzo[a,l]pyrene  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
Enterolactone  (ISO)
erythromycin estolate  (EXP)
fluoranthene  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
glucose  (ISO)
hydralazine  (ISO)
indometacin  (ISO)
leflunomide  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylphenidate  (ISO)
nicotine  (ISO)
paracetamol  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
quercitrin  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP)
tetraphene  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:19137022   PMID:22569126   PMID:22658674   PMID:22681889   PMID:23376485  


Genomics

Comparative Map Data
Chd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01134,757,934 - 134,873,053 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1134,757,934 - 134,871,167 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01135,782,462 - 135,897,354 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41128,609,727 - 128,720,325 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11128,688,083 - 128,798,804 (-)NCBI
Celera1119,322,047 - 119,431,932 (-)NCBICelera
Cytogenetic Map1q31NCBI
CHD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1592,900,189 - 93,027,996 (+)EnsemblGRCh38hg38GRCh38
GRCh381592,900,324 - 93,027,996 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371593,442,286 - 93,571,237 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361591,244,555 - 91,372,241 (+)NCBINCBI36hg18NCBI36
Build 341591,244,422 - 91,366,396NCBI
Celera1569,855,404 - 69,982,772 (+)NCBI
Cytogenetic Map15q26.1NCBI
HuRef1569,580,061 - 69,707,674 (+)NCBIHuRef
CHM1_11593,284,562 - 93,411,895 (+)NCBICHM1_1
Chd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39773,076,400 - 73,191,494 (-)NCBI
GRCm38773,426,652 - 73,541,746 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl773,426,638 - 73,541,830 (-)EnsemblGRCm38mm10GRCm38
MGSCv37780,571,538 - 80,686,632 (-)NCBIGRCm37mm9NCBIm37
MGSCv36773,303,121 - 73,415,343 (-)NCBImm8
Celera770,874,423 - 70,989,778 (-)NCBICelera
Cytogenetic Map7D1NCBI
Chd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495541621,085,570 - 21,210,321 (+)NCBIChiLan1.0ChiLan1.0
CHD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11590,780,220 - 90,906,863 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1590,781,169 - 90,903,569 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01571,568,560 - 71,713,330 (+)NCBIMhudiblu_PPA_v0panPan3
CHD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl347,105,046 - 47,221,385 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1347,101,789 - 47,221,473 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Chd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364839,803,887 - 9,931,132 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1785,980,759 - 86,107,886 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2791,874,318 - 92,002,341 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CHD2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2911,450,799 - 11,579,594 (+)Ensembl
ChlSab1.12911,436,170 - 11,579,468 (+)NCBI
Chd2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476810,786,139 - 10,922,558 (-)NCBI

Position Markers
RH143573  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01134,872,486 - 134,872,631NCBIRnor6.0
Rnor_5.01135,896,784 - 135,896,929UniSTSRnor5.0
RGSC_v3.41128,721,643 - 128,721,788UniSTSRGSC3.4
Celera1119,433,250 - 119,433,395UniSTS
Cytogenetic Map1q31UniSTS
RH 3.4 Map1994.1UniSTS
AW535385  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01134,775,197 - 134,775,390NCBIRnor6.0
Rnor_5.01135,799,725 - 135,799,918UniSTSRnor5.0
RGSC_v3.41128,624,096 - 128,624,289UniSTSRGSC3.4
Celera1119,336,416 - 119,336,609UniSTS
Cytogenetic Map1q31UniSTS
RH 3.4 Map1984.0UniSTS
RH141602  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01134,869,319 - 134,869,509NCBIRnor6.0
Rnor_5.01135,893,617 - 135,893,807UniSTSRnor5.0
RGSC_v3.41128,718,476 - 128,718,666UniSTSRGSC3.4
Celera1119,430,083 - 119,430,273UniSTS
Cytogenetic Map1q31UniSTS
RH 3.4 Map1974.5UniSTS
MARC_17499-17500:1016469992:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01134,813,025 - 134,813,614NCBIRnor6.0
Rnor_5.01135,837,553 - 135,838,142UniSTSRnor5.0
RGSC_v3.41128,661,098 - 128,661,687UniSTSRGSC3.4
Celera1119,373,414 - 119,374,003UniSTS
Cytogenetic Map1q31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)190804143161321256Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)191093646136093646Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)194201400184846632Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)194201400197187904Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194364073153076991Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)195304961156446783Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)199983293188289386Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)199983293198656062Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)199983293216213510Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)199983293216325819Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100131562236763528Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100354344145354344Rat
8655649Arrd1Age-related retinal degeneration QTL 14.89retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1106002252202571904Rat
61370Mcs3Mammary carcinoma susceptibility QTL 32.15mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1108057233167517487Rat
1641897Alcrsp1Alcohol response QTL 1response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1108417193153417193Rat
2317833Alcrsp19Alcohol response QTL 1912.40.001response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1108417193153417193Rat
1354623Rf46Renal function QTL 463.8blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)1108986301161784422Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1108986301219232156Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1108986301219232156Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1108986301238830534Rat
2303591Gluco41Glucose level QTL 412blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1109634374154634374Rat
9590300Scort16Serum corticosterone level QTL 164.390.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1110620749155620749Rat
8694370Bw154Body weight QTL 1548.910.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)1110620749155620749Rat
61399Tcat1Tongue tumor resistance QTL 13.3tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 5 mm (CMO:0001879)1111446783156446783Rat
61346Rf2Renal disease susceptibility QTL 23.7urine protein amount (VT:0005160)urine protein level (CMO:0000591)1111446783156446783Rat
631496Bp97Blood pressure QTL 973.08arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1113593576158593576Rat
1300158Bp173Blood pressure QTL 1733.48arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1122614824201146953Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1122614824262664716Rat
2313060Bss71Bone structure and strength QTL 712.60.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)1124090312169090312Rat
631199Cm23Cardiac mass QTL 234.60.0004heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1124603592188289386Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1125875758262433692Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1126240667217054291Rat
2293140Bp313Blood pressure QTL 313arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1129208943174208943Rat
2325726Eae30Experimental allergic encephalomyelitis QTL 30nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1130458716135612014Rat
631544Bp84Blood pressure QTL 845.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130779148198585664Rat
1358189Cstrr1Cold stress response QTL 10.0001catecholamine amount (VT:0010543)urine norepinephrine level (CMO:0001629)1130779148199254774Rat
1578770Stresp23Stress response QTL 23kidney sympathetic nerve activity (VT:0004050)stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)1130779148199254774Rat
1641895Bp298Blood pressure QTL 298arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1130779148199254774Rat
631549Bp89Blood pressure QTL 895.7arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130779320219238476Rat
631570Bp94Blood pressure QTL 940.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130917121152871103Rat
1598850Bp297Blood pressure QTL 2972.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1131334152176334152Rat
1598866Bp287Blood pressure QTL 2875.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1131334152176334152Rat
631654Bp107Blood pressure QTL 107arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1133076978178076978Rat
9685799Bp375Blood pressure QTL 375arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1133076978178076978Rat
634348Bp138Blood pressure QTL 138arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1133076978184188922Rat
61442Strs1Sensitivity to stroke QTL 17.4cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)1133946489178946489Rat
9685802Bp376Blood pressure QTL 376arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1134089429179089429Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:56
Count of miRNA genes:51
Interacting mature miRNAs:55
Transcripts:ENSRNOT00000055829
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.


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 42 53 37 19 37 8 10 74 35 36 11 8
Low 1 4 4 4 1 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000055829   ⟹   ENSRNOP00000052684
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1134,760,842 - 134,870,255 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076300   ⟹   ENSRNOP00000068303
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1134,757,934 - 134,871,167 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090149   ⟹   ENSRNOP00000075309
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1134,760,084 - 134,867,001 (-)Ensembl
RefSeq Acc Id: NM_001107523   ⟹   NP_001100993
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01134,760,828 - 134,871,168 (-)NCBI
Rnor_5.01135,782,462 - 135,897,354 (-)NCBI
RGSC_v3.41128,609,727 - 128,720,325 (-)RGD
Celera1119,322,047 - 119,431,932 (-)RGD
Sequence:
RefSeq Acc Id: XM_006229369   ⟹   XP_006229431
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01134,757,934 - 134,870,382 (-)NCBI
Rnor_5.01135,782,462 - 135,897,354 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229370   ⟹   XP_006229432
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01134,757,934 - 134,873,053 (-)NCBI
Rnor_5.01135,782,462 - 135,897,354 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229371   ⟹   XP_006229433
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01134,757,934 - 134,873,053 (-)NCBI
Rnor_5.01135,782,462 - 135,897,354 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229372   ⟹   XP_006229434
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01134,757,934 - 134,870,382 (-)NCBI
Rnor_5.01135,782,462 - 135,897,354 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008759519   ⟹   XP_008757741
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01134,760,597 - 134,870,382 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008759520   ⟹   XP_008757742
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01134,827,923 - 134,870,382 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001100993   ⟸   NM_001107523
- UniProtKB: D4AD08 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229433   ⟸   XM_006229371
- Peptide Label: isoform X2
- UniProtKB: A0A096MJY0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229432   ⟸   XM_006229370
- Peptide Label: isoform X2
- UniProtKB: A0A096MJY0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229434   ⟸   XM_006229372
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006229431   ⟸   XM_006229369
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KA92 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008757741   ⟸   XM_008759519
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008757742   ⟸   XM_008759520
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000052684   ⟸   ENSRNOT00000055829
RefSeq Acc Id: ENSRNOP00000075309   ⟸   ENSRNOT00000090149
RefSeq Acc Id: ENSRNOP00000068303   ⟸   ENSRNOT00000076300
Transcriptome

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

Promoters
RGD ID:13690116
Promoter ID:EPDNEW_R639
Type:multiple initiation site
Name:Chd2_2
Description:chromodomain helicase DNA binding protein 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R640  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01134,867,098 - 134,867,158EPDNEW
RGD ID:13690117
Promoter ID:EPDNEW_R640
Type:multiple initiation site
Name:Chd2_1
Description:chromodomain helicase DNA binding protein 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R639  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01134,871,167 - 134,871,227EPDNEW

Strain Variation

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


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 135826313 135826314 G T snv KFRS3B/Kyo (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310056 AgrOrtholog
Ensembl Genes ENSRNOG00000012716 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000052684 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068303 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075309 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055829 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000076300 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000090149 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.10810 UniProtKB/TrEMBL
InterPro CDH1_2_SANT_HL1 UniProtKB/TrEMBL
  Chromo_domain UniProtKB/TrEMBL
  Chromo_domain/shadow UniProtKB/TrEMBL
  Chromodomain-like UniProtKB/TrEMBL
  Chromodomain_CS UniProtKB/TrEMBL
  DUF4208 UniProtKB/TrEMBL
  Helicase_ATP-bd UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  SNF2-like_sf UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
KEGG Report rno:308738 UniProtKB/TrEMBL
NCBI Gene 308738 ENTREZGENE
Pfam CDH1_2_SANT_HL1 UniProtKB/TrEMBL
  Chromo UniProtKB/TrEMBL
  DUF4208 UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
PhenoGen Chd2 PhenoGen
PROSITE CHROMO_1 UniProtKB/TrEMBL
  CHROMO_2 UniProtKB/TrEMBL
  HELICASE_ATP_BIND_1 UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/TrEMBL
SMART CHROMO UniProtKB/TrEMBL
  DEXDc UniProtKB/TrEMBL
  DUF4208 UniProtKB/TrEMBL
  HELICc UniProtKB/TrEMBL
Superfamily-SCOP Chromodomain-like UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniGene Rn.225034 ENTREZGENE
UniProt A0A096MJY0 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2KA92 ENTREZGENE, UniProtKB/TrEMBL
  D4AD08 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Chd2  chromodomain helicase DNA binding protein 2   Chd2_predicted  chromodomain helicase DNA binding protein 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Chd2_predicted  chromodomain helicase DNA binding protein 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED