Mbd4 (methyl-CpG binding domain 4 DNA glycosylase) - Rat Genome Database

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Gene: Mbd4 (methyl-CpG binding domain 4 DNA glycosylase) Rattus norvegicus
Analyze
Symbol: Mbd4
Name: methyl-CpG binding domain 4 DNA glycosylase
RGD ID: 1585874
Description: Predicted to enable DNA binding activity and pyrimidine-specific mismatch base pair DNA N-glycosylase activity. Involved in response to estradiol. Predicted to be located in cytoplasm and nuclear speck. Predicted to be part of chromatin. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in colorectal carcinoma; esophagus squamous cell carcinoma; lung cancer; rheumatoid arthritis; and uveal melanoma. Orthologous to human MBD4 (methyl-CpG binding domain 4, DNA glycosylase); PARTICIPATES IN altered DNA modification pathway; DNA modification pathway; base excision repair pathway; INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC680915; methyl-CpG binding domain protein 4; methyl-CpG-binding domain protein 4; similar to Methyl-CpG-binding domain protein 4 (Methyl-CpG-binding protein MBD4) (Mismatch-specific DNA N-glycosylase)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
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
GRCr84150,565,646 - 150,577,433 (-)NCBIGRCr8
mRatBN7.24148,893,049 - 148,904,833 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4148,894,280 - 148,904,982 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.04147,744,673 - 147,756,462 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4147,746,186 - 147,756,294 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04211,028,384 - 211,040,158 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44151,972,272 - 151,981,633 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4137,783,059 - 137,794,850 (-)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-hydroxypropanoic acid  (ISO)
3,N(4)-ethenocytosine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
5-iodo-2'-deoxyuridine  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP)
bortezomib  (ISO)
caffeine  (ISO)
carbon nanotube  (ISO)
cisplatin  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
crocidolite asbestos  (ISO)
cypermethrin  (ISO)
decabromodiphenyl ether  (EXP)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
folic acid  (ISO)
FR900359  (ISO)
gentamycin  (EXP)
glyphosate  (ISO)
hydrogen peroxide  (ISO)
leflunomide  (ISO)
mercury dichloride  (ISO)
methimazole  (EXP)
methylmercury chloride  (ISO)
monosodium L-glutamate  (ISO)
morphine  (ISO)
paracetamol  (ISO)
pirinixic acid  (ISO)
quercetin  (EXP,ISO)
rac-lactic acid  (ISO)
resveratrol  (EXP)
SB 431542  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
sulfadimethoxine  (EXP)
temozolomide  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
topotecan  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (ISO)
cytoplasm  (ISO)
nuclear speck  (IEA,ISO)
nucleus  (IBA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Inter-individual variation in nucleotide excision repair pathway is modulated by non-synonymous polymorphisms in ERCC4 and MBD4 genes. Allione A, etal., Mutat Res. 2013 Nov-Dec;751-752:49-54. doi: 10.1016/j.mrfmmm.2013.08.005. Epub 2013 Sep 1.
2. Somatic frameshift mutations in the MBD4 gene of sporadic colon cancers with mismatch repair deficiency. Bader S, etal., Oncogene. 1999 Dec 23;18(56):8044-7.
3. On how mammalian transcription factors recognize methylated DNA. Buck-Koehntop BA and Defossez PA, Epigenetics. 2013 Feb;8(2):131-7. doi: 10.4161/epi.23632. Epub 2013 Jan 16.
4. Peptidylarginine deiminase type 4 and methyl-CpG binding domain 4 polymorphisms in Chinese patients with rheumatoid arthritis. Cheng J, etal., J Rheumatol. 2012 Jun;39(6):1159-65. doi: 10.3899/jrheum.120007. Epub 2012 Apr 15.
5. 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.
6. Identification of genetic variants in base excision repair pathway and their associations with risk of esophageal squamous cell carcinoma. Hao B, etal., Cancer Res. 2004 Jun 15;64(12):4378-84.
7. MBD4 gene is associated with rheumatoid arthritis in Chinese patients in Taiwan. Huang CM, etal., Rheumatol Int. 2012 Jan;32(1):117-22. doi: 10.1007/s00296-010-1545-8. Epub 2010 Jul 30.
8. Tagging single nucleotide polymorphisms in MBD4 are associated with risk of lung cancer in a Chinese population. Miao R, etal., Lung Cancer. 2008 Dec;62(3):281-6. doi: 10.1016/j.lungcan.2008.03.027. Epub 2008 May 20.
9. Enhanced CpG mutability and tumorigenesis in MBD4-deficient mice. Millar CB, etal., Science. 2002 Jul 19;297(5580):403-5.
10. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Comprehensive gene review and curation RGD comprehensive gene curation
13. The Glu346Lys polymorphism and frameshift mutations of the Methyl-CpG Binding Domain 4 gene in gastrointestinal cancer. Song JH, etal., Neoplasma. 2009;56(4):343-7.
14. Neonatal exposure to estradiol/bisphenol A alters promoter methylation and expression of Nsbp1 and Hpcal1 genes and transcriptional programs of Dnmt3a/b and Mbd2/4 in the rat prostate gland throughout life. Tang WY, etal., Endocrinology. 2012 Jan;153(1):42-55. doi: 10.1210/en.2011-1308. Epub 2011 Nov 22.
15. Validation of biomarkers associated with 5-fluorouracil and thymidylate synthase in colorectal cancer. Xi Y, etal., Oncol Rep. 2008 Jan;19(1):257-62.
16. Methyl-CpG binding domain 4 tagging polymorphisms and esophageal cancer risk in a Chinese population. Yin J, etal., Eur J Cancer Prev. 2014 Aug 26.
Additional References at PubMed
PMID:9774669   PMID:12477932   PMID:14562041   PMID:14614141   PMID:17546630  


Genomics

Comparative Map Data
Mbd4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84150,565,646 - 150,577,433 (-)NCBIGRCr8
mRatBN7.24148,893,049 - 148,904,833 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4148,894,280 - 148,904,982 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.04147,744,673 - 147,756,462 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4147,746,186 - 147,756,294 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04211,028,384 - 211,040,158 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44151,972,272 - 151,981,633 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4137,783,059 - 137,794,850 (-)NCBICelera
Cytogenetic Map4q42NCBI
MBD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383129,430,947 - 129,439,948 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3129,430,947 - 129,440,179 (-)EnsemblGRCh38hg38GRCh38
GRCh373129,149,790 - 129,158,791 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363130,632,483 - 130,641,542 (-)NCBINCBI36Build 36hg18NCBI36
Build 343130,632,490 - 130,641,550NCBI
Celera3127,576,629 - 127,585,688 (-)NCBICelera
Cytogenetic Map3q21.3NCBI
HuRef3126,533,265 - 126,542,500 (-)NCBIHuRef
CHM1_13129,112,922 - 129,122,157 (-)NCBICHM1_1
T2T-CHM13v2.03132,175,773 - 132,184,774 (-)NCBIT2T-CHM13v2.0
Mbd4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396115,817,658 - 115,830,361 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6115,817,658 - 115,830,332 (-)EnsemblGRCm39 Ensembl
GRCm386115,840,697 - 115,853,400 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6115,840,697 - 115,853,371 (-)EnsemblGRCm38mm10GRCm38
MGSCv376115,790,715 - 115,803,359 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366115,808,047 - 115,819,340 (-)NCBIMGSCv36mm8
Celera6117,677,344 - 117,690,709 (-)NCBICelera
Cytogenetic Map6E3NCBI
cM Map653.72NCBI
Mbd4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542917,858,937 - 17,869,262 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542917,858,656 - 17,868,111 (+)NCBIChiLan1.0ChiLan1.0
MBD4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22127,363,949 - 127,372,866 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13127,368,337 - 127,377,271 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03126,489,125 - 126,498,034 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13133,842,156 - 133,851,450 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3133,839,643 - 133,851,450 (-)Ensemblpanpan1.1panPan2
MBD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1205,716,162 - 5,725,068 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl205,716,239 - 5,724,881 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha205,753,617 - 5,762,527 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0205,745,974 - 5,754,885 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl205,745,978 - 5,754,919 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1205,461,788 - 5,470,699 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0205,814,748 - 5,823,669 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0205,790,467 - 5,799,355 (+)NCBIUU_Cfam_GSD_1.0
MBD4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1368,816,679 - 68,828,580 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11368,816,677 - 68,828,559 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
MBD4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12251,616,840 - 51,626,232 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2251,616,803 - 51,626,224 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041114,838,792 - 114,848,231 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Mbd4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624872451,118 - 462,509 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624872453,303 - 462,661 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Mbd4
48 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:253
Count of miRNA genes:167
Interacting mature miRNAs:183
Transcripts:ENSRNOT00000014537, ENSRNOT00000071994
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)482798864152731274Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)485253748150276390Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
2302049Pia32Pristane induced arthritis QTL 325.10.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)4105789505150789505Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106649412151649412Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4106805662151805662Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109827074154827074Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109827074154827074Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
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
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4116179486151161268Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
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
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
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
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
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
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
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
61446Coreg2Compensatory renal growth QTL 23.5kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)4148423102157580971Rat

Markers in Region
Mbd4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24148,897,195 - 148,897,395 (+)MAPPERmRatBN7.2
Rnor_6.04147,748,820 - 147,749,019NCBIRnor6.0
Rnor_5.04211,032,531 - 211,032,730UniSTSRnor5.0
RGSC_v3.44151,975,099 - 151,975,298UniSTSRGSC3.4
Celera4137,787,204 - 137,787,403UniSTS
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 2 4 11 4 17 4 28 18 38 2
Low 1 39 46 37 2 37 8 11 46 17 3 9 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000014537   ⟹   ENSRNOP00000014537
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4148,894,280 - 148,904,982 (-)Ensembl
Rnor_6.0 Ensembl4147,746,186 - 147,756,294 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103876   ⟹   ENSRNOP00000092006
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4148,894,280 - 148,904,904 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106971   ⟹   ENSRNOP00000082100
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4148,894,584 - 148,904,746 (-)Ensembl
RefSeq Acc Id: NM_001427248   ⟹   NP_001414177
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84150,565,646 - 150,577,426 (-)NCBI
RefSeq Acc Id: XM_063286678   ⟹   XP_063142748
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84150,565,646 - 150,572,848 (-)NCBI
RefSeq Acc Id: XM_063286679   ⟹   XP_063142749
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84150,565,646 - 150,572,559 (-)NCBI
RefSeq Acc Id: XR_010065702
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84150,569,764 - 150,577,433 (-)NCBI
RefSeq Acc Id: XR_010065703
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84150,569,764 - 150,577,433 (-)NCBI
RefSeq Acc Id: XR_010065704
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84150,569,764 - 150,577,433 (-)NCBI
RefSeq Acc Id: XR_010065705
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84150,569,764 - 150,577,433 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001414177 (Get FASTA)   NCBI Sequence Viewer  
  XP_063142748 (Get FASTA)   NCBI Sequence Viewer  
  XP_063142749 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000014537.7
  ENSRNOP00000082100.1
  ENSRNOP00000092006.1
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000014537   ⟸   ENSRNOT00000014537
RefSeq Acc Id: ENSRNOP00000092006   ⟸   ENSRNOT00000103876
RefSeq Acc Id: ENSRNOP00000082100   ⟸   ENSRNOT00000106971
RefSeq Acc Id: NP_001414177   ⟸   NM_001427248
- UniProtKB: A6IL01 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063142748   ⟸   XM_063286678
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063142749   ⟸   XM_063286679
- Peptide Label: isoform X2
Protein Domains
MBD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A9W8-F1-model_v2 AlphaFold D4A9W8 1-566 view protein structure

Transcriptome

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

Promoters
RGD ID:13693328
Promoter ID:EPDNEW_R3852
Type:multiple initiation site
Name:Mbd4_1
Description:methyl-CpG binding domain 4 DNA glycosylase
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_6.04147,756,350 - 147,756,410EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1585874 AgrOrtholog
BioCyc Gene G2FUF-43309 BioCyc
Ensembl Genes ENSRNOG00000010919 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014537.8 UniProtKB/TrEMBL
  ENSRNOT00000103876.1 UniProtKB/TrEMBL
  ENSRNOT00000106971.1 UniProtKB/TrEMBL
InterPro DNA-bd_integrase-typ UniProtKB/TrEMBL
  DNA_glycosylase UniProtKB/TrEMBL
  Me_CpG-bd_MBD4 UniProtKB/TrEMBL
  MeCP2/MBD4 UniProtKB/TrEMBL
  Methyl_CpG_DNA-bd UniProtKB/TrEMBL
NCBI Gene 680915 ENTREZGENE
PANTHER METHYL-CPG-BINDING DOMAIN PROTEIN 4 UniProtKB/TrEMBL
  PTHR15074 UniProtKB/TrEMBL
Pfam MBD UniProtKB/TrEMBL
PharmGKB MBD4 RGD
PhenoGen Mbd4 PhenoGen
PIRSF Methyl_CpG_bd_MBD4 UniProtKB/TrEMBL
PROSITE MBD UniProtKB/TrEMBL
RatGTEx ENSRNOG00000010919 RatGTEx
SMART MBD UniProtKB/TrEMBL
Superfamily-SCOP DNA-binding_integrase-type UniProtKB/TrEMBL
  DNA_glycsylse UniProtKB/TrEMBL
UniProt A0A8I5ZTJ7_RAT UniProtKB/TrEMBL
  A0A8I6AH85_RAT UniProtKB/TrEMBL
  A6IL01 ENTREZGENE, UniProtKB/TrEMBL
  D4A9W8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-01 Mbd4  methyl-CpG binding domain 4 DNA glycosylase  Mbd4  methyl-CpG binding domain protein 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Mbd4  methyl-CpG binding domain protein 4  LOC680915  similar to Methyl-CpG-binding domain protein 4 (Methyl-CpG-binding protein MBD4) (Mismatch-specific DNA N-glycosylase)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC680915  similar to Methyl-CpG-binding domain protein 4 (Methyl-CpG-binding protein MBD4) (Mismatch-specific DNA N-glycosylase)  LOC679015  similar to Methyl-CpG-binding domain protein 4 (Methyl-CpG-binding protein MBD4) (Mismatch-specific DNA N-glycosylase)  Data merged from RGD:1593109 1643240 APPROVED
2006-11-20 LOC679015  similar to Methyl-CpG-binding domain protein 4 (Methyl-CpG-binding protein MBD4) (Mismatch-specific DNA N-glycosylase)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC680915  similar to Methyl-CpG-binding domain protein 4 (Methyl-CpG-binding protein MBD4) (Mismatch-specific DNA N-glycosylase)      Symbol and Name status set to provisional 70820 PROVISIONAL