Mbd3 (methyl-CpG binding domain protein 3) - Chinchilla Research Resource Database
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Gene: Mbd3 (methyl-CpG binding domain protein 3) Rattus norvegicus
Analyze
Symbol: Mbd3
Name: methyl-CpG binding domain protein 3
CRRD ID: 1307389
Description: Predicted to have chromatin binding activity and methyl-CpG binding activity. Involved in several processes, including animal organ development; regulation of DNA methylation; and response to estradiol. Predicted to localize to NuRD complex; cytoplasm; and heterochromatin. Biomarker of transient cerebral ischemia and visual epilepsy. Orthologous to human MBD3 (methyl-CpG binding domain protein 3); PARTICIPATES IN CHD family mediated chromatin remodeling pathway; INTERACTS WITH 2,6-dinitrotoluene; 4-amino-2,6-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC362834; methyl-CpG-binding domain protein 3
Orthologs:
Homo sapiens (human) : MBD3 (methyl-CpG binding domain protein 3)  HGNC  Alliance
Mus musculus (house mouse) : Mbd3 (methyl-CpG binding domain protein 3)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Mbd3 (methyl-CpG binding domain protein 3)
Pan paniscus (bonobo/pygmy chimpanzee) : MBD3 (methyl-CpG binding domain protein 3)
Canis lupus familiaris (dog) : MBD3 (methyl-CpG binding domain protein 3)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Mbd3 (methyl-CpG binding domain protein 3)
Sus scrofa (pig) : MBD3 (methyl-CpG binding domain protein 3)
Chlorocebus sabaeus (African green monkey) : MBD3 (methyl-CpG binding domain protein 3)
Heterocephalus glaber (naked mole-rat) : Mbd3 (methyl-CpG binding domain protein 3)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0712,179,046 - 12,186,251 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,179,203 - 12,186,656 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0712,349,101 - 12,356,306 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,824,260 - 10,831,460 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1710,824,538 - 10,830,878 (+)NCBI
Celera77,491,653 - 7,498,865 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View


Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9774669   PMID:12477932   PMID:14643676   PMID:16217013   PMID:16322236   PMID:16462733   PMID:17287250   PMID:17546630   PMID:19796622   PMID:20720167   PMID:22770845   PMID:24307175  
PMID:24991957   PMID:27650712  


Genomics

Comparative Map Data
Mbd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0712,179,046 - 12,186,251 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,179,203 - 12,186,656 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0712,349,101 - 12,356,306 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,824,260 - 10,831,460 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1710,824,538 - 10,830,878 (+)NCBI
Celera77,491,653 - 7,498,865 (+)NCBICelera
Cytogenetic Map7q11NCBI
MBD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl191,573,596 - 1,592,865 (-)EnsemblGRCh38hg38GRCh38
GRCh38191,573,596 - 1,592,865 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37191,576,670 - 1,592,760 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36191,527,678 - 1,543,652 (-)NCBINCBI36hg18NCBI36
Build 34191,527,677 - 1,543,652NCBI
Celera191,511,530 - 1,527,508 (-)NCBI
Cytogenetic Map19p13.3NCBI
HuRef191,350,749 - 1,366,844 (-)NCBIHuRef
CHM1_1191,576,471 - 1,592,573 (-)NCBICHM1_1
Mbd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391080,228,373 - 80,235,365 (-)NCBI
GRCm381080,392,539 - 80,399,531 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1080,392,539 - 80,399,550 (-)EnsemblGRCm38mm10GRCm38
MGSCv371079,855,286 - 79,862,224 (-)NCBIGRCm37mm9NCBIm37
MGSCv361079,795,670 - 79,802,608 (-)NCBImm8
Celera1081,409,909 - 81,416,847 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Mbd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554956,336,367 - 6,389,056 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554956,385,449 - 6,388,911 (+)NCBIChiLan1.0ChiLan1.0
MBD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1191,549,184 - 1,565,601 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl191,549,184 - 1,559,254 (-)Ensemblpanpan1.1panPan2
MBD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2057,296,713 - 57,307,110 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12057,296,713 - 57,312,988 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Mbd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936588865,046 - 873,821 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MBD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl276,906,644 - 76,923,435 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1276,913,880 - 76,923,435 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2278,156,278 - 78,165,819 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MBD3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl61,357,204 - 1,371,777 (-)Ensembl
ChlSab1.161,357,388 - 1,371,835 (-)NCBI
Mbd3
(Heterocephalus glaber - naked mole-rat)
No map positions available.

Position Markers
RH126839  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0712,186,015 - 12,186,234NCBIRnor6.0
Rnor_6.0223,926,119 - 23,926,338NCBIRnor6.0
Rnor_5.0712,356,070 - 12,356,289UniSTSRnor5.0
Rnor_5.0243,097,162 - 43,097,381UniSTSRnor5.0
RGSC_v3.4710,831,227 - 10,831,446UniSTSRGSC3.4
RGSC_v3.4224,571,860 - 24,572,079UniSTSRGSC3.4
Celera77,498,632 - 7,498,851UniSTS
Celera221,573,686 - 21,573,905UniSTS
Cytogenetic Map7q11UniSTS
Cytogenetic Map2q12UniSTS
RH133854  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0712,186,008 - 12,186,222NCBIRnor6.0
Rnor_6.0223,926,112 - 23,926,326NCBIRnor6.0
Rnor_5.0712,356,063 - 12,356,277UniSTSRnor5.0
Rnor_5.0243,097,155 - 43,097,369UniSTSRnor5.0
RGSC_v3.4710,831,220 - 10,831,434UniSTSRGSC3.4
RGSC_v3.4224,571,853 - 24,572,067UniSTSRGSC3.4
Celera77,498,625 - 7,498,839UniSTS
Celera221,573,679 - 21,573,893UniSTS
Cytogenetic Map7q11UniSTS
Cytogenetic Map2q12UniSTS
BE121221  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0712,178,256 - 12,178,412NCBIRnor6.0
Rnor_5.0712,348,311 - 12,348,467UniSTSRnor5.0
RGSC_v3.4710,823,470 - 10,823,626UniSTSRGSC3.4
Celera77,490,863 - 7,491,019UniSTS
Cytogenetic Map7q11UniSTS
RH 3.4 Map727.7UniSTS
Mbd3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0712,185,880 - 12,186,217NCBIRnor6.0
Rnor_6.0223,925,984 - 23,926,321NCBIRnor6.0
Rnor_5.0712,355,935 - 12,356,272UniSTSRnor5.0
Rnor_5.0243,097,027 - 43,097,364UniSTSRnor5.0
RGSC_v3.4710,831,092 - 10,831,429UniSTSRGSC3.4
RGSC_v3.4224,571,725 - 24,572,062UniSTSRGSC3.4
Celera77,498,497 - 7,498,834UniSTS
Celera221,573,551 - 21,573,888UniSTS
Cytogenetic Map7q11UniSTS
Cytogenetic Map2q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
CRRD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7134147172Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7134828535Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7134828535Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7137009673Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7138119654Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7265313832258115Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7591147750911477Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7595196950951969Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7975804554758045Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)71164710256647102Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:202
Count of miRNA genes:126
Interacting mature miRNAs:137
Transcripts:ENSRNOT00000049170
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.


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 35 48 33 19 33 6 9 74 35 41 11 6
Low 8 9 8 8 2 2 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000049170   ⟹   ENSRNOP00000041242
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl712,179,203 - 12,186,656 (+)Ensembl
RefSeq Acc Id: NM_001108735   ⟹   NP_001102205
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0712,179,046 - 12,186,248 (+)NCBI
Rnor_5.0712,349,101 - 12,356,306 (+)NCBI
RGSC_v3.4710,824,260 - 10,831,460 (+)RGD
Celera77,491,653 - 7,498,865 (+)RGD
Sequence:
RefSeq Acc Id: XM_006240965   ⟹   XP_006241027
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0712,179,052 - 12,186,251 (+)NCBI
Rnor_5.0712,349,101 - 12,356,306 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006240966   ⟹   XP_006241028
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0712,179,057 - 12,186,251 (+)NCBI
Rnor_5.0712,349,101 - 12,356,306 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765119   ⟹   XP_008763341
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0712,179,119 - 12,186,251 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765120   ⟹   XP_008763342
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0712,179,222 - 12,186,251 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765121   ⟹   XP_008763343
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0712,179,190 - 12,186,251 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001102205   ⟸   NM_001108735
- Sequence:
RefSeq Acc Id: XP_006241027   ⟸   XM_006240965
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006241028   ⟸   XM_006240966
- Peptide Label: isoform X5
- UniProtKB: F7EY92 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763343   ⟸   XM_008765121
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008763341   ⟸   XM_008765119
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008763342   ⟸   XM_008765120
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000041242   ⟸   ENSRNOT00000049170
Protein Domains
MBD

Transcriptome

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

Promoters
RGD ID:13695019
Promoter ID:EPDNEW_R5544
Type:initiation region
Name:Mbd3_1
Description:methyl-CpG binding domain protein 3
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_6.0712,179,117 - 12,179,177EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
7 12355594 12355595 C T snv SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), WKY/NHsd (KNAW), SHRSP/Gcrc (KNAW), WKY/Gcrc (KNAW), WKY/NCrl (KNAW), SHR/OlaIpcvPrin (KNAW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 10830751 10830752 C T snv SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), HCR/2Mco (UMich), WKY/NHsd (ICL), WKY/NCrl (ICL), LCR/1Mco (UMich), WKY/Gcrc (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307389 AgrOrtholog
Ensembl Genes ENSRNOG00000028956 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000041242 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000049170 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8363656 IMAGE-MGC_LOAD
InterPro DNA-bd_integrase-typ UniProtKB/TrEMBL
  MBD2/MBD3_p55-bd UniProtKB/TrEMBL
  MeCpG_bd_2/3_C_dom UniProtKB/TrEMBL
  Methyl_CpG_DNA-bd UniProtKB/TrEMBL
MGC_CLONE MGC:189306 IMAGE-MGC_LOAD
NCBI Gene 362834 ENTREZGENE
Pfam MBD_C UniProtKB/TrEMBL
  MBDa UniProtKB/TrEMBL
PhenoGen Mbd3 PhenoGen
PROSITE MBD UniProtKB/TrEMBL
SMART MBD UniProtKB/TrEMBL
Superfamily-SCOP DNA-binding_integrase-type UniProtKB/TrEMBL
UniGene Rn.231656 ENTREZGENE
UniProt B2RZ64_RAT UniProtKB/TrEMBL
  F7EY92 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Mbd3  methyl-CpG binding domain protein 3   Mbd3_predicted  methyl-CpG binding domain protein 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Mbd3_predicted  methyl-CpG binding domain protein 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED

 



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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.