Mbd3l2 (methyl-CpG binding domain protein 3-like 2) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Mbd3l2 (methyl-CpG binding domain protein 3-like 2) Rattus norvegicus
Analyze
Symbol: Mbd3l2
Name: methyl-CpG binding domain protein 3-like 2
RGD ID: 1308833
Description: Predicted to be involved in regulation of chromatin organization and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Orthologous to several human genes including MBD3L2 (methyl-CpG binding domain protein 3 like 2); INTERACTS WITH bisphenol A; vinclozolin; 2,3',4,4',5-Pentachlorobiphenyl (ortholog).
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: INFERRED
Previously known as: LOC300375; Mbd3l3; methyl-CpG binding domain protein 3-like 3; putative methyl-CpG-binding domain protein 3-like 3
RGD Orthologs
Human
Mouse
Alliance Genes
More Info more info ...
Related Functional Gene: Mbd3  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8823,883,809 - 23,890,378 (+)NCBIGRCr8
mRatBN7.2815,607,477 - 15,614,046 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl815,611,214 - 15,612,563 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0817,928,027 - 17,929,783 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl817,928,358 - 17,929,704 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0818,003,538 - 18,005,098 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4815,975,721 - 15,977,070 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1815,976,452 - 15,977,070 (+)NCBI
Celera817,039,315 - 17,041,071 (+)NCBICelera
Cytogenetic Map8q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Mbd3l2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8823,883,809 - 23,890,378 (+)NCBIGRCr8
mRatBN7.2815,607,477 - 15,614,046 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl815,611,214 - 15,612,563 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0817,928,027 - 17,929,783 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl817,928,358 - 17,929,704 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0818,003,538 - 18,005,098 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4815,975,721 - 15,977,070 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1815,976,452 - 15,977,070 (+)NCBI
Celera817,039,315 - 17,041,071 (+)NCBICelera
Cytogenetic Map8q13NCBI
MBD3L2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38197,049,321 - 7,051,735 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl197,049,321 - 7,051,735 (+)EnsemblGRCh38hg38GRCh38
GRCh37197,049,332 - 7,051,746 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36197,000,351 - 7,002,746 (+)NCBINCBI36Build 36hg18NCBI36
Celera196,961,220 - 6,963,675 (-)NCBICelera
Cytogenetic Map19p13.2NCBI
CHM1_1197,048,996 - 7,051,391 (+)NCBICHM1_1
T2T-CHM13v2.0197,039,410 - 7,041,824 (+)NCBIT2T-CHM13v2.0
Mbd3l2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39918,341,911 - 18,357,612 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl918,341,950 - 18,357,612 (+)EnsemblGRCm39 Ensembl
GRCm38918,430,615 - 18,446,316 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl918,430,654 - 18,446,316 (+)EnsemblGRCm38mm10GRCm38
MGSCv37918,235,059 - 18,250,760 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36918,181,056 - 18,196,718 (+)NCBIMGSCv36mm8
Celera915,714,253 - 15,729,954 (+)NCBICelera
Cytogenetic Map9A2NCBI
cM Map97.05NCBI

Variants

.
Variants in Mbd3l2
20 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:155
Count of miRNA genes:106
Interacting mature miRNAs:112
Transcripts:ENSRNOT00000029911
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat


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 endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 1 1 1 6 1
Below cutoff 4 3 1 3 2 2 3 3 10 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000029911   ⟹   ENSRNOP00000037810
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl815,611,214 - 15,612,563 (+)Ensembl
Rnor_6.0 Ensembl817,928,358 - 17,929,704 (+)Ensembl
RefSeq Acc Id: XM_039082237   ⟹   XP_038938165
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2815,607,477 - 15,614,046 (+)NCBI
Protein Sequences
Ensembl Protein ENSRNOP00000037810.1
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000037810   ⟸   ENSRNOT00000029911
RefSeq Acc Id: XP_038938165   ⟸   XM_039082237
Protein Domains
Methyl-CpG binding protein 2/3 C-terminal   Methyl-CpG-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZHU7-F1-model_v2 AlphaFold D3ZHU7 1-226 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308833 AgrOrtholog
BioCyc Gene G2FUF-31600 BioCyc
Ensembl Genes ENSRNOG00000026629 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029911.3 UniProtKB/TrEMBL
InterPro MBD2/MBD3_p55-bd UniProtKB/TrEMBL
  MeCpG-bd_2/3_C_dom UniProtKB/TrEMBL
NCBI Gene 300375 ENTREZGENE
Pfam MBD_C UniProtKB/TrEMBL
  MBDa UniProtKB/TrEMBL
PhenoGen Mbd3l2 PhenoGen
RatGTEx ENSRNOG00000026629 RatGTEx
UniProt D3ZHU7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-01-22 Mbd3l2  methyl-CpG binding domain protein 3-like 2  Mbd3l3  methyl-CpG binding domain protein 3-like 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-14 Mbd3l3  methyl-CpG binding domain protein 3-like 3  Mbd3l2_predicted  methyl-CpG binding domain protein 3-like 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Mbd3l2_predicted  methyl-CpG binding domain protein 3-like 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED