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

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Gene: Mbd3l2 (methyl-CpG binding domain protein 3-like 2) Rattus norvegicus
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Symbol: Mbd3l2
Name: methyl-CpG binding domain protein 3-like 2
RGD ID: 1308833
Description: Predicted to enable methyl-CpG binding activity. Predicted to be involved in DNA methylation-dependent constitutive heterochromatin formation; negative regulation of transcription by RNA polymerase II; and regulation of chromatin organization. Predicted to be active 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 Orthologs
More Info more info ...
Related Functional Gene: Mbd3  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8823,883,809 - 23,890,378 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl823,881,161 - 23,888,901 (+)EnsemblGRCr8
mRatBN7.2815,607,477 - 15,614,046 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl815,611,214 - 15,612,563 (+)EnsemblmRatBN7.2
Rnor_6.0817,928,027 - 17,929,783 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl817,928,358 - 17,929,704 (+)Ensemblrn6Rnor6.0
Rnor_5.0818,003,538 - 18,005,098 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4815,975,721 - 15,977,070 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera817,039,315 - 17,041,071 (+)NCBICelera
RGSC_v3.1815,976,452 - 15,977,070 (+)NCBI
Cytogenetic Map8q13NCBI
JBrowse:




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,IEA,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 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl823,881,161 - 23,888,901 (+)EnsemblGRCr8
mRatBN7.2815,607,477 - 15,614,046 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl815,611,214 - 15,612,563 (+)EnsemblmRatBN7.2
Rnor_6.0817,928,027 - 17,929,783 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl817,928,358 - 17,929,704 (+)Ensemblrn6Rnor6.0
Rnor_5.0818,003,538 - 18,005,098 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4815,975,721 - 15,977,070 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera817,039,315 - 17,041,071 (+)NCBICelera
RGSC_v3.1815,976,452 - 15,977,070 (+)NCBI
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 (+)Ensemblhg38GRCh38
GRCh37197,049,332 - 7,051,746 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36197,000,351 - 7,002,746 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm38918,430,615 - 18,446,316 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl918,430,654 - 18,446,316 (+)Ensemblmm10GRCm38
MGSCv37918,235,059 - 18,250,760 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36918,181,056 - 18,196,718 (+)NCBIMGSCv36mm8
Celera915,714,253 - 15,729,954 (+)NCBICelera
Cytogenetic Map9A2NCBI
cM Map97.05NCBI

Variants

.
Variants in Mbd3l2
75 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81699464261994642Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)81038254055382540Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)81296416557964165Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)81595227960952279Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)81296416557964165Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81799386262252873Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)81038254055382540Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8132882639Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)81038254055382540Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81699464261994642Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)81296416557964165Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)81038254055382540Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
2 2 1 6 6 7 3 1 3 15 4 4 4 29 4

Sequence


Ensembl Acc Id: ENSRNOT00000029911   ⟹   ENSRNOP00000037810
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl823,881,161 - 23,888,901 (+)Ensembl
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 ENSRNOP00000037810.2
Ensembl Acc Id: ENSRNOP00000037810   ⟸   ENSRNOT00000029911
RefSeq Acc Id: XP_038938165   ⟸   XM_039082237

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 ENSRNOT00000029911.4 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