Mbd3 methyl-CpG binding domain protein 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Mbd3provided by RGD
Official Full Name: methyl-CpG binding domain protein 3provided by RGD
Primary source: RGD:1307389
See related: EnsemblRapid:ENSRNOG00000028956 AllianceGenome:RGD:1307389
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable chromatin binding activity and methyl-CpG binding activity. Involved in several processes, including epigenetic regulation of gene expression; response to estradiol; and ventricular cardiac muscle tissue development. Predicted to be located in cytoplasm and heterochromatin. Predicted to be part of NuRD complex. Predicted to be active in nucleus. Biomarker of transient cerebral ischemia and visual epilepsy. Orthologous to human MBD3 (methyl-CpG binding domain protein 3). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Muscle (RPKM 96.5), Kidney (RPKM 91.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q11

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (9961053..9970845)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (9312961..9320166)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (12179046..12186251)

Chromosome 7 - NC_086025.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

data demonstrate for the first time alterations in the MBD3 expression and DNA occupancy in the experimental model of epilepsy.
Title: MBD3 expression and DNA binding patterns are altered in a rat model of temporal lobe epilepsy.
Endogenous Mta1/2 forms a complex with chromodomain helicase (Chd)4, histone deacetylase (Hdac)1/2, RbAp46/48, and Mbd3 in the rat cerebellum
Title: Promoter decommissioning by the NuRD chromatin remodeling complex triggers synaptic connectivity in the mammalian brain.
MBD3 displays a selective spatial and temporal pattern of expression in the embryonic and adult brain, thereby strengthening the possibility of MBD3 playing an important role in neuronal development
Title: Differential expression of methyl CpG-binding domain containing factor MBD3 in the developing and adult rat brain.
Methyl CpG binding protein 3 (Mecp3, MBD3)displays a selective spatial and temporal pattern of expression in the embryonic and adult brain, thereby strengthening the possibility of MBD3 playing an important role in neuronal development.
Title: Differential expression of methyl CpG-binding domain containing factor MBD3 in the developing and adult rat brain.

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General gene information

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Markers

RH133854 (e-PCR)
- UniSTS:217137

Mbd3 (e-PCR), detects polymorphism
- UniSTS:498797

RH126839 (e-PCR)
- UniSTS:208574

BE121221 (e-PCR)
- UniSTS:248037

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables methyl-CpG binding	IBA Inferred from Biological aspect of Ancestor more info
enables methyl-CpG binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent constitutive heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in embryonic organ development	IEP Inferred from Expression Pattern more info	PubMed
involved_in epigenetic regulation of gene expression	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to estradiol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to nutrient levels	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to organic cyclic compound	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within tissue development	ISO Inferred from Sequence Orthology more info
involved_in ventricular cardiac muscle tissue development	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
part_of NuRD complex	ISO Inferred from Sequence Orthology more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in heterochromatin	ISO Inferred from Sequence Orthology more info
NOT located_in nucleolus	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: methyl-CpG-binding domain protein 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001108735.1 → NP_001102205.1 methyl-CpG-binding domain protein 3

See identical proteins and their annotated locations for NP_001102205.1

Status: PROVISIONAL

Source sequence(s)

CH474029

UniProtKB/TrEMBL

A0A8I6ANN7, A6K8L1

Conserved Domains (3) summary

cd01396
Location:5 → 79

MeCP2_MBD; MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding ...

pfam14048
Location:153 → 243

MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3

pfam16564
Location:82 → 148

MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086025.1 Reference GRCr8

Range

9961053..9970845

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006240965.3 → XP_006241027.1 methyl-CpG-binding domain protein 3 isoform X1

See identical proteins and their annotated locations for XP_006241027.1

UniProtKB/TrEMBL

A0A8I6ANN7, A6K8L1

Conserved Domains (3) summary

cd01396
Location:5 → 79

MeCP2_MBD; MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding ...

pfam14048
Location:153 → 243

MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3

pfam16564
Location:82 → 148

MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD
XM_006240966.2 → XP_006241028.1 methyl-CpG-binding domain protein 3 isoform X3

See identical proteins and their annotated locations for XP_006241028.1

UniProtKB/TrEMBL

A0A8I6ANN7, A6K8L3

Conserved Domains (3) summary

pfam14048
Location:121 → 211

MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3

pfam16564
Location:50 → 116

MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD

cl00110
Location:5 → 47

MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...
XM_039079396.2 → XP_038935324.1 methyl-CpG-binding domain protein 3 isoform X4

Related

ENSRNOP00000041242.7, ENSRNOT00000049170.7
XM_008765120.3 → XP_008763342.1 methyl-CpG-binding domain protein 3 isoform X2

UniProtKB/TrEMBL

A0A8I6ANN7, F7EY92

Related

ENSRNOP00000094795.2, ENSRNOT00000100050.2

Conserved Domains (3) summary

pfam14048
Location:149 → 239

MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3

pfam16564
Location:87 → 144

MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD

cl00110
Location:5 → 47

MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...