Mbd1 methyl-CpG binding domain protein 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Mbd1provided by RGD
Official Full Name: methyl-CpG binding domain protein 1provided by RGD
Primary source: RGD:1305980
See related: EnsemblRapid:ENSRNOG00000024104 AllianceGenome:RGD:1305980
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: Enables chromatin binding activity. Involved in several processes, including negative regulation of astrocyte differentiation; regulation of gene expression; and response to estradiol. Located in chromatin. Biomarker of transient cerebral ischemia and visual epilepsy. Human ortholog(s) of this gene implicated in lung cancer. Orthologous to human MBD1 (methyl-CpG binding domain protein 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Adrenal (RPKM 176.9), Spleen (RPKM 103.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 18q12.2

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	18	NC_086036.1 (70145093..70159744)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	18	NC_051353.1 (67869870..67884501)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	18	NC_005117.4 (70248568..70263190)

Chromosome 18 - NC_086036.1 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?

Adolescent chronic intermittent toluene inhalation dynamically regulates the transcriptome and neuronal methylome within the rat medial prefrontal cortex.
Title: Adolescent chronic intermittent toluene inhalation dynamically regulates the transcriptome and neuronal methylome within the rat medial prefrontal cortex.
Mbd1 and DNA methylation-mediated epigenetic mechanism regulated the expression of stem cell mitogen Fgf-2 in adult neural stem/progenitor cells.
Title: Epigenetic regulation of the stem cell mitogen Fgf-2 by Mbd1 in adult neural stem/progenitor cells.

Submit: New GeneRIF Correction

General gene information

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Markers

RH135120 (e-PCR)
- UniSTS:218397

BF389035 (e-PCR)
- UniSTS:245351

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded methylated 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
enables unmethylated CpG binding	ISO Inferred from Sequence Orthology more info
enables zinc ion 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 epigenetic regulation of gene expression	IEP Inferred from Expression Pattern more info	PubMed
involved_in negative regulation of astrocyte differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to cocaine	IEP Inferred from Expression Pattern more info	PubMed
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
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in ventricular cardiac muscle tissue development	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
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
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nuclear matrix	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
NOT located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	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

General protein information

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Preferred Names: methyl-CpG-binding domain protein 1

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_001011924.1 → NP_001011924.1 methyl-CpG-binding domain protein 1

See identical proteins and their annotated locations for NP_001011924.1

Status: PROVISIONAL

Source sequence(s)

BC081932

UniProtKB/TrEMBL

A0A8I6GMJ2, Q66HB8

Conserved Domains (2) summary

smart00391
Location:3 → 72

MBD; Methyl-CpG binding domain

pfam02008
Location:186 → 233

zf-CXXC; CXXC zinc finger domain

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_086036.1 Reference GRCr8

Range

70145093..70159744

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006254911.5 → XP_006254973.1 methyl-CpG-binding domain protein 1 isoform X3

UniProtKB/TrEMBL

A0A8I6A3W5, A0A8I6AS94

Related

ENSRNOP00000097211.2, ENSRNOT00000113558.2

Conserved Domains (2) summary

cd01396
Location:5 → 66

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 ...

pfam02008
Location:349 → 393

zf-CXXC; CXXC zinc finger domain
XM_006254913.5 → XP_006254975.1 methyl-CpG-binding domain protein 1 isoform X8

UniProtKB/TrEMBL

A0A8I6GMJ2

Related

ENSRNOP00000037640.5, ENSRNOT00000032202.6

Conserved Domains (2) summary

cd01396
Location:5 → 66

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 ...

pfam02008
Location:235 → 280

zf-CXXC; CXXC zinc finger domain
XM_039096640.2 → XP_038952568.1 methyl-CpG-binding domain protein 1 isoform X5

UniProtKB/TrEMBL

A0A8I6AS94

Conserved Domains (2) summary

cd01396
Location:5 → 66

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 ...

pfam02008
Location:347 → 393

zf-CXXC; CXXC zinc finger domain
XM_006254909.5 → XP_006254971.1 methyl-CpG-binding domain protein 1 isoform X1

UniProtKB/TrEMBL

A0A8I6AS94

Related

ENSRNOP00000019573.7, ENSRNOT00000019573.9

Conserved Domains (2) summary

cd01396
Location:5 → 66

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 ...

pfam02008
Location:349 → 393

zf-CXXC; CXXC zinc finger domain
XM_017600883.3 → XP_017456372.1 methyl-CpG-binding domain protein 1 isoform X4

UniProtKB/TrEMBL

A0A8I6AS94
XM_063277172.1 → XP_063133242.1 methyl-CpG-binding domain protein 1 isoform X11

UniProtKB/TrEMBL

A0A8I6AS94
XM_006254910.5 → XP_006254972.1 methyl-CpG-binding domain protein 1 isoform X2

UniProtKB/TrEMBL

A0A8I6AS94

Conserved Domains (2) summary

cd01396
Location:5 → 66

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 ...

pfam02008
Location:348 → 392

zf-CXXC; CXXC zinc finger domain
XM_006254914.5 → XP_006254976.1 methyl-CpG-binding domain protein 1 isoform X9

UniProtKB/TrEMBL

A0A8I5ZMU8

Related

ENSRNOP00000078508.2, ENSRNOT00000102132.2

Conserved Domains (2) summary

cd01396
Location:5 → 66

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 ...

pfam02008
Location:235 → 280

zf-CXXC; CXXC zinc finger domain
XM_017600882.3 → XP_017456371.1 methyl-CpG-binding domain protein 1 isoform X6

UniProtKB/TrEMBL

A0A8I6AS94
XM_063277170.1 → XP_063133240.1 methyl-CpG-binding domain protein 1 isoform X7

UniProtKB/TrEMBL

A0A8I6AS94
XM_063277171.1 → XP_063133241.1 methyl-CpG-binding domain protein 1 isoform X10

UniProtKB/TrEMBL

A0A8I5ZMU8