Mbd1 methyl-CpG binding domain protein 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Mbd1provided by MGI
Official Full Name: methyl-CpG binding domain protein 1provided by MGI
Primary source: MGI:MGI:1333811
See related: Ensembl:ENSMUSG00000024561 AllianceGenome:MGI:1333811
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: PCM1; Cxxc3
Summary: Enables DNA binding activity. Predicted to be involved in negative regulation of astrocyte differentiation and negative regulation of gene expression. Located in cytoplasm; heterochromatin; and nuclear lumen. Is expressed in several structures, including central nervous system; early conceptus; genitourinary system; and retina. 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: Ubiquitous expression in thymus adult (RPKM 15.4), genital fat pad adult (RPKM 13.7) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 18 E2; 18 50.7 cM

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	18	NC_000084.7 (74400676..74415808)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	18	NC_000084.6 (74267605..74282737)

Chromosome 18 - NC_000084.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Forward genetic screen of homeostatic antibody levels in the Collaborative Cross identifies MBD1 as a novel regulator of B cell homeostasis.
Title: Forward genetic screen of homeostatic antibody levels in the Collaborative Cross identifies MBD1 as a novel regulator of B cell homeostasis.
Knock-out MBD1 mice displayed reduced responses in the dorsal root ganglia to acute pain and neuropathic pain.
Title: MBD1 Contributes to the Genesis of Acute Pain and Neuropathic Pain by Epigenetic Silencing of Oprm1 and Kcna2 Genes in Primary Sensory Neurons.
MBD1 regulates localization and activity of Tet1 in a CXXC3 domain-dependent manner.
Title: Methyl-CpG binding domain protein 1 regulates localization and activity of Tet1 in a CXXC3 domain-dependent manner.
MBD1 has a role in neural stem cell maintenance and epigenetic regulation.
Title: Methyl-CpG-Binding Protein MBD1 Regulates Neuronal Lineage Commitment through Maintaining Adult Neural Stem Cell Identity.
MBD1 targets short interspersed nuclear elements, but does not exclude RNA Polymerase III.
Title: SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation.
We demonstrated the importance of Aire's interaction with the ATF7ip-MBD1 protein complex in maintaining central tolerance
Title: The transcriptional regulator Aire coopts the repressive ATF7ip-MBD1 complex for the induction of immunotolerance.
H19 lncRNA controls gene expression of the Imprinted Gene Network by recruiting MBD1.
Title: H19 lncRNA controls gene expression of the Imprinted Gene Network by recruiting MBD1.
regulatory loop formed by MBD1 and miR-195 is an important component of the epigenetic network that controls aNSC fate
Title: An epigenetic feedback regulatory loop involving microRNA-195 and MBD1 governs neural stem cell differentiation.
MBD1, miR-184, and Numbl form a regulatory network that helps control the balance between proliferation and differentiation of adult neural stem/progenitor cells.
Title: Epigenetic regulation of miR-184 by MBD1 governs neural stem cell proliferation and differentiation.
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 See all GeneRIFs (13)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2) 1 citation
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AF072240 (e-PCR)
- UniSTS:163604

Mbd1 (e-PCR), detects polymorphism
- UniSTS:525692

Mbd1 (e-PCR), detects polymorphism
- UniSTS:143834

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables double-stranded methylated DNA binding	ISO Inferred from Sequence Orthology more info	PubMed
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 protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables unmethylated CpG binding	ISO Inferred from Sequence Orthology more info
enables unmethylated CpG binding	ISS Inferred from Sequence or Structural Similarity more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity 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 negative regulation of astrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression	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

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	IDA Inferred from Direct Assay more info	PubMed
located_in heterochromatin	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nuclear matrix	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear speck	IDA Inferred from Direct Assay more info	PubMed
NOT located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: methyl-CpG-binding domain protein 1

Names: methyl-CpG-binding protein MBD1

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_001357421.2 → NP_001344350.1 methyl-CpG-binding domain protein 1 isoform 2

Status: VALIDATED

Source sequence(s)

AC147367

UniProtKB/Swiss-Prot

Q3TMA4, Q3U101, Q6NSW0, Q792D6, Q8CCL9, Q9DC19, Q9Z2E2

Conserved Domains (2) summary

pfam02008
Location:359 → 403

zf-CXXC; CXXC zinc finger domain

pfam01429
Location:1 → 72

MBD; Methyl-CpG binding domain
NM_001357422.2 → NP_001344351.1 methyl-CpG-binding domain protein 1 isoform 3

Status: VALIDATED

Source sequence(s)

AC147367

UniProtKB/TrEMBL

A0A286YCP6

Conserved Domains (1) summary

pfam02008
Location:164 → 208

zf-CXXC; CXXC zinc finger domain
NM_001357423.2 → NP_001344352.1 methyl-CpG-binding domain protein 1 isoform 4

Status: VALIDATED

Source sequence(s)

AC147367

Consensus CDS

CCDS89280.1

UniProtKB/Swiss-Prot

Q3TMA4, Q3U101, Q6NSW0, Q792D6, Q8CCL9, Q9DC19, Q9Z2E2

UniProtKB/TrEMBL

A0A286YDI1

Related

ENSMUSP00000153428.2, ENSMUST00000224047.2

Conserved Domains (2) summary

pfam02008
Location:359 → 403

zf-CXXC; CXXC zinc finger domain

pfam01429
Location:1 → 72

MBD; Methyl-CpG binding domain
NM_001402889.1 → NP_001389818.1 methyl-CpG-binding domain protein 1 isoform 5

Status: VALIDATED

Source sequence(s)

AC147367

UniProtKB/Swiss-Prot

Q3TMA4, Q3U101, Q6NSW0, Q792D6, Q8CCL9, Q9DC19, Q9Z2E2
NM_001402890.1 → NP_001389819.1 methyl-CpG-binding domain protein 1 isoform 6

Status: VALIDATED

Source sequence(s)

AC147367

UniProtKB/TrEMBL

A0A5F8MPN9
NM_001402891.1 → NP_001389820.1 methyl-CpG-binding domain protein 1 isoform 7

Status: VALIDATED

Source sequence(s)

AC147367

UniProtKB/TrEMBL

A0A5F8MPN9

Related

ENSMUSP00000153085.2, ENSMUST00000224332.2
NM_001402892.1 → NP_001389821.1 methyl-CpG-binding domain protein 1 isoform 8

Status: VALIDATED

Source sequence(s)

AC147367

UniProtKB/Swiss-Prot

Q3TMA4, Q3U101, Q6NSW0, Q792D6, Q8CCL9, Q9DC19, Q9Z2E2
NM_001402894.1 → NP_001389823.1 methyl-CpG-binding domain protein 1 isoform 9

Status: VALIDATED

Source sequence(s)

AC147367
NM_001402895.1 → NP_001389824.1 methyl-CpG-binding domain protein 1 isoform 10

Status: VALIDATED

Source sequence(s)

AC147367
NM_013594.4 → NP_038622.2 methyl-CpG-binding domain protein 1 isoform 1

See identical proteins and their annotated locations for NP_038622.2

Status: VALIDATED

Source sequence(s)

AC147367

Consensus CDS

CCDS50321.1

UniProtKB/TrEMBL

A0A0R4J159, A0A5F8MPN9

Related

ENSMUSP00000095137.4, ENSMUST00000097530.5

Conserved Domains (2) summary

pfam02008
Location:243 → 288

zf-CXXC; CXXC zinc finger domain

pfam01429
Location:5 → 69

MBD; Methyl-CpG binding domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000084.7 Reference GRCm39 C57BL/6J

Range

74400676..74415808

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006525707.3 → XP_006525770.1 methyl-CpG-binding domain protein 1 isoform X3

UniProtKB/Swiss-Prot

Q3TMA4, Q3U101, Q6NSW0, Q792D6, Q8CCL9, Q9DC19, Q9Z2E2

Conserved Domains (2) summary

pfam01429
Location:1 → 72

MBD; Methyl-CpG binding domain

pfam02008
Location:314 → 360

zf-CXXC; CXXC zinc finger domain
XM_030250354.2 → XP_030106214.1 methyl-CpG-binding domain protein 1 isoform X7

Conserved Domains (1) summary

pfam02008
Location:119 → 165

zf-CXXC; CXXC zinc finger domain