Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene miRNA Transcription factors Gene ontology Other IDs Protein Pathways
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	4152
Gene name Gene Name - the full gene name approved by the HGNC.	Methyl-CpG binding domain protein 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	MBD1
Synonyms (NCBI Gene) Gene synonyms aliases	CXXC3, PCM1, RFT
Chromosome Chromosome number	18
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	18q21.1
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene is a member of a family of nuclear proteins related by the presence of a methyl-CpG binding domain (MBD). These proteins are capable of binding specifically to methylated DNA, and some members can also repress transcriptio

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miRTarBase ID	miRNA	Experiments	Reference
MIRT007219	hsa-miR-195-5p	Luciferase reporter assay	23349673
MIRT050283	hsa-miR-25-3p	CLASH	23622248
MIRT047606	hsa-miR-10a-5p	CLASH	23622248
MIRT040325	hsa-miR-615-3p	CLASH	23622248
MIRT690077	hsa-miR-18a-5p	HITS-CLIP	23313552
MIRT690076	hsa-miR-18b-5p	HITS-CLIP	23313552
MIRT690075	hsa-miR-4735-3p	HITS-CLIP	23313552
MIRT690074	hsa-miR-6504-3p	HITS-CLIP	23313552
MIRT690073	hsa-miR-4761-5p	HITS-CLIP	23313552
MIRT690072	hsa-miR-6814-5p	HITS-CLIP	23313552
MIRT690071	hsa-miR-1234-3p	HITS-CLIP	23313552
MIRT690070	hsa-miR-7107-5p	HITS-CLIP	23313552
MIRT690069	hsa-miR-150-5p	HITS-CLIP	23313552
MIRT690068	hsa-miR-1913	HITS-CLIP	23313552
MIRT690067	hsa-miR-324-3p	HITS-CLIP	23313552
MIRT690066	hsa-miR-18a-3p	HITS-CLIP	23313552
MIRT690065	hsa-miR-619-5p	HITS-CLIP	23313552
MIRT690064	hsa-miR-6506-5p	HITS-CLIP	23313552
MIRT690063	hsa-miR-4707-3p	HITS-CLIP	23313552
MIRT690062	hsa-miR-6778-3p	HITS-CLIP	23313552
MIRT690061	hsa-miR-4731-5p	HITS-CLIP	23313552
MIRT690060	hsa-miR-5589-5p	HITS-CLIP	23313552
MIRT690059	hsa-miR-5095	HITS-CLIP	23313552
MIRT690058	hsa-miR-7151-3p	HITS-CLIP	23313552
MIRT690057	hsa-miR-5089-5p	HITS-CLIP	23313552
MIRT678996	hsa-miR-4797-5p	HITS-CLIP	23824327
MIRT678994	hsa-miR-5007-5p	HITS-CLIP	23824327
MIRT678995	hsa-miR-4524a-3p	HITS-CLIP	23824327
MIRT678992	hsa-miR-3672	HITS-CLIP	23824327
MIRT678993	hsa-miR-6864-3p	HITS-CLIP	23824327
MIRT678991	hsa-miR-8055	HITS-CLIP	23824327
MIRT290618	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT690077	hsa-miR-18a-5p	HITS-CLIP	23313552
MIRT690076	hsa-miR-18b-5p	HITS-CLIP	23313552
MIRT690075	hsa-miR-4735-3p	HITS-CLIP	23313552
MIRT690074	hsa-miR-6504-3p	HITS-CLIP	23313552
MIRT690073	hsa-miR-4761-5p	HITS-CLIP	23313552
MIRT690072	hsa-miR-6814-5p	HITS-CLIP	23313552
MIRT690071	hsa-miR-1234-3p	HITS-CLIP	23313552
MIRT690070	hsa-miR-7107-5p	HITS-CLIP	23313552
MIRT690069	hsa-miR-150-5p	HITS-CLIP	23313552
MIRT690068	hsa-miR-1913	HITS-CLIP	23313552
MIRT690067	hsa-miR-324-3p	HITS-CLIP	23313552
MIRT690066	hsa-miR-18a-3p	HITS-CLIP	23313552
MIRT690065	hsa-miR-619-5p	HITS-CLIP	23313552
MIRT690064	hsa-miR-6506-5p	HITS-CLIP	23313552
MIRT690063	hsa-miR-4707-3p	HITS-CLIP	23313552
MIRT690062	hsa-miR-6778-3p	HITS-CLIP	23313552
MIRT690061	hsa-miR-4731-5p	HITS-CLIP	23313552
MIRT690060	hsa-miR-5589-5p	HITS-CLIP	23313552
MIRT690059	hsa-miR-5095	HITS-CLIP	23313552
MIRT690058	hsa-miR-7151-3p	HITS-CLIP	23313552
MIRT690057	hsa-miR-5089-5p	HITS-CLIP	23313552
MIRT678996	hsa-miR-4797-5p	HITS-CLIP	23824327
MIRT678994	hsa-miR-5007-5p	HITS-CLIP	23824327
MIRT678995	hsa-miR-4524a-3p	HITS-CLIP	23824327
MIRT678992	hsa-miR-3672	HITS-CLIP	23824327
MIRT678993	hsa-miR-6864-3p	HITS-CLIP	23824327
MIRT678991	hsa-miR-8055	HITS-CLIP	23824327
MIRT290618	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT1134787	hsa-miR-1343	CLIP-seq
MIRT1134788	hsa-miR-4268	CLIP-seq
MIRT1134789	hsa-miR-4286	CLIP-seq
MIRT1134790	hsa-miR-4448	CLIP-seq
MIRT1134791	hsa-miR-498	CLIP-seq
MIRT1134792	hsa-miR-4676-5p	CLIP-seq
MIRT1134793	hsa-miR-575	CLIP-seq
MIRT1134794	hsa-miR-634	CLIP-seq
MIRT1134795	hsa-miR-125a-3p	CLIP-seq
MIRT1134796	hsa-miR-3157-5p	CLIP-seq
MIRT1134797	hsa-miR-33a	CLIP-seq
MIRT1134798	hsa-miR-33b	CLIP-seq
MIRT1134799	hsa-miR-3934	CLIP-seq
MIRT1134800	hsa-miR-4291	CLIP-seq
MIRT1134801	hsa-miR-4310	CLIP-seq
MIRT1134802	hsa-miR-4424	CLIP-seq
MIRT1134803	hsa-miR-4461	CLIP-seq
MIRT1134804	hsa-miR-4468	CLIP-seq
MIRT1134805	hsa-miR-4519	CLIP-seq
MIRT1134806	hsa-miR-4691-3p	CLIP-seq
MIRT1134807	hsa-miR-4792	CLIP-seq
MIRT1134808	hsa-miR-764	CLIP-seq
MIRT2442351	hsa-miR-3124-3p	CLIP-seq
MIRT2442352	hsa-miR-4274	CLIP-seq
MIRT1134805	hsa-miR-4519	CLIP-seq
MIRT2465608	hsa-miR-1915	CLIP-seq
MIRT2465609	hsa-miR-624	CLIP-seq
MIRT2465610	hsa-miR-720	CLIP-seq
MIRT2567884	hsa-miR-1287	CLIP-seq
MIRT2567885	hsa-miR-1293	CLIP-seq
MIRT2567886	hsa-miR-216b	CLIP-seq
MIRT2567887	hsa-miR-3135b	CLIP-seq
MIRT1134796	hsa-miR-3157-5p	CLIP-seq
MIRT1134797	hsa-miR-33a	CLIP-seq
MIRT1134798	hsa-miR-33b	CLIP-seq
MIRT2567888	hsa-miR-376a	CLIP-seq
MIRT2567889	hsa-miR-376b	CLIP-seq
MIRT2567890	hsa-miR-4314	CLIP-seq
MIRT2567891	hsa-miR-4417	CLIP-seq
MIRT2567892	hsa-miR-4483	CLIP-seq
MIRT1134792	hsa-miR-4676-5p	CLIP-seq
MIRT2567893	hsa-miR-541	CLIP-seq
MIRT1134793	hsa-miR-575	CLIP-seq
MIRT1134794	hsa-miR-634	CLIP-seq
MIRT2567894	hsa-miR-642b	CLIP-seq
MIRT2567895	hsa-miR-654-5p	CLIP-seq

Transcription factors

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Transcription factor	Regulation	Reference
HDAC3	Unknown	16432238

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IBA
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	TAS	9774669
GO:0005515	Function	Protein binding	IPI	12665582, 12711603, 16432238, 19498464, 19666599, 21653829, 23275563
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	10454587
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0006346	Process	DNA methylation-dependent constitutive heterochromatin formation	IBA
GO:0006366	Process	Transcription by RNA polymerase II	TAS	9774669
GO:0008270	Function	Zinc ion binding	IDA	29276034
GO:0008270	Function	Zinc ion binding	IEA
GO:0008327	Function	Methyl-CpG binding	IBA
GO:0008327	Function	Methyl-CpG binding	IDA	25284789
GO:0008327	Function	Methyl-CpG binding	NAS	10454587
GO:0010385	Function	Double-stranded methylated DNA binding	IDA	11371345
GO:0016363	Component	Nuclear matrix	IEA
GO:0016363	Component	Nuclear matrix	ISS
GO:0016607	Component	Nuclear speck	IEA
GO:0016607	Component	Nuclear speck	ISS
GO:0045322	Function	Unmethylated CpG binding	IDA	29276034
GO:0045892	Process	Negative regulation of DNA-templated transcription	NAS	10454587
GO:0046872	Function	Metal ion binding	IEA

MIM	HGNC	e!Ensembl
156535	6916	ENSG00000141644

Protein

UniProt ID

Q9UIS9

Protein name

Methyl-CpG-binding domain protein 1 (CXXC-type zinc finger protein 3) (Methyl-CpG-binding protein MBD1) (Protein containing methyl-CpG-binding domain 1)

Protein function

Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (

PDB

1D9N , 1IG4 , 4D4W , 5W9Q , 6D1T

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01429	MBD	1 → 88	Methyl-CpG binding domain	Domain
PF02008	zf-CXXC	168 → 215	CXXC zinc finger domain	Domain
PF02008	zf-CXXC	217 → 262	CXXC zinc finger domain	Domain
PF02008	zf-CXXC	330 → 377	CXXC zinc finger domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:9207790}.

Sequence

MAEDWLDCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPACDLT
LFDFKQGILCYPAPKAHPVAVASKKRKKPSRPAKTRKRQVGPQSGEVRKEAPRDETKADT
DTAPASFPAPGCCENCGISFSGDGTQRQRLKTLCKDCRAQRIAFNREQRMFKRVGCGECA
ACQVTEDCGACSTCLLQLPHDVASGLFCKCERRRCLRIVERSRGCGVCRGCQTQEDCGHC
PICLRPPRPGLRRQWKCVQRRCLRGKHARRKGGCDSKMAARRRPGAQPLPPPPPSQSPEP
TEPHPRALAPSPPAEFIYYCVDEDELQPYTNRRQNRKCGACAACLRRMDCGRCDFCCDKP
KFGGSNQKRQKCRWRQCLQFAMKRLLPSVWSESEDGAGSPPPYRRRKRPSSARRHHLGPT
LKPTLATRTAQPDHTQAPTKQEAGGGFVLPPPGTDLVFLREGASSPVQVPGPVAASTEAL
LQEAQCSGLSWVVALPQVKQEKADTQDEWTPGTAVLTSPVLVPGCPSKAVDPGLPSVKQE
PPDPEEDKEENKDDSASKLAPEEEAGGAGTPVITEIFSLGGTRFRDTAVWLPRSKDLKKP
GARKQ

Sequence length

605

Interactions

View interactions

	Reactome
			SUMOylation of transcription cofactors

MBD1 (methyl-CpG binding domain protein 1)