Human Gene MBD1 (uc002lem.4) Description and Page Index
  Description: Homo sapiens methyl-CpG binding domain protein 1 (MBD1), transcript variant 6, mRNA.
RefSeq Summary (NM_001204136): 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 transcription from methylated gene promoters. This protein contains multiple domains: MBD at the N-terminus that functions both in binding to methylated DNA and in protein interactions; several CXXC-type zinc finger domains that mediate binding to non-methylated CpG dinucleotides; transcriptional repression domain (TRD) at the C-terminus that is involved in transcription repression and in protein interactions. Numerous alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Feb 2011].
Transcript (Including UTRs)
   Position: hg19 chr18:47,795,216-47,808,144 Size: 12,929 Total Exon Count: 16 Strand: -
Coding Region
   Position: hg19 chr18:47,795,999-47,806,362 Size: 10,364 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:47,795,216-47,808,144)mRNA (may differ from genome)Protein (655 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: MBD1_HUMAN
DESCRIPTION: RecName: Full=Methyl-CpG-binding domain protein 1; AltName: Full=CXXC-type zinc finger protein 3; AltName: Full=Methyl-CpG-binding protein MBD1; AltName: Full=Protein containing methyl-CpG-binding domain 1;
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 (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.
SUBUNIT: Interacts with OASL, AFT7IP, AFT7IP2 and BAHD1. Binds CHAF1A and the SUV39H1-CBX5 complex via the MBD domain. Binds MGP via the TRD domain. May be part of the MeCP1 complex. During DNA replication, it recruits SETDB1 to form a S phase-specific complex that facilitates methylation of H3 'Lys-9' during replication- coupled chromatin assembly and is at least composed of the CAF-1 subunit CHAF1A, MBD1 and SETDB1.
INTERACTION: P45973:CBX5; NbExp=5; IntAct=EBI-867196, EBI-78219; Q13547:HDAC1; NbExp=2; IntAct=EBI-867196, EBI-301834; Q92769:HDAC2; NbExp=2; IntAct=EBI-867196, EBI-301821; O15379:HDAC3; NbExp=3; IntAct=EBI-867196, EBI-607682; Q15156:PML-RAR; NbExp=4; IntAct=EBI-867196, EBI-867256; O43463:SUV39H1; NbExp=5; IntAct=EBI-867196, EBI-349968;
SUBCELLULAR LOCATION: Nucleus speckle. Chromosome. Note=Nuclear, in a punctate pattern. Associated with euchromatic regions of the chromosomes, with pericentromeric regions on chromosome 1 and with telomeric regions from several chromosomes.
TISSUE SPECIFICITY: Widely expressed.
INDUCTION: Up-regulated by interferon.
DOMAIN: The methyl-CpG-binding domain (MBD) functions both in binding to methylated DNA and in protein interactions.
DOMAIN: The third CXXC-type zinc finger mediates binding to non- methylated CpG dinucleotides.
DOMAIN: The transcriptional repression domain (TRD) is involved in transcription repression and in protein interactions.
PTM: Sumoylated with SUMO1 by PIAS1 and PIAS3. Sumoylation affects transcriptional silencing by preventing the interaction with SETDB1. In contrast, sumoylation may increase interaction with AFT7IP.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Contains 3 CXXC-type zinc fingers.
SIMILARITY: Contains 1 MBD (methyl-CpG-binding) domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): MBD1
CDC HuGE Published Literature: MBD1
Positive Disease Associations: Chronic lymphocytic leukemia
Related Studies:
  1. Chronic lymphocytic leukemia
    Crowther-Swanepoel ,et al. 2010, Common variants at 2q37.3, 8q24.21, 15q21.3 abd 16q24.1 influence chronic lymphocytic leukemia risk, Nature genetics 2010 42- 2 : 132-6. [PubMed 20062064]

-  MalaCards Disease Associations
  MalaCards Gene Search: MBD1
Diseases sorted by gene-association score: trigeminal nerve disease (13), trigeminal neuralgia (8), subacute cutaneous lupus erythematosus (8), cranial nerve disease (1), autistic disorder (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 47.28 RPKM in Testis
Total median expression: 801.37 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -209.70437-0.480 Picture PostScript Text
3' UTR -243.47783-0.311 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016177 - DNA-bd_integrase-typ
IPR001739 - Methyl_CpG_DNA-bd
IPR002857 - Znf_CXXC

Pfam Domains:
PF01429 - Methyl-CpG binding domain
PF02008 - CXXC zinc finger domain

SCOP Domains:
54171 - DNA-binding domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1D9N
- NMR MuPIT

1IG4
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9UIS9
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008327 methyl-CpG binding
GO:0010385 double-stranded methylated DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0045892 negative regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus
GO:0005694 chromosome
GO:0016363 nuclear matrix
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  BC047353 - Homo sapiens methyl-CpG binding domain protein 1, mRNA (cDNA clone IMAGE:4510451).
AB209765 - Homo sapiens mRNA for methyl-CpG binding domain protein 1 isoform PCM1 variant protein.
AK291519 - Homo sapiens cDNA FLJ75178 complete cds, highly similar to Homo sapiens methyl-CpG binding protein splice variant 1 (MBD1) mRNA.
Y10746 - H.sapiens mRNA for protein containing MBD 1.
AK225948 - Homo sapiens mRNA for Splice isoform 6 of Q9UIS9 variant, clone: FCC115E03.
AJ564845 - Homo sapiens mRNA for methyl-CpG binding domain protein 1, splice form 6 (MBD1 gene).
AK225889 - Homo sapiens mRNA for methyl-CpG binding domain protein 1 isoform 1 variant, clone: FCC121D05.
BC033242 - Homo sapiens methyl-CpG binding domain protein 1, mRNA (cDNA clone MGC:45928 IMAGE:5432943), complete cds.
JD181915 - Sequence 162939 from Patent EP1572962.
JD273096 - Sequence 254120 from Patent EP1572962.
JD559517 - Sequence 540541 from Patent EP1572962.
JD504872 - Sequence 485896 from Patent EP1572962.
JD511738 - Sequence 492762 from Patent EP1572962.
JD398286 - Sequence 379310 from Patent EP1572962.
JD127206 - Sequence 108230 from Patent EP1572962.
JD039480 - Sequence 20504 from Patent EP1572962.
JD267623 - Sequence 248647 from Patent EP1572962.
JD540513 - Sequence 521537 from Patent EP1572962.
AK300759 - Homo sapiens cDNA FLJ55386 complete cds, highly similar to Homo sapiens methyl-CpG binding domain protein 1 (MBD1), transcript variant 4, mRNA.
JD437094 - Sequence 418118 from Patent EP1572962.
AF078831 - Homo sapiens methyl-CpG binding protein splice variant 2 (MBD1) mRNA, complete cds.
AK295401 - Homo sapiens cDNA FLJ55972 complete cds, highly similar to Methyl-CpG-binding domain protein 1.
JD170482 - Sequence 151506 from Patent EP1572962.
JD475052 - Sequence 456076 from Patent EP1572962.
AK302004 - Homo sapiens cDNA FLJ60940 complete cds, highly similar to Methyl-CpG-binding domain protein 1.
AF078830 - Homo sapiens methyl-CpG binding protein splice variant 1 (MBD1) mRNA, complete cds.
AF078832 - Homo sapiens methyl-CpG binding protein splice variant 3 (MBD1) mRNA, complete cds.
AF078833 - Homo sapiens methyl-CpG binding protein splice variant 4 (MBD1) mRNA, complete cds.
EF488685 - Homo sapiens methyl-CpG binding domain protein 1 variant 8 (MBD1) mRNA, complete cds, alternatively spliced.
AB527669 - Synthetic construct DNA, clone: pF1KB6174, Homo sapiens MBD1 gene for methyl-CpG binding domain protein 1, without stop codon, in Flexi system.
BC012487 - Homo sapiens methyl-CpG binding domain protein 1, mRNA (cDNA clone IMAGE:4509171), **** WARNING: chimeric clone ****.
AF072241 - Homo sapiens methyl-CpG binding protein MBD1 (MBD1) mRNA, partial cds.
JD145272 - Sequence 126296 from Patent EP1572962.
JD239942 - Sequence 220966 from Patent EP1572962.
JD045606 - Sequence 26630 from Patent EP1572962.
JD129573 - Sequence 110597 from Patent EP1572962.
JD476172 - Sequence 457196 from Patent EP1572962.
JD142376 - Sequence 123400 from Patent EP1572962.
JD462540 - Sequence 443564 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A4UTZ0, B4DXJ5, CXXC3, E9PEC5, MBD1_HUMAN, NM_001204136, NP_001191065, O15248, O95241, PCM1, Q7Z7B5, Q8N4W4, Q9UIS9, Q9UNZ6, Q9UNZ7, Q9UNZ8, Q9UNZ9
UCSC ID: uc002lem.4
RefSeq Accession: NM_001204136
Protein: Q9UIS9 (aka MBD1_HUMAN)
CCDS: CCDS59320.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001204136.1
exon count: 16CDS single in 3' UTR: no RNA size: 3207
ORF size: 1968CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4026.00frame shift in genome: no % Coverage: 99.41
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.