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MBD3L1 Gene

protein-coding   GIFtS: 44
GCID: GC19P008953

Methyl-CpG Binding Domain Protein 3-Like 1

(Previous name: methyl-CpG binding domain protein 3-like)
(Previous symbol: MBD3L)
  Search for MBD3L1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Methyl-CpG Binding Domain Protein 3-Like 11 2
MBD3L1 2 3
MBD3-Like Protein 12 3
Methyl-CpG Binding Domain Protein 3-Like1
Methyl-CpG-Binding Domain Protein 3-Like 12

External Ids:    HGNC: 157741   Entrez Gene: 855092   Ensembl: ENSG000001709487   OMIM: 6079635   UniProtKB: Q8WWY63   

Export aliases for MBD3L1 gene to outside databases

Previous GC identifers: GC19U900020 GC19P008798 GC19P008814 GC19P008530


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for MBD3L1 Gene:
This gene encodes a protein that is related to methyl-CpG-binding proteins but lacks the methyl-CpG binding
domain. The protein is localized to discrete areas in the nucleus, and expression appears to be restricted to
round spermatids, suggesting that the protein plays a role in the postmeiotic stages of male germ cell
development. (provided by RefSeq, Jul 2008)

GeneCards Summary for MBD3L1 Gene:
MBD3L1 (methyl-CpG binding domain protein 3-like 1) is a protein-coding gene. An important paralog of this gene is MBD3L4.

UniProtKB/Swiss-Prot: MB3L1_HUMAN, Q8WWY6
Function: Transcriptional repressor




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000019.10  NC_018930.2  NT_011295.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the MBD3L1 gene promoter:
         ISGF-3   AML1a   IRF-1   STAT5A   LCR-F1   Arnt   GATA-1   RORalpha2   RORalpha1   HOXA5   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidMBD3L1 promoter sequence
   Search Chromatin IP Primers for MBD3L1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat MBD3L1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19p13.2   Ensembl cytogenetic band:  19p13.2   HGNC cytogenetic band: 19p13.2

MBD3L1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
MBD3L1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P008953:  view genomic region     (about GC identifiers)

Start:
8,943,074 bp from pter      End:
8,954,016 bp from pter
Size:
10,943 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: MB3L1_HUMAN, Q8WWY6 (See protein sequence)
Recommended Name: Methyl-CpG-binding domain protein 3-like 1  
Size: 194 amino acids; 21616 Da
Miscellaneous: Does not bind methylated DNA
Miscellaneous: The MBD3L proteins are encoded by strongly repeated regions of the 19p13 chromosome. The exact
number of functional copies is unclear, and some of them may represent pseudogenes
Secondary accessions: B5BUM6 Q2M291

Explore the universe of human proteins at neXtProt for MBD3L1: NX_Q8WWY6

Explore proteomics data for MBD3L1 at MOPED


See MBD3L1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_660209.2  
ENSEMBL proteins: 
 ENSP00000471575   ENSP00000304198  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR025884 MeCpG-bd_2/3_C_dom

Graphical View of Domain Structure for InterPro Entry Q8WWY6

ProtoNet protein and cluster: Q8WWY6

UniProtKB/Swiss-Prot: MB3L1_HUMAN, Q8WWY6
Domain: The N-terminal half of the protein mediates transcription repression
Similarity: Belongs to the MBD3L family


MBD3L1 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: MB3L1_HUMAN, Q8WWY6
Function: Transcriptional repressor

Phenotypes:
     1 GenomeRNAi human phenotype for MBD3L1:

 Increased HPV18 LCR reporter a 

     1 MGI mutant phenotype (inferred from 1 allele(MGI details for Mbd3l1):
 normal 

MBD3L1 for phenotypes           About GeneDecksing

Animal Models:
     MGI mouse knock-out Mbd3l1tm1Gpp for MBD3L1

   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for MBD3L1
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   genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for MBD3L1
   genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for MBD3L1

miRNA
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hsa-miR-518a-5p
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Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat MBD3L1

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GenScript: all cDNA clones in your preferred vector: MBD3L1 (NM_145208)
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat MBD3L1

Cell Line
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MBD3L1


(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
MB3L1_HUMAN, Q8WWY6: Nucleus. Note=Nuclear, in large foci
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus5
cytosol3
plasma membrane3
extracellular1
mitochondrion1

Gene Ontology (GO): 4 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IDA--
GO:0005730NOT nucleolus IDA--
GO:0005737cytoplasm IDA--
GO:0005886plasma membrane IDA--

MBD3L1 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for MBD3L1
Interactions:

    GeneGlobe Interaction Network for MBD3L1

STRING Interaction Network Preview (showing 5 interactants - click image to see 11)

Selected Interacting proteins for MBD3L1 (Q8WWY63 ENSP000003041984) via UniProtKB, MINT, STRING, and/or I2D (see all 11)
InteractantInteraction Details
GeneCardExternal ID(s)
MBD2Q9UBB53, ENSP000002564294I2D: score=2 STRING: ENSP00000256429
MBD3O959833, ENSP000001568254I2D: score=2 STRING: ENSP00000156825
CHD3Q128733, ENSP000003697164I2D: score=1 STRING: ENSP00000369716
MTA1Q133303, ENSP000003336334I2D: score=1 STRING: ENSP00000333633
MTA2O947763, ENSP000002788234I2D: score=1 STRING: ENSP00000278823
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Gene Ontology (GO): 2 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006351transcription, DNA-templated IEA--
GO:0006355regulation of transcription, DNA-templated IEA--

MBD3L1 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for MBD3L1 (MB3L1)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for MBD3L1 gene: 
NM_145208.2  

Unigene Cluster for MBD3L1:

Methyl-CpG binding domain protein 3-like 1
Hs.133912  [show with all ESTs]
Unigene Representative Sequence: BC112064
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000595891 ENST00000305625(uc002mko.2)
miRNA
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hsa-miR-518a-5p
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Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat MBD3L1
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GenScript: all cDNA clones in your preferred vector: MBD3L1 (NM_145208)
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Primer
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  QuantiTect SYBR Green Assays in human, mouse, rat MBD3L1
  QuantiFast Probe-based Assays in human, mouse, rat MBD3L1

Additional mRNA sequence: 

AB451462.1 AY038022.1 BC112058.1 BC112064.1 

2 DOTS entries:

DT.75144810  DT.121499601 

4 AceView cDNA sequences:

NM_145208 AY038022 AI073495 AW263178 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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MBD3L1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ATTTATTTTA
MBD3L1 Expression
About this image

MBD3L1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

MBD3L1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.133912

UniProtKB/Swiss-Prot: MB3L1_HUMAN, Q8WWY6
Tissue specificity: Highly expressed in testis. Detected at low levels in pancreas. Not detected in the other
tissues tested

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MBD3L1

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals.

Orthologs for MBD3L1 gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Mbd3l11 , 5 methyl-CpG binding domain protein 3-like 11, 5 73.74(n)1
64.8(a)1
  9 (7.06 cM)5
735031  NM_028557.21  NP_082833.11 
 184783955 
chicken
(Gallus gallus)
Aves MBD36
Gallus gallus methyl-CpG binding domain protein 3 ...
38(a)
1 → many
28(2378593-2393466)
zebrafish
(Danio rerio)
Actinopterygii mbd3b6
mbd3a6
methyl-CpG binding domain protein 3a
33(a)
30(a)
many ↔ many
many ↔ many
22(20610857-20627983) ENSDARG00000042029
2(57737888-57762598) ENSDARG00000061774
fruit fly
(Drosophila melanogaster)
Insecta MBD-like6
MBD-like
14(a)
1 → many
3R(5385487-5387255)


ENSEMBL Gene Tree for MBD3L1 (if available)
TreeFam Gene Tree for MBD3L1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for MBD3L1 gene
MBD3L42  MBD22  MBD3L32  MBD32  MBD3L52  MBD3L22  
7 SIMAP similar genes for MBD3L1 using alignment to 1 protein entry:     MB3L1_HUMAN:
DKFZp586O0821    MBD3    NY-CO-41    MBD3L2    MBD3L3    MBD3L4
MBD3L5

MBD3L1 for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for MBD3L1 (see all 101)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1833975351,2
--8951269(+) AGCCAC/GCATGC 1 -- us2k10--------
rs1473662831,2
C--8951344(+) TATTTG/TCAGAT 1 -- us2k10--------
rs1381366051,2
--8951502(+) TTCTAC/TGCATG 1 -- us2k10--------
rs1174546471,2
C,F--8951509(+) CATGAT/CGGATT 1 -- us2k11Minor allele frequency- C:0.03EA 120
rs1435956201,2
--8951571(+) TGTCAC/TGTGAT 1 -- us2k10--------
rs1471892141,2
--8951575(+) ACGTGA/CTTCTT 1 -- us2k10--------
rs1880454851,2
--8951617(+) CATGGC/TGTCAC 1 -- us2k10--------
rs1396480671,2
--8951643(+) TCCAAA/GTTTGA 1 -- us2k10--------
rs1164429031,2
C,F--8951678(+) GTGGTA/GAGGAA 1 -- us2k11Minor allele frequency- G:0.07WA 118
rs592991551,2
C--8951721(+) TTTTTTT/-AGACA 1 -- us2k11Minor allele frequency- -:0.50NA 2

HapMap Linkage Disequilibrium report for MBD3L1 (8943074 - 8954016 bp)

Structural Variations
     Database of Genomic Variants (DGV) 6 variations for MBD3L1:    About this table    
Variant IDTypeSubtypePubMed ID
dgv48n68CNV Gain17160897
nsv911019CNV Gain21882294
nsv428362CNV Gain+Loss18775914
dgv1056e1CNV Complex17122850
nsv469648CNV Complex16826518
nsv483078CNV Complex15286789

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing MBD3L1
DNA2.0 Custom Variant and Variant Library Synthesis for MBD3L1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 607963    OMIM disorders: --


MBD3L1 for disorders           About GeneDecksing


Export disorders for MBD3L1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for MBD3L1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with MBD3L1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. MBD3L1 and MBD3L2, two new proteins homologous to the methyl-CpG- binding proteins MBD2 and MBD3: characterization of MBD3L1 as a testis-specific transcriptional repressor. (PubMed id 12504854)1, 2, 3, 9 Jiang C.-L.... Pfeifer G.P. (Genomics 2002)
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  3. Unique features of the anti-parallel, heterodimeric coiled-coil interaction between methyl-cytosine binding domain 2 (MBD2) homologues and GATA zinc finger domain containing 2A (GATAD2A/p66I+). (PubMed id 23239876)1 Walavalkar N.M....Williams D.C. (J. Biol. Chem. 2013)
  4. Human protein factory for converting the transcriptome into an in vitro-expressed proteome. (PubMed id 19054851)2 Goshima N.... Nomura N. (Nat. Methods 2008)
  5. MBD3L1 is a transcriptional repressor that interacts with methyl-CpG- binding protein 2 (MBD2) and components of the NuRD complex. (PubMed id 15456747)1 Jiang C.-L.... Pfeifer G.P. (J. Biol. Chem. 2004)
  6. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)2 Grimwood J.... Lucas S.M. (Nature 2004)
  7. The metastasis-associated proteins 1 and 2 form distinct protein complexes with histone deacetylase activity. (PubMed id 12920132)1 Yao Y.-L. and Yang W.-M. (J. Biol. Chem. 2003)
  8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  9. Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. (PubMed id 16025148)9 Rauch T. and Pfeifer G.P. ( a journal of technical methods and pathology 2005)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 85509 HGNC: 15774 AceView: MBD3L1 Ensembl:ENSG00000170948 euGenes: HUgn85509
ECgene: MBD3L1 H-InvDB: MBD3L1

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for MBD3L1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for MBD3L1 gene:
Search GeneIP for patents involving MBD3L1

GeneCards and IP:
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(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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