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MBD3L4 Gene

protein-coding   GIFtS: 27
GCID: GC19M007037

Methyl-CpG Binding Domain Protein 3-Like 4

  Search for MBD3L4
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 41 2
MBD3-Like Protein 42 3
MBD3-Like 42
Putative Methyl-CpG-Binding Domain Protein 3-Like 42

External Ids:    HGNC: 372061   Entrez Gene: 6536562   Ensembl: ENSG000002057187   UniProtKB: A6NDZ83   

Export aliases for MBD3L4 gene to outside databases

Previous GC identifer: GC19M006990


(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 MBD3L4 Gene:
This gene encodes a member of a family of proteins that are related to methyl-CpG-binding proteins but lack the
methyl-CpG binding domain. There is no definitive support for transcription of this locus, and the transcript
structure is inferred from other family members. (provided by RefSeq, Aug 2009)

GeneCards Summary for MBD3L4 Gene:
MBD3L4 (methyl-CpG binding domain protein 3-like 4) is a protein-coding gene. An important paralog of this gene is MBD2.




(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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Regulatory elements:
   Regulatory transcription factor binding sites in the MBD3L4 gene promoter:
         STAT1   STAT1beta   STAT3   STAT1alpha   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for MBD3L4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat MBD3L4


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

MBD3L4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
MBD3L4 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M007037:  view genomic region     (about GC identifiers)

Start:
7,037,755 bp from pter      End:
7,040,190 bp from pter
Size:
2,436 bases      Orientation:
minus 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: MB3L4_HUMAN, A6NDZ8 (See protein sequence)
Recommended Name: Putative methyl-CpG-binding domain protein 3-like 4  
Size: 208 amino acids; 23121 Da
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
Caution: Could be the product of a pseudogene

Explore the universe of human proteins at neXtProt for MBD3L4: NX_A6NDZ8

Explore proteomics data for MBD3L4 at MOPED


See MBD3L4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001157891.1  
ENSEMBL proteins: 
 ENSP00000370801  

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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 A6NDZ8

ProtoNet protein and cluster: A6NDZ8

UniProtKB/Swiss-Prot: MB3L4_HUMAN, A6NDZ8
Similarity: Belongs to the MBD3L family


Find genes that share domains with MBD3L4           About GenesLikeMe


(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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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(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 COMPARTMENTS: 

CompartmentConfidence
cytosol2
nucleus2
mitochondrion1

(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 MBD3L4
Interactions:

    Search GeneGlobe Interaction Network for MBD3L4

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--

Find genes that share ontologies with MBD3L4           About GenesLikeMe



(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 MBD3L4 (MB3L4)



(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,
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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for MBD3L4 gene: 
NM_001164419.1  

1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000381394(uc021unr.1)
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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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MBD3L4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
MBD3L4 Expression
About this image

MBD3L4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

MBD3L4 Protein Expression
    Custom PCR Arrays for MBD3L4
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In Situ
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(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 MBD3L4 gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Mbd3l21 methyl-CpG binding domain protein 3-like 2 56.91(n)
39.51(a)
  234988  NM_144934.3  NP_659183.3 
chicken
(Gallus gallus)
Aves MBD36
Gallus gallus methyl-CpG binding domain protein 3 ...
25(a)
1 → many
28(2378593-2393466)
zebrafish
(Danio rerio)
Actinopterygii mbd3b6
mbd3a6
methyl-CpG binding domain protein 3a
24(a)
22(a)
many ↔ many
many ↔ many
22(20610857-20627983) ENSDARG00000042029
2(57737888-57762598) ENSDARG00000061774
fruit fly
(Drosophila melanogaster)
Insecta MBD-like6
MBD-like
12(a)
1 → many
3R(5385487-5387255)


ENSEMBL Gene Tree for MBD3L4 (if available)
TreeFam Gene Tree for MBD3L4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for MBD3L4 gene
MBD3L51 2  MBD3L31 2  MBD3L21 2  LOC729458  MBD22  MBD3L12  MBD32  
5 SIMAP similar genes for MBD3L4 using alignment to 1 protein entry:     MB3L4_HUMAN:
MBD3L3    MBD3L5    MBD3L2    MBD3L1    NY-CO-41

Find genes that share paralogs with MBD3L4           About GenesLikeMe



(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 MBD3L4 (see all 17)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs2014181221,2
C--7037333(+) TTAACA/GGCCGG 1 -- ds50010--------
rs2004727521,2
C--7037655(+) AAATCA/GTGGTA 1 -- ds50010--------
rs2014692841,2
C--7037868(+) GACTGA/CGCTTC 1 -- ut310--------
rs1152436091,2
C--7039982(+) TATTAA/CCACCT 1 -- int10--------
rs2010428581,2
C--7041692(+) CTTTGC/GTTTCC 1 -- us2k10--------
rs766997041,2
C--7042087(+) TTCCTT/GTCTTC 1 -- us2k11Minor allele frequency- G:0.00NA 2
rs777346191,2
C--7042092(+) GTCTTC/TCTTTC 1 -- us2k11Minor allele frequency- T:0.50NA 2
rs284210141,2
----7037284(+) GCCACA/GGCGCC 1 -- ds50010--------
rs3769086761,2
----7037634(+) ACAAAA/CAAAAA 1 -- ds50010--------
rs3768080641,2
----7037600(+) CAGAGC/GAGACT 1 -- ds50010--------

HapMap Linkage Disequilibrium report for MBD3L4 (7037755 - 7040190 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for MBD3L4 (see all 12):    About this table    
Variant IDTypeSubtypePubMed ID
nsv821572CNV Duplication20802225
esv2751810CNV Loss17911159
nsv910954CNV Loss21882294
dgv393n27CNV Gain19166990
dgv3708n71CNV Gain21882294
esv2751809CNV Gain17911159
dgv136e55CNV Gain17911159
dgv3707n71CNV Gain21882294
nsv517794CNV Gain+Loss19592680
esv33729CNV Gain+Loss17666407

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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  --

(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 article for MBD3L4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with MBD3L4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)1, 2 Grimwood J.... Lucas S.M. (Nature 2004)

(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: 653656 HGNC: 37206 Ensembl:ENSG00000205718 euGenes: HUgn653656 ECgene: MBD3L4
H-InvDB: MBD3L4

(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 MBD3L4 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 MBD3L4 gene:
Search GeneIP for patents involving MBD3L4

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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The GeneCards human gene database gene index: 1 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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