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Aliases for DNMT3L Gene

Aliases for DNMT3L Gene

  • DNA (Cytosine-5-)-Methyltransferase 3-Like 2 3 5
  • Human Cytosine-5-Methyltransferase 3-Like Protein 2
  • Cytosine-5-Methyltransferase 3-Like Protein 2

External Ids for DNMT3L Gene

Previous GeneCards Identifiers for DNMT3L Gene

  • GC21M042176
  • GC21M042259
  • GC21M044522
  • GC21M044490
  • GC21M045666
  • GC21M031037

Summaries for DNMT3L Gene

Entrez Gene Summary for DNMT3L Gene

  • CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a nuclear protein with similarity to DNA methyltransferases, but is not thought to function as a DNA methyltransferase as it does not contain the amino acid residues necessary for methyltransferase activity. However, it does stimulate de novo methylation by DNA cytosine methyltransferase 3 alpha and is thought to be required for the establishment of maternal genomic imprints. This protein also mediates transcriptional repression through interaction with histone deacetylase 1. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012]

GeneCards Summary for DNMT3L Gene

DNMT3L (DNA (Cytosine-5-)-Methyltransferase 3-Like) is a Protein Coding gene. Diseases associated with DNMT3L include Testicular Spermatocytic Seminoma and Testis Seminoma. Among its related pathways are Gene Expression and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include enzyme binding and enzyme activator activity. An important paralog of this gene is LOC102724184.

UniProtKB/Swiss-Prot for DNMT3L Gene

  • Catalytically inactive regulatory factor of DNA methyltransferases. It is essential for the function of DNMT3A and DNMT3B. Activates DNMT3A and DNMT3B by binding to their catalytic domain. Accelerates the binding of DNA and AdoMet to the methyltransferases and dissociates from the complex after DNA binding to the methyltransferases. Recognizes unmethylated histone H3 lysine 4 (H3K4) and induces de novo DNA methylation by recruitment or activation of DNMT3.

Gene Wiki entry for DNMT3L Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DNMT3L Gene

Genomics for DNMT3L Gene

Regulatory Elements for DNMT3L Gene

Enhancers for DNMT3L Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around DNMT3L on UCSC Golden Path with GeneCards custom track

Genomic Location for DNMT3L Gene

Chromosome:
21
Start:
44,246,339 bp from pter
End:
44,267,138 bp from pter
Size:
20,800 bases
Orientation:
Minus strand

Genomic View for DNMT3L Gene

Genes around DNMT3L on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DNMT3L Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DNMT3L Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DNMT3L Gene

Proteins for DNMT3L Gene

  • Protein details for DNMT3L Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UJW3-DNM3L_HUMAN
    Recommended name:
    DNA (cytosine-5)-methyltransferase 3-like
    Protein Accession:
    Q9UJW3
    Secondary Accessions:
    • E9PB42
    • Q9BUJ4

    Protein attributes for DNMT3L Gene

    Size:
    386 amino acids
    Molecular mass:
    43583 Da
    Quaternary structure:
    • Homodimer. Heterotetramer composed of 1 DNMT3A homodimer and 2 DNMT3L subunits (DNMT3L-DNMT3A-DNMT3A-DNMT3L). Interacts with histone H3 (via N-terminus).
    Miscellaneous:
    • Interaction with histone H3 is strongly inhibited by methylation at lysine 4 (H3K4me).

    Three dimensional structures from OCA and Proteopedia for DNMT3L Gene

    Alternative splice isoforms for DNMT3L Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DNMT3L Gene

Proteomics data for DNMT3L Gene at MOPED

Post-translational modifications for DNMT3L Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DNMT3L Gene

No data available for DME Specific Peptides for DNMT3L Gene

Domains & Families for DNMT3L Gene

Protein Domains for DNMT3L Gene

Suggested Antigen Peptide Sequences for DNMT3L Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UJW3

UniProtKB/Swiss-Prot:

DNM3L_HUMAN :
  • Contains 1 ADD domain.
  • Contains 1 GATA-type zinc finger.
Domain:
  • Contains 1 ADD domain.
Similarity:
  • Contains 1 GATA-type zinc finger.
  • Contains 1 PHD-type zinc finger.
genes like me logo Genes that share domains with DNMT3L: view

No data available for Gene Families for DNMT3L Gene

Function for DNMT3L Gene

Molecular function for DNMT3L Gene

UniProtKB/Swiss-Prot Function:
Catalytically inactive regulatory factor of DNA methyltransferases. It is essential for the function of DNMT3A and DNMT3B. Activates DNMT3A and DNMT3B by binding to their catalytic domain. Accelerates the binding of DNA and AdoMet to the methyltransferases and dissociates from the complex after DNA binding to the methyltransferases. Recognizes unmethylated histone H3 lysine 4 (H3K4) and induces de novo DNA methylation by recruitment or activation of DNMT3.

Gene Ontology (GO) - Molecular Function for DNMT3L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030234 enzyme regulator activity IEA --
genes like me logo Genes that share ontologies with DNMT3L: view
genes like me logo Genes that share phenotypes with DNMT3L: view

Animal Models for DNMT3L Gene

MGI Knock Outs for DNMT3L:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for DNMT3L Gene

Localization for DNMT3L Gene

Subcellular locations from UniProtKB/Swiss-Prot for DNMT3L Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for DNMT3L Gene COMPARTMENTS Subcellular localization image for DNMT3L gene
Compartment Confidence
cytosol 5
nucleus 5
extracellular 1

No data available for Gene Ontology (GO) - Cellular Components for DNMT3L Gene

Pathways & Interactions for DNMT3L Gene

genes like me logo Genes that share pathways with DNMT3L: view

Pathways by source for DNMT3L Gene

1 BioSystems pathway for DNMT3L Gene

Gene Ontology (GO) - Biological Process for DNMT3L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006306 DNA methylation IEA,NAS 12202768
GO:0006349 regulation of gene expression by genetic imprinting NAS 12202768
GO:0032776 DNA methylation on cytosine TAS --
GO:0043085 positive regulation of catalytic activity IDA 16543361
GO:0050790 regulation of catalytic activity IEA --
genes like me logo Genes that share ontologies with DNMT3L: view

No data available for SIGNOR curated interactions for DNMT3L Gene

Drugs & Compounds for DNMT3L Gene

(5) Drugs for DNMT3L Gene - From: ApexBio, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
S-Adenosylmethionine Approved Nutra 0
Thioguanine Approved Pharma Purine antimetabolite 79
s-adenosylhomocysteine Experimental Pharma 0
Lomeguatrib Pharma MGMT inhibitor 0

(1) Additional Compounds for DNMT3L Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(2) ApexBio Compounds for DNMT3L Gene

Compound Action Cas Number
Lomeguatrib MGMT inhibitor 192441-08-0
Thioguanine Purine antimetabolite 154-42-7
genes like me logo Genes that share compounds with DNMT3L: view

Transcripts for DNMT3L Gene

Unigene Clusters for DNMT3L Gene

DNA (cytosine-5-)-methyltransferase 3-like:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for DNMT3L Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b
SP1:
SP2:

Relevant External Links for DNMT3L Gene

GeneLoc Exon Structure for
DNMT3L
ECgene alternative splicing isoforms for
DNMT3L

Expression for DNMT3L Gene

mRNA expression in normal human tissues for DNMT3L Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for DNMT3L Gene

This gene is overexpressed in Liver (x21.0) and Kidney - Cortex (x20.0).

Protein differential expression in normal tissues from HIPED for DNMT3L Gene

This gene is overexpressed in Plasma (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for DNMT3L Gene



SOURCE GeneReport for Unigene cluster for DNMT3L Gene Hs.592165

mRNA Expression by UniProt/SwissProt for DNMT3L Gene

Q9UJW3-DNM3L_HUMAN
Tissue specificity: Expressed at low levels in several tissues including testis, ovary, and thymus.
genes like me logo Genes that share expression patterns with DNMT3L: view

Protein tissue co-expression partners for DNMT3L Gene

Orthologs for DNMT3L Gene

This gene was present in the common ancestor of chordates.

Orthologs for DNMT3L Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia DNMT3L 35
  • 81.84 (n)
  • 79.47 (a)
DNMT3L 36
  • 70 (a)
OneToOne
dog
(Canis familiaris)
Mammalia DNMT3L 35
  • 80.26 (n)
  • 75.3 (a)
DNMT3L 36
  • 75 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Dnmt3l 35
  • 71.63 (n)
  • 65.16 (a)
Dnmt3l 16
Dnmt3l 36
  • 54 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia DNMT3L 35
  • 99.4 (n)
  • 99.22 (a)
DNMT3L 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Dnmt3l 35
  • 72.37 (n)
  • 66.84 (a)
oppossum
(Monodelphis domestica)
Mammalia DNMT3L 36
  • 58 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DNMT3L 36
  • 39 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.20876 35
zebrafish
(Danio rerio)
Actinopterygii dnmt3 36
  • 9 (a)
ManyToMany
dnmt3b 36
  • 9 (a)
ManyToMany
dnmt5 36
  • 10 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 17 (a)
OneToMany
Species with no ortholog for DNMT3L:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for DNMT3L Gene

ENSEMBL:
Gene Tree for DNMT3L (if available)
TreeFam:
Gene Tree for DNMT3L (if available)

Paralogs for DNMT3L Gene

Paralogs for DNMT3L Gene

(1) SIMAP similar genes for DNMT3L Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with DNMT3L: view

Variants for DNMT3L Gene

Sequence variations from dbSNP and Humsavar for DNMT3L Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type
VAR_051962 -
rs2276247 -- 44,259,207(+) CACAG(C/T)GATGT intron-variant
rs2276248 -- 44,259,375(+) ATGAG(C/T)AGCTG intron-variant
rs4818894 -- 44,265,609(+) TTTTT(G/T)GAGAT intron-variant
rs5844180 -- 44,268,688(+) TTTTT(-/T/TT)GAGAA upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for DNMT3L Gene

Variant ID Type Subtype PubMed ID
esv33817 CNV Loss 17666407
nsv913887 CNV Loss 21882294
nsv913898 CNV Loss 21882294
nsv913902 CNV Loss 21882294
dgv4767n71 CNV Loss 21882294
nsv913906 CNV Loss 21882294
nsv526276 CNV Loss 19592680
nsv913907 CNV Loss 21882294
esv2723638 CNV Deletion 23290073
dgv4768n71 CNV Loss 21882294
dgv4769n71 CNV Loss 21882294
dgv4770n71 CNV Loss 21882294
esv2659125 CNV Deletion 23128226
esv23445 CNV Gain+Loss 19812545

Variation tolerance for DNMT3L Gene

Residual Variation Intolerance Score: 80.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.06; 68.82% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for DNMT3L Gene

Human Gene Mutation Database (HGMD)
DNMT3L

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DNMT3L Gene

Disorders for DNMT3L Gene

MalaCards: The human disease database

(6) MalaCards diseases for DNMT3L Gene - From: DISEASES

Disorder Aliases PubMed IDs
testicular spermatocytic seminoma
  • spermatocytic seminoma
testis seminoma
  • seminoma
testicular malignant germ cell cancer
  • malignant germ cell tumor of testis
choline deficiency disease
  • choline deficiency
diabetes mellitus, transient neonatal, 1
  • diabetes mellitus, transient neonatal
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for DNMT3L

Genetic Association Database (GAD)
DNMT3L
Human Genome Epidemiology (HuGE) Navigator
DNMT3L
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
DNMT3L
genes like me logo Genes that share disorders with DNMT3L: view

No data available for UniProtKB/Swiss-Prot and Genatlas for DNMT3L Gene

Publications for DNMT3L Gene

  1. Isolation and initial characterization of a novel zinc finger gene, DNMT3L, on 21q22.3, related to the cytosine-5-methyltransferase 3 gene family. (PMID: 10857753) Aapola U. … Peterson P. (Genomics 2000) 2 3 4 23 67
  2. DNA methyltransferase 3-like affects promoter methylation of thymine DNA glycosylase independently of DNMT1 and DNMT3B in cancer cells. (PMID: 20428781) Kim H. … Kim T.Y. (Int. J. Oncol. 2010) 3 23
  3. A systematic search for DNA methyltransferase polymorphisms reveals a rare DNMT3L variant associated with subtelomeric hypomethylation. (PMID: 19246518) El-Maarri O. … ChAcdin F. (Hum. Mol. Genet. 2009) 3 23
  4. CG dinucleotide periodicities recognized by the Dnmt3a-Dnmt3L complex are distinctive at retroelements and imprinted domains. (PMID: 19921333) Glass J.L. … Greally J.M. (Mamm. Genome 2009) 3 23
  5. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. (PMID: 17687327) Ooi S.K. … Bestor T.H. (Nature 2007) 3 23

Products for DNMT3L Gene

Sources for DNMT3L Gene

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