Human Gene DNMT3L (ENST00000270172.7) from GENCODE V44
  Description: Homo sapiens DNA methyltransferase 3 like (DNMT3L), transcript variant 1, mRNA. (from RefSeq NM_013369)
RefSeq Summary (NM_013369): 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].
Gencode Transcript: ENST00000270172.7
Gencode Gene: ENSG00000142182.9
Transcript (Including UTRs)
   Position: hg38 chr21:44,246,339-44,262,216 Size: 15,878 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg38 chr21:44,246,397-44,261,259 Size: 14,863 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:44,246,339-44,262,216)mRNA (may differ from genome)Protein (387 aa)
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HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DNM3L_HUMAN
DESCRIPTION: RecName: Full=DNA (cytosine-5)-methyltransferase 3-like;
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.
SUBUNIT: Homodimer. Heterotetramer composed of 1 DNMT3A homodimer and 2 DNMT3L subunits (DNMT3L-DNMT3A-DNMT3A-DNMT3L). Interacts with histone H3 (via N-terminus).
INTERACTION: Q13547:HDAC1; NbExp=3; IntAct=EBI-740967, EBI-301834;
SUBCELLULAR LOCATION: Nucleus (Probable).
TISSUE SPECIFICITY: Expressed at low levels in several tissues including testis, ovary, and thymus.
MISCELLANEOUS: Interaction with histone H3 is strongly inhibited by methylation at lysine 4 (H3K4me).
SIMILARITY: Belongs to the C5-methyltransferase family.
SIMILARITY: Contains 1 ADD domain.
SIMILARITY: Contains 1 GATA-type zinc finger.
SIMILARITY: Contains 1 PHD-type zinc finger.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: DNMT3L
Diseases sorted by gene-association score: testicular spermatocytic seminoma (17), testis seminoma (16), testicular malignant germ cell cancer (11), alpha thalassemia-x-linked intellectual disability syndrome (7), conjunctival squamous cell carcinoma (6), immunodeficiency-centromeric instability-facial anomalies syndrome (5), diabetes mellitus, transient neonatal, 1 (4), thalassemias, alpha- (1)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.75 RPKM in Kidney - Cortex
Total median expression: 2.40 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 -138.50484-0.286 Picture PostScript Text
3' UTR -7.3058-0.126 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
IPR025766 - ADD
IPR011011 - Znf_FYVE_PHD
IPR013083 - Znf_RING/FYVE/PHD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2PV0 - X-ray MuPIT 2PVC - X-ray MuPIT 2QRV - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9UJW3
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0008047 enzyme activator activity
GO:0019899 enzyme binding
GO:0030234 enzyme regulator activity
GO:0046872 metal ion binding

Biological Process:
GO:0006306 DNA methylation
GO:0006349 regulation of gene expression by genetic imprinting
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007141 male meiosis I
GO:0007283 spermatogenesis
GO:0030154 cell differentiation
GO:0032776 DNA methylation on cytosine
GO:0043046 DNA methylation involved in gamete generation
GO:0043085 positive regulation of catalytic activity
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048863 stem cell differentiation
GO:0050790 regulation of catalytic activity
GO:1905642 negative regulation of DNA methylation
GO:1905643 positive regulation of DNA methylation

Cellular Component:
GO:0005634 nucleus
GO:0005829 cytosol
GO:0035098 ESC/E(Z) complex


-  Descriptions from all associated GenBank mRNAs
  AF194032 - Homo sapiens cytosine-5-methyltransferase 3-like protein (DNMT3L) mRNA, complete cds.
BC002560 - Homo sapiens DNA (cytosine-5-)-methyltransferase 3-like, mRNA (cDNA clone MGC:1090 IMAGE:3138514), complete cds.
JD435290 - Sequence 416314 from Patent EP1572962.
DQ892177 - Synthetic construct clone IMAGE:100004807; FLH183719.01X; RZPDo839F10142D DNA (cytosine-5-)-methyltransferase 3-like (DNMT3L) gene, encodes complete protein.
DQ895372 - Synthetic construct Homo sapiens clone IMAGE:100009832; FLH183715.01L; RZPDo839F10141D DNA (cytosine-5-)-methyltransferase 3-like (DNMT3L) gene, encodes complete protein.
AB528324 - Synthetic construct DNA, clone: pF1KB6520, Homo sapiens DNMT3L gene for DNA (cytosine-5-)-methyltransferase 3-like, without stop codon, in Flexi system.
JD320676 - Sequence 301700 from Patent EP1572962.
JD318919 - Sequence 299943 from Patent EP1572962.
JD423138 - Sequence 404162 from Patent EP1572962.
JD399902 - Sequence 380926 from Patent EP1572962.
JD392034 - Sequence 373058 from Patent EP1572962.
JD415981 - Sequence 397005 from Patent EP1572962.
JD191211 - Sequence 172235 from Patent EP1572962.
JD381518 - Sequence 362542 from Patent EP1572962.
JD111704 - Sequence 92728 from Patent EP1572962.
JD386035 - Sequence 367059 from Patent EP1572962.
JD324743 - Sequence 305767 from Patent EP1572962.
JD115898 - Sequence 96922 from Patent EP1572962.
JD386602 - Sequence 367626 from Patent EP1572962.
JD122610 - Sequence 103634 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00270 - Cysteine and methionine metabolism
hsa01100 - Metabolic pathways

Reactome (by CSHL, EBI, and GO)

Protein Q9UJW3 (Reactome details) participates in the following event(s):

R-HSA-5334164 DNMT3B:DNMT3L binds chromatin
R-HSA-5334179 DNMT3A:DNMT3L binds chromatin
R-HSA-5334097 DNMT3B:DNMT3L methylates cytosine in DNA
R-HSA-5334152 DNMT3A:DNMT3L methylates cytosine in DNA
R-HSA-5334118 DNA methylation
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: DNM3L_HUMAN, E9PB42, ENST00000270172.1, ENST00000270172.2, ENST00000270172.3, ENST00000270172.4, ENST00000270172.5, ENST00000270172.6, NM_013369, Q9BUJ4, Q9UJW3, uc002zeh.1, uc002zeh.2
UCSC ID: ENST00000270172.7
RefSeq Accession: NM_013369
Protein: Q9UJW3 (aka DNM3L_HUMAN or DM3L_HUMAN)
CCDS: CCDS13705.1, CCDS46650.1

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