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DNMT3L DNA methyltransferase 3 like [ Homo sapiens (human) ]

Gene ID: 29947, updated on 10-Dec-2019

Summary

Official Symbol
DNMT3Lprovided by HGNC
Official Full Name
DNA methyltransferase 3 likeprovided by HGNC
Primary source
HGNC:HGNC:2980
See related
Ensembl:ENSG00000142182 MIM:606588
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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]
Expression
Biased expression in liver (RPKM 1.3), kidney (RPKM 1.0) and 3 other tissues See more
Orthologs

Genomic context

See DNMT3L in Genome Data Viewer
Location:
21q22.3
Exon count:
12
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 21 NC_000021.9 (44246339..44261897, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (45666222..45682099, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107983952 Neighboring gene uncharacterized LOC102725065 Neighboring gene inducible T cell costimulator ligand Neighboring gene DNMT3L antisense RNA 1 Neighboring gene autoimmune regulator Neighboring gene phosphofructokinase, liver type

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from BioSystems

  • DNA methylation, organism-specific biosystem (from REACTOME)
    DNA methylation, organism-specific biosystemMethylation of cytosine is catalyzed by a family of DNA methyltransferases (DNMTs): DNMT1, DNMT3A, and DNMT3B transfer methyl groups from S-adenosylmethionine to cytosine, producing 5-methylcytosine ...
  • Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
    Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Preimplantation Embryo, organism-specific biosystem (from WikiPathways)
    Preimplantation Embryo, organism-specific biosystemThe source of this pathway is RNA-Seq data from single-cell pre-implantation embryos (Supplemental Table 1): http://www.nature.com/nsmb/journal/v20/n9/full/nsmb.2660.html Analysis options for runnin...
  • Trans-sulfuration and one carbon metabolism, organism-specific biosystem (from WikiPathways)
    Trans-sulfuration and one carbon metabolism, organism-specific biosystem
    Trans-sulfuration and one carbon metabolism

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Clone Names

  • MGC1090

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enzyme activator activity IDA
Inferred from Direct Assay
more info
PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
DNA methylation NAS
Non-traceable Author Statement
more info
PubMed 
DNA methylation involved in gamete generation ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA methylation on cytosine ISS
Inferred from Sequence or Structural Similarity
more info
 
male meiosis I ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of DNA methylation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of DNA methylation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of catalytic activity IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression by genetic imprinting NAS
Non-traceable Author Statement
more info
PubMed 
spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
spermatogenesis NAS
Non-traceable Author Statement
more info
PubMed 
stem cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
colocalizes_with ESC/E(Z) complex ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol HDA PubMed 
nucleus HDA PubMed 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
DNA (cytosine-5)-methyltransferase 3-like
Names
DNA (cytosine-5-)-methyltransferase 3-like
cytosine-5-methyltransferase 3-like protein
human cytosine-5-methyltransferase 3-like protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_013369.4NP_037501.2  DNA (cytosine-5)-methyltransferase 3-like isoform 1

    See identical proteins and their annotated locations for NP_037501.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AF194032, BC002560, BQ028660
    Consensus CDS
    CCDS13705.1
    UniProtKB/Swiss-Prot
    Q9UJW3
    Related
    ENSP00000270172.3, ENST00000270172.7
    Conserved Domains (1) summary
    cl22851
    Location:47169
    PHD_SF; PHD finger superfamily
  2. NM_175867.3NP_787063.1  DNA (cytosine-5)-methyltransferase 3-like isoform 2

    See identical proteins and their annotated locations for NP_787063.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site at the 3' terminal exon compared to variant 1, which results in an isoform (2) that is 1 aa shorter than isoform 1.
    Source sequence(s)
    AF194032, BC002560, BQ028660
    Consensus CDS
    CCDS46650.1
    UniProtKB/Swiss-Prot
    Q9UJW3
    Related
    ENSP00000486001.1, ENST00000628202.2
    Conserved Domains (1) summary
    cl22851
    Location:47169
    PHD_SF; PHD finger superfamily

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p13 Primary Assembly

    Range
    44246339..44261897 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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