FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\Hen1
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General Information
Symbol
Dmel\Hen1
Species
D. melanogaster
Name
Hen1 methyltransferase
Annotation Symbol
CG12367
Feature Type
protein_coding_gene
FlyBase ID
FBgn0033686
Gene Model Status
Current
Stock Availability
11 publicly available
Enzyme Name (EC)
small RNA 2'-O-methyltransferase (2.1.1.386)
Gene Summary
Hen1 methyltransferase (Hen1) encodes a methyltransferase that methylates the terminal 2' hydroxyl group of small interfering RNAs and Piwi-interacting RNAs. It probably protects the 3' ends of small RNAs from degradation. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)
All Summaries
Also Known As

Pimet, DmHen1, piRNA methyltransferase

Key Links
Genomic Location
Cytogenetic map
48E2-48E3
Sequence location
Recombination map
2-66
RefSeq locus
NT_033778 REGION:12145710..12152752
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (11 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables small RNA 2'-O-methyltransferase activity
inferred from direct assay
(Horwich et al., 2007, Saito et al., 2007, Kimbrell and Beutler, 2001)
inferred from mutant phenotype
(Wang et al., 2016)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables O-methyltransferase activity
inferred from electronic annotation with InterPro:IPR026610
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN000483941
(GO Reference Genome Project, 2011-)
enables RNA methyltransferase activity
inferred from biological aspect of ancestor with PANTHER:PTN000483941
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR026610
(InterPro Project Members, 2004-)
Biological Process (6 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
involved_in piRNA processing
inferred from direct assay
(Horwich et al., 2007)
inferred from direct assay
(Saito et al., 2007)
inferred from mutant phenotype
(Wang et al., 2016)
involved_in RNA methylation
inferred from direct assay
(Horwich et al., 2007, Kimbrell and Beutler, 2001)
inferred from mutant phenotype
(Horwich et al., 2007)
involved_in siRNA processing
inferred from direct assay
(Horwich et al., 2007)
involved_in transposable element silencing
inferred from mutant phenotype
(Wang et al., 2016)
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
involved_in piRNA processing
inferred from biological aspect of ancestor with PANTHER:PTN000483941
(GO Reference Genome Project, 2011-)
involved_in primary piRNA processing
traceable author statement
(Yang and Pillai, 2014)
involved_in RNA methylation
inferred from electronic annotation with InterPro:IPR026610
(InterPro Project Members, 2004-)
involved_in secondary piRNA processing
traceable author statement
(Yang and Pillai, 2014)
involved_in siRNA processing
inferred from biological aspect of ancestor with PANTHER:PTN000483941
(GO Reference Genome Project, 2011-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
is_active_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000483941
(GO Reference Genome Project, 2011-)
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000483941
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the methyltransferase superfamily. HEN1 family. (Q7K175)
Protein Signatures (InterPro)
Catalytic Activity (EC/Rhea)
small RNA 2'-O-methyltransferase activity
small RNA 3'-end nucleotide + S-adenosyl-L-methionine = small RNA 3'-end 2'-O-methylnucleotide + S-adenosyl-L-homocysteine + H(+) (2.1.1.386)
RHEA 37887:
Summaries
Gene Snapshot
Hen1 methyltransferase (Hen1) encodes a methyltransferase that methylates the terminal 2' hydroxyl group of small interfering RNAs and Piwi-interacting RNAs. It probably protects the 3' ends of small RNAs from degradation. [Date last reviewed: 2019-03-07]
Gene Group (FlyBase)
UNCLASSIFIED RNA METHYLTRANSFERASES -
This group comprises RNA methyltransferases that do not classify under other groups in FlyBase.
Protein Function (UniProtKB)
Methyltransferase that adds a 2'-O-methyl group at the 3'-end of selected small RNAs. Mediates 2'-O-methylation of piRNAs, single-stranded siRNAs and long hairpin RNA genes (hpRNAs). Methylation protects the 3'-end of small RNAs from tailing and trimming and could constitute a recognition signal for appropriate argonaute machineries.
(UniProt, Q7K175)
Summary (Interactive Fly)

RNA methyltransferase - carries out methylation of small interfering RNAs, the final step in assembly of RISC occurring after the Argonaute-bound siRNA duplex is converted to single-stranded RNA

Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Hen1 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q7K175)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.46

Gene model reviewed during 5.55

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Hen1-RA
FBtr0087984
NM_136888
1573
391
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
Hen1-PA
FBpp0087092
45.6
391
4.44
Q7K175
NP_610732
AAF58575
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Hen1 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

0.99

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 4 -- 6
organism
(Fisher et al., 2012)
RT-PCR
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage | female
ovary
(Horwich et al., 2007)
adult stage | male
testis
(Horwich et al., 2007)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Hen1 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 11 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Hen1
Transgenic constructs containing regulatory region of Hen1
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 4 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
fertile
Phenotype manifest in
Allele
embryonic/larval hemocyte | third instar larval stage, with Scer\GAL4Pxn.PS
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (1)
Hsap\HENMT1
13 of 14
Yes
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (1)
Rnor\Henmt1
10 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Henmt1
11 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\henmt1
10 of 13
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\henmt1
13 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\henn-1
7 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (2)
Agam\AgaP_AGAP005646
7 of 12
Yes
Yes
Agam\AgaP_AGAP010537
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (2)
Atha\HEN1
7 of 13
Yes
Yes
Atha\AT4G20920
4 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\SPBC336.05c
9 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Hen1. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    HENMT1; HEN methyltransferase 1
    13 of 14
    612178
        Functional Complementation Data
        Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
        Interactions
        Summary of Physical Interactions
        Summary of Genetic Interactions
        Interaction Browsers
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        FlyBase
        External Links
        External Data
        Linkouts
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        2R
        Recombination map
        2-66
        Cytogenetic map
        48E2-48E3
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        48E2-48E3
        Limits computationally determined from genome sequence between P{lacW}jebk05644 and P{PZ}SmD302833
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        2-66

        (FlyBase, 2016)

        2-67.4

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (11)
        Genomic Clones (13)
         

        Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

        cDNA Clones (20)
         

        Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

        cDNA clones, fully sequenced
        BDGP DGC clones
        Other clones
        Drosophila Genomics Resource Center cDNA clones

        For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

        cDNA Clones, End Sequenced (ESTs)
        BDGP DGC clones
        Other clones
        RNAi and Array Information
        Linkouts
        DRSC - Results frm RNAi screens
        Antibody Information
        Laboratory Generated Antibodies
         

        monoclonal

        (Alberti et al., 2018)
        Commercially Available Antibodies
         
        Cell Line Information
        Publicly Available Cell Lines
         
          Other Stable Cell Lines
           
          Other Comments

          Production of mature siRNAs from endogenous long hairpin RNA genes is a hybrid mechanism that combines canonical RNA interference factors (Dcr-2, Hen1 and AGO2) and a canonical microRNA factor loqs.

          (Okamura et al., 2008)

          hen1 methylates the 3' termini of siRNAs and piRNAs. hen1 acts on single strands and not duplexes.

          (Horwich et al., 2007)

          hen1 is required for piRNA-directed silencing of transposable elements in the germline.

          (Horwich et al., 2007)

          Pimet shows single-stranded small RNA methylation activity in vitro.

          (Saito et al., 2007)
          Relationship to Other Genes
          Source for database merge of
          Additional comments
          Nomenclature History
          Source for database identify of

          Source for identity of: hen1 CG12367

          (Horwich et al., 2007)

          Source for identity of: Pimet hen1

          (Saito et al., 2007)

          Source for identity of: Hen1 Pimet

          (FlyBase, 2009-)
          Nomenclature comments

          Renamed from 'Pimet/piRNA methyltransferase' to 'Hen1' because: i) the former is misleading because the gene product methylates both siRNAs and piRNAs in flies (see FBrf0202202); and ii) PubMed searches show that the wider research community clearly favours 'Hen1' over 'Pimet'.

          (FlyBase, 2009-)
          Etymology
          Synonyms and Secondary IDs (13)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 35 )
          Sequence Crossreferences
          NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
          GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
          GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
          RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
          UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
          UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
          Other crossreferences
          AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
          BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
          DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
          EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
          FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
          FlyMine - An integrated database for Drosophila genomics
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          MARRVEL_MODEL - MARRVEL (model organism gene)
          Linkouts
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
          Flygut - An atlas of the Drosophila adult midgut
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
          MIST (protein-protein) - An integrated Molecular Interaction Database
          References (80)