FB2020_06, released Dec 22, 2020

Gene: Dmel\Lhr

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General Information
Symbol
Dmel\Lhr
Species
D. melanogaster
Name
Lethal hybrid rescue
Annotation Symbol
CG18468
Feature Type
protein_coding_gene
FlyBase ID
FBgn0034217
Gene Model Status
Current
Stock Availability
8 publicly available
Gene Snapshot
Lethal hybrid rescue (Lhr) encodes a protein required to repress transposable element and satellite DNA expression. It also has a gain-of-function phenotype of causing lethality in F1 male hybrids between D. melanogaster and D. simulans. [Date last reviewed: 2019-03-14]
Other Summaries
Also Known As

HP3, mel-Lhr

Key Links
Genomic Location
Cytogenetic map
54B7-54B7
Sequence location
2R:17,431,032..17,432,219 [+]
Recombination map

2-82

RefSeq locus
NT_033778 REGION:17431032..17432219
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
GO Summary Ribbons
Gene Ontology (GO) Annotations (12 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables protein binding
inferred from physical interaction with FLYBASE:Hmr; FB:FBgn0001206
(Satyaki et al., 2014, Thomae et al., 2013)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables DNA binding
inferred from electronic annotation with InterPro:IPR004210
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Biological Process (5 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
involved_in heterochromatin organization involved in chromatin silencing
inferred from mutant phenotype
(Swenson et al., 2016)
involved_in mitotic sister chromatid segregation
inferred from mutant phenotype
(Thomae et al., 2013)
involved_in negative regulation of transposition
inferred from mutant phenotype
(Satyaki et al., 2014)
involved_in regulation of transposition
inferred from mutant phenotype
(Thomae et al., 2013)
involved_in telomere maintenance
inferred from mutant phenotype
(Satyaki et al., 2014)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (5 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
located_in chromocenter
inferred from direct assay
(Greil et al., 2007, Brideau et al., 2006)
located_in chromosome, telomeric region
inferred from direct assay
(Thomae et al., 2013)
located_in chromosome, telomeric repeat region
inferred from direct assay
(Satyaki et al., 2014)
located_in heterochromatin
inferred from direct assay
(Swenson et al., 2016, Maheshwari and Barbash, 2012, Brideau and Barbash, 2011, Brideau et al., 2006)
located_in pericentric heterochromatin
inferred from direct assay
(Satyaki et al., 2014)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
MADF-BESS DOMAIN TRANSCRIPTION REGULATORS -
The MADF-BESS domain transcription regulators include a variety of activators and corepressors and chromatin modifying proteins. BESS domains are often present in combination with MADF domains. The BESS domain mediates protein-protein interactions. (Adapted from FBrf0155780 and FBrf0224045).
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
Lhr: Lethal hybrid rescue
When Drosophila simulans carries Lhr, classes of hybrids between D. simulans and D. melanogaster that do not ordinarily survive are recovered. Crosses of D. melanogaster females by D. simulans males, which ordinarily produce only daughters, produce sons and daughters in a 1:1 ratio. Crosses of D. simulans females to D. melanogaster males, which ordinarily produce only sons, produce 86% sons and 14% daughters. Crosses of C(1)RM - bearing D. melanogaster females to D. simulans males, which normally produce only sons, yield a few daughters when the D. simulans males carry Lhr.
Summary (Interactive Fly)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Lhr 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
Comments on Gene Model

Gene model reviewed during 5.44

Gene model reviewed during 5.50

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Lhr-RA
FBtr0086917
NM_137366
1188
334
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
RefSeq ID
GenBank
Lhr-PA
FBpp0086073
38.6
334
9.90
NP_611210
AAF57867
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\Lhr 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
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
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 | ubiquitous
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 9 -- 10
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 11 -- 12
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 13 -- 16
organism | ubiquitous
(Fisher et al., 2012)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
day 5 of adulthood & male -- day 7 of adulthood & male
spermatozoon
(Wasbrough et al., 2010)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in chromocenter
inferred from direct assay
(Greil et al., 2007, Brideau et al., 2006)
located_in chromosome, telomeric region
inferred from direct assay
(Thomae et al., 2013)
located_in chromosome, telomeric repeat region
inferred from direct assay
(Satyaki et al., 2014)
located_in heterochromatin
inferred from direct assay
(Swenson et al., 2016, Maheshwari and Barbash, 2012, Brideau and Barbash, 2011, Brideau et al., 2006)
located_in pericentric heterochromatin
inferred from direct assay
(Satyaki et al., 2014)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Lhr in GBrowse 2
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
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, and Transgenic Constructs
Classical and Insertion Alleles ( 1 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 15 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Lhr
Transgenic constructs containing regulatory region of Lhr
Deletions and Duplications ( 2 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
Sterility
Allele
female semi-sterile | progressive
female semi-sterile | recessive
Other Phenotypes
Allele
suppressor of variegation, with P{SUPor-P}KV00108, Scer\GAL4Act.PU
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (0)
No records found.
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (0)
No records found.
Rattus norvegicus (Norway rat) (0)
No records found.
Xenopus tropicalis (Western clawed frog) (0)
No records found.
Danio rerio (Zebrafish) (0)
No records found.
Caenorhabditis elegans (Nematode, roundworm) (0)
No records found.
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190DN4 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00003564
Drosophila simulans
Dsim\Lhr
Drosophila sechellia
Dsec\GM21773
Drosophila erecta
Dere\Lhr
Drosophila yakuba
Dyak\Lhr
Drosophila ananassae
Dana\Lhr
Drosophila pseudoobscura pseudoobscura
Dpse\Lhr
Drosophila persimilis
Dper\GL11424
Drosophila willistoni
Dwil\GK22897
Drosophila virilis
Dvir\Lhr
Drosophila mojavensis
Dmoj\GI18576
Drosophila grimshawi
Dgri\GH21397
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091507G4 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17014995
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_05802
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( None identified )
No non-Dipteran orthologies identified
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( None identified )
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (0)
No records found.
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    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 v8.0 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?
    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
    esyN Network Diagram
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2R
    Recombination map

    2-82

    Cytogenetic map
    54B7-54B7
    Sequence location
    2R:17,431,032..17,432,219 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    54B7-54B7
    Limits computationally determined from genome sequence between P{EP}l(2)k01209EP2177&P{lacW}k11012a and P{lacW}l(2)k07433k07433
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    2-82

    (FlyBase, 2016)

    2-86.2

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (8)
    Genomic Clones (14)
     

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

    cDNA Clones (4)
     

    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 GBrowse 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
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        Antibody Information
        Laboratory Generated Antibodies
         

        polyclonal

        (Satyaki et al., 2014)

        monoclonal

        (Thomae et al., 2013)
        Commercially Available Antibodies
         
        Other Information
        Relationship to Other Genes
        Source for database identify of

        Source for identity of: Lhr CG18468

        (Barbash et al., 2006)
        Source for database merge of
        Additional comments
        Other Comments

        The Hmr and Lhr proteins form a heterochromatic complex with Su(var)205 in D. melanogaster. Hmr and Lhr are required to repress transcripts from satellite DNAs and many families of transposable elements. They are also required to help regulate the length of telomeres (which in Drosophila are composed of domesticated transposable elements).

        (Satyaki et al., 2014)

        The Dsim\Lhr ortholog of Lhr does not appear to affect satellite DNA transcription in D. simulans, but it does have a role in repressing transcription of transposable elements in this species.

        (Satyaki et al., 2014)

        Upregulation of transposable element transcription is seen in hybrids between D. melanogaster and D. simulans, but this is unlikely to be the direct cause of hybrid lethality.

        (Satyaki et al., 2014)

        The Hmr and Lhr proteins form a centromeric complex in D. melanogaster which is required for proper chromosome segregation during mitosis. Both an increase and a decrease in complex levels result in mitotic defects, indicating that this function is extremely dose sensitive. Alteration of the levels of the complex also result in an increase in transcription from transposable elements.

        (Thomae et al., 2013)

        The orthologous D. simulans Dsim\Hmr and Dsim\Lhr proteins also bind each other in coimmunoprecipitation experiments and also localise to the centromere (although Dsim\Hmr also shows a prominent non-centromeric localisation).

        (Thomae et al., 2013)

        The level of Hmr expression in D melanogaster is substantially higher than the expression of the orthologous Dsim\Hmr gene in D. simulans. Conversely, the expression of the D. simulans Dsim\Lhr gene is higher than the expression of the orthologous Lhr gene in D. melanogaster. Hybrids derived from a cross between D. melanogaster females and D. simulans males thus have an elevated amount of the Hmr-Lhr protein complex compared to the parent species, and the complex is delocalised, being bound to numerous interbands along all chromosome arms in the hybrids. Hybrid males and females show a massive increase in transcription from transposable elements, but as the effect is not sex-specific, this is presumably not the the main cause of the lethality of hybrid males.

        (Thomae et al., 2013)

        DNA-protein interactions: genome-wide binding profile assayed for Lhr protein in Kc167 cells; see Chromatin_types_NKI collection report. Individual protein-binding experiments listed under "Samples" at GEO_GSE22069 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22069).

        (Filion et al., 2010)
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 28 )
        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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
        Other crossreferences
        BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        InterPro - A database of protein families, domains and functional sites
        KEGG Genes - Molecular building blocks of life in the genomic space.
        modMine - A data warehouse for the modENCODE project
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        FlyMine - An integrated database for Drosophila genomics
        Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Synonyms and Secondary IDs (8)
        Datasets (1)
        Study focus (1)
        Experimental Role
        Project
        Project Type
        Title
        • transgene_used
        FBGSE22069
        Protein profiling reveals five principal chromatin types in Drosophila cells.
        References (54)