FB2024_02 , released April 23, 2024
Gene: Dmel\lilli
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General Information
Symbol
Dmel\lilli
Species
D. melanogaster
Name
lilliputian
Annotation Symbol
CG8817
Feature Type
FlyBase ID
FBgn0041111
Gene Model Status
Stock Availability
Gene Summary
Has a role in transcriptional regulation. Acts in parallel with the Ras/MAPK and the PI3K/PKB pathways in the control of cell identity and cellular growth. Essential for regulation of the cytoskeleton and cell growth but not for cell proliferation or growth rate. Required specifically for the microtubule-based basal transport of lipid droplets. Plays a partially redundant function downstream of Raf in cell fate specification in the developing eye. Pair-rule protein that regulates embryonic cellularization, gastrulation and segmentation. (UniProt, Q9VQI9)
Contribute a Gene Snapshot for this gene.
Also Known As

l(2)00632, Su(Raf)2A, SS2-1, l(2)23Cc, SY2-1

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
2-8
RefSeq locus
NT_033779 REGION:2885929..2954406
Sequence
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
Gene Ontology (GO) Annotations (16 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (0 terms)
Biological Process (10 terms)
Terms Based on Experimental Evidence (9 terms)
CV Term
Evidence
References
involved_in learning or memory
inferred from mutant phenotype
inferred from mutant phenotype
inferred from genetic interaction with FLYBASE:E(spl)mγ-HLH; FB:FBgn0002735,FLYBASE:Su(Tpl); FB:FBgn0014037
inferred from genetic interaction with FLYBASE:N; FB:FBgn0004647
inferred from genetic interaction with FLYBASE:N; FB:FBgn0004647,FLYBASE:lilli; FB:FBgn0041111
inferred from genetic interaction with FLYBASE:Su(Tpl); FB:FBgn0014037
inferred from mutant phenotype
inferred from mutant phenotype
inferred from genetic interaction with FLYBASE:Su(Tpl); FB:FBgn0014037
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from high throughput mutant phenotype
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000829417
inferred from electronic annotation with InterPro:IPR007797
Cellular Component (4 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
part_of euchromatin
inferred from direct assay
located_in nucleus
inferred from direct assay
inferred from physical interaction with FLYBASE:Su(Tpl); FB:FBgn0014037
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
located_in nucleus
inferred from electronic annotation with InterPro:IPR043640
inferred from biological aspect of ancestor with PANTHER:PTN000829417
Protein Family (UniProt)
Belongs to the AF4 family. (Q9VQI9)
Summaries
Gene Group (FlyBase)
UNCLASSIFIED DNA BINDING DOMAIN TRANSCRIPTION FACTORS -
This group comprises DNA-binding transcription factors that do not classify under other domain-based transcription factor groups in FlyBase.
SUPER ELONGATION COMPLEX -
The super elongation complex (SEC) is one of the most active forms of positive transcription elongation factor b (P-TEFb)-containing complexes that acts as a positive regulator of the release of RNA polymerase II from promoter-proximal pausing. (Adapted from FBrf0235091, FBrf0217100, PMID:27223670 and PMID:22895430).
Protein Function (UniProtKB)
Has a role in transcriptional regulation. Acts in parallel with the Ras/MAPK and the PI3K/PKB pathways in the control of cell identity and cellular growth. Essential for regulation of the cytoskeleton and cell growth but not for cell proliferation or growth rate. Required specifically for the microtubule-based basal transport of lipid droplets. Plays a partially redundant function downstream of Raf in cell fate specification in the developing eye. Pair-rule protein that regulates embryonic cellularization, gastrulation and segmentation.
(UniProt, Q9VQI9)
Summary (Interactive Fly)

transcription factor - Fragile X mental retardation 2 (Fmr2) family - Functions in MAPK and Dpp signaling pathways - affects growth, a function associated with the insulin pathway - affects the cytoskeleton early in development.

Gene Model and Products
Number of Transcripts
9
Number of Unique Polypeptides
3

Please see the JBrowse view of Dmel\lilli 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 Q9VQI9)

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

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Gene model reviewed during 5.45

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Gene model reviewed during 6.13

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0077632
7956
1673
FBtr0077633
9683
1673
FBtr0077634
7243
1673
FBtr0290038
5228
1614
FBtr0290039
6134
1614
FBtr0290040
5337
1614
FBtr0290041
7438
1673
FBtr0332458
7591
1614
FBtr0452101
7025
1626
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
FBpp0077317
180.1
1673
9.69
FBpp0077318
180.1
1673
9.69
FBpp0077319
180.1
1673
9.69
FBpp0288477
173.0
1614
9.76
FBpp0288478
173.0
1614
9.76
FBpp0288479
173.0
1614
9.76
FBpp0288480
180.1
1673
9.69
FBpp0304731
173.0
1614
9.76
FBpp0402856
174.5
1626
9.84
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

1673 aa isoforms: lilli-PA, lilli-PB, lilli-PC, lilli-PG
1614 aa isoforms: lilli-PD, lilli-PE, lilli-PF, lilli-PH
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Component of the super elongation complex (SEC), at least composed of Ell, Cdk9, cyclin-T (CycT), lilli and ear.

(UniProt, Q9VQI9)
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\lilli 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).

1.92

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of euchromatin
inferred from direct assay
located_in nucleus
inferred from direct assay
inferred from physical interaction with FLYBASE:Su(Tpl); FB:FBgn0014037
Expression Deduced from Reporters
Reporter: P{GawB}lilli189Y
Stage
Tissue/Position (including subcellular localization)
Reference
Reporter: P{GMR44E10-GAL4}
Stage
Tissue/Position (including subcellular localization)
Reference
Reporter: P{PZ}lilli00632
Stage
Tissue/Position (including subcellular localization)
Reference
Stage
Tissue/Position (including subcellular localization)
Reference
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\lilli in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 73 )
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 lilli
Transgenic constructs containing regulatory region of lilli
Aberrations (Deficiencies and Duplications) ( 20 )
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
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (4)
8 of 14
Yes
Yes
8 of 14
Yes
Yes
8 of 14
Yes
Yes
1  
7 of 14
No
Yes
1  
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (4)
7 of 14
Yes
Yes
7 of 14
Yes
Yes
7 of 14
Yes
Yes
7 of 14
Yes
Yes
Mus musculus (laboratory mouse) (4)
8 of 14
Yes
Yes
8 of 14
Yes
Yes
8 of 14
Yes
Yes
7 of 14
No
Yes
Xenopus tropicalis (Western clawed frog) (8)
7 of 13
Yes
Yes
6 of 13
No
Yes
6 of 13
No
Yes
5 of 13
No
Yes
4 of 13
No
No
3 of 13
No
Yes
1 of 13
No
No
1 of 13
No
Yes
Danio rerio (Zebrafish) (3)
8 of 14
Yes
Yes
8 of 14
Yes
Yes
8 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (0)
Anopheles gambiae (African malaria mosquito) (1)
7 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (0)
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:lilli. Refer to their site for version information.
Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 2 )
Potential Models Based on Orthology ( 2 )
Modifiers Based on Experimental Evidence ( 5 )
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.
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
esyN Network Diagram
Show neighbor-neighbor interactions:
Show/hide secondary interactors 
(data from AllianceMine provided by esyN)
Select Layout:
Legend:
Protein
RNA
Selected Interactor(s)
Interactions Browser

Please see the Physical Interaction reports below for full details
MIST Molecular Interaction Search Tool

Please see the Physical Interaction reports below for full details
protein-protein
Physical Interaction
Assay
References
Summary of Genetic Interactions
esyN Network Diagram
Show/hide secondary interactors 
(data from AllianceMine provided by esyN)
esyN Network Key:
Suppression
Enhancement

Please look at the allele data for full details of the genetic interactions
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
External Data
Subunit Structure (UniProtKB)
Component of the super elongation complex (SEC), at least composed of Ell, Cdk9, cyclin-T (CycT), lilli and ear.
(UniProt, Q9VQI9 )
Linkouts
BioGRID - A database of protein and genetic interactions.
DroID - A comprehensive database of gene and protein interactions.
MIST (genetic) - An integrated Molecular Interaction Database
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)
2L
Recombination map
2-8
Cytogenetic map
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
23C1-23C3
Limits computationally determined from genome sequence between P{PZ}oho23B03575 and P{PZ}lilli00632
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
23C1-23C2
(determined by in situ hybridisation)
Experimentally Determined Recombination Data
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (29)
Genomic Clones (54)
cDNA Clones (42)
 

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
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    Antibody Information
    Laboratory Generated Antibodies
    Commercially Available Antibodies
     
    Cell Line Information
    Publicly Available Cell Lines
     
      Other Stable Cell Lines
       
        Other Comments

        lilli is acutely required at the blastoderm stage for the run-dependent activation of ftz.

        lilli is required for transcriptional activation of the Sxl embryonic promoter.

        Embryos lacking maternal lilli function show specific defects in the establishment of a functional cytoskeleton during cellularisation, and show a pair-rule segmentation phenotype.

        Loss of lilli function causes an autonomous reduction in cell size.

        Maternal contribution of the lilli gene is important for formation of segmentation pattern during embryogenesis.

        lilli homozygous clones produce small cells.

        40 "SS2-1" alleles of lilli have been isolated in a screen for dominant modifiers of the sinaGMR.PN eye phenotype.

        Identified in a genetic screen for modifiers of the phl::tor12D.sev rough eye mutant phenotype. Clonal analysis reveals that lilli is not required for normal eye development.

        The autosomal "FLP-DFS" technique (using the P{ovoD1-18} P{FRT(whs)} P{hsFLP} chromosomes) has been used to identify the specific maternal effect phenotype for the zygotic lethal mutation.

        Relationship to Other Genes
        Source for database merge of

        Source for merge of: lilli SY2-1 Su(Raf)2A l(2)k07920

        Source for merge of: lilli l(2)23Cc

        Source for merge of: lilli BEST:GH09955

        Source for merge of: lilli BcDNA:GM02019

        Additional comments

        Source for identity of lilli CG8817 was sequence comparison ( date:010129 ).

        Source for merge of lilli BcDNA:GM02019 was a shared cDNA ( date:030728 ).

        Nomenclature History
        Source for database identify of

        Source for identity of: lilli CG8817

        Nomenclature comments
        Etymology

        The gene is named "lilliputian" based on the small size of homozygous mutant cells.

        Synonyms and Secondary IDs (25)
        Reported As
        Symbol Synonym
        BEST:GH09955
        BcDNA:GM02019
        l(2)k07920
        l(2)k16124
        Secondary FlyBase IDs
        • FBgn0010466
        • FBgn0016741
        • FBgn0026635
        • FBgn0026643
        • FBgn0031481
        • FBgn0040119
        • FBgn0045826
        • FBgn0047289
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        External Crossreferences and Linkouts ( 106 )
        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 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
        UniProt/TrEMBL - Automatically annotated and unreviewed 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
        BioGRID - A database of protein and genetic interactions.
        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
        FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
        Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
        MIST (genetic) - An integrated Molecular Interaction Database
        MIST (protein-protein) - An integrated Molecular Interaction Database
        References (163)