FB2024_02 , released April 23, 2024
Gene: Dmel\lili
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General Information
Symbol
Dmel\lili
Species
D. melanogaster
Name
lilipod
Annotation Symbol
CG5807
Feature Type
protein_coding_gene
FlyBase ID
FBgn0027539
Gene Model Status
Current
Stock Availability
13 publicly available
Gene Summary
lilipod (lili) encodes a multi-pass transmembrane protein required for Dpp signal transduction in the female germline to promote ovarian stem cell maintenance. [Date last reviewed: 2018-09-27] (FlyBase Gene Snapshot)
All Summaries
Also Known As

BcDNA:GH12663

Key Links
Genomic Location
Cytogenetic map
96A23-96A23
Sequence location
Recombination map
3-85
RefSeq locus
NT_033777 REGION:24805445..24814012
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 (5 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables transmembrane signaling receptor activity
inferred from biological aspect of ancestor with PANTHER:PTN000290121
(GO Reference Genome Project, 2011-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in female germ-line stem cell population maintenance
inferred from mutant phenotype
(Dolezal et al., 2015)
involved_in positive regulation of BMP signaling pathway
inferred from genetic interaction with FLYBASE:tkv; FB:FBgn0003716
(Dolezal et al., 2015)
inferred from genetic interaction with FLYBASE:Dad; FB:FBgn0020493
(Dolezal et al., 2015)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in signal transduction
inferred from biological aspect of ancestor with PANTHER:PTN000290121
(GO Reference Genome Project, 2011-)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
is_active_in plasma membrane
inferred from biological aspect of ancestor with PANTHER:PTN000290121
(GO Reference Genome Project, 2011-)
located_in plasma membrane
inferred from sequence or structural similarity with UniProtKB:Q6UX01
(Gene Ontology Curators, 2002-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the LIMR family. (Q9VC35)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
lilipod (lili) encodes a multi-pass transmembrane protein required for Dpp signal transduction in the female germline to promote ovarian stem cell maintenance. [Date last reviewed: 2018-09-27]
Gene Group (FlyBase)
Positive Regulators of BMP Signaling Pathway -
Positive regulators of Bone Morphogenetic Protein (BMP) signaling up-regulate the pathway, ultimately resulting in the increased nuclear activity of the Mad/Med transcription factor complex.
UNCLASSIFIED TRANSMEMBRANE RECEPTORS -
This group comprises transmembrane receptors that do not classify under other groups in FlyBase.
Protein Function (UniProtKB)
Required during oogenesis to promote self-renewal of germline stem cells, probably by enhancing BMP signaling activity.
(UniProt, Q9VC35)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\lili 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 Q9VC35)

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

Gene model reviewed during 5.45

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

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
lili-RA
FBtr0084739
NM_143033
2690
527
lili-RB
FBtr0331697
NM_001276001
2035
519
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
lili-PA
FBpp0084114
60.0
527
7.99
Q9VC35
NP_651290
AAF56340
lili-PB
FBpp0304086
58.9
519
8.19
A0A0B4KGZ8
NP_001262930
AGB96310
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

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\lili 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).

4.42

Transcript Expression
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
Reporter: P{lili-eGFP.nls}
Stage
Tissue/Position (including subcellular localization)
Reference
oogenesis
female germline stem cell
(Dolezal et al., 2015)
follicle cell
(Dolezal et al., 2015)
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\lili 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
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 ( 17 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 9 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of lili
Transgenic constructs containing regulatory region of lili
Aberrations (Deficiencies and Duplications) ( 2 )
Inferred from experimentation ( 2 )
Gene disrupted in
Df(3R)Exel6200
(Ryder, 2004.4.26)
Gene partially disrupted in
Df(3R)96ST
(Zhang et al., 2005)
Inferred from location ( 0 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
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) (2)
Hsap\LMBR1L
13 of 14
Yes
Yes
Hsap\LMBR1
12 of 14
No
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) (2)
Rnor\Lmbr1l
11 of 14
Yes
Yes
Rnor\Lmbr1
11 of 14
Yes
Yes
Mus musculus (laboratory mouse) (2)
Mmus\Lmbr1l
13 of 14
Yes
Yes
Mmus\Lmbr1
12 of 14
No
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\lmbr1
9 of 13
Yes
Yes
Xtro\lmbr1l
7 of 13
No
Yes
Danio rerio (Zebrafish) (2)
Drer\lmbr1l
13 of 14
Yes
Yes
Drer\lmbr1
11 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\R05D3.2
14 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP006880
12 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:lili. 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 ( 3 )
    Human Ortholog
    Disease
    Evidence
    References
    LMBR1; limb development membrane protein 1
    model of  syndactyly type 4
    IEA
    (FlyBase, 2019-)
    model of  acheiropody
    IEA
    (FlyBase, 2019-)
    model of  Laurin-Sandrow syndrome
    IEA
    (FlyBase, 2019-)
    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?
    LMBR1L; limb development membrane protein 1 like
    13 of 14
    610007
        LMBR1; limb development membrane protein 1
        12 of 14
        605522
        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
        Other Interaction Browsers
        Summary of Genetic Interactions
        esyN Network Diagram
        Show/hide secondary interactors 
        (data from AllianceMine provided by esyN)
        esyN Network Key:
        Suppression
        Enhancement
        Other Interaction Browsers
        View in FlyBase Interactions Browser   View in MIST tool (external link)
        Please look at the allele data for full details of the genetic interactions
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        lili
        suppressible
        bam
        (Dolezal et al., 2015)
        lili
        suppressible
        Dad
        (Dolezal et al., 2015)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        tkv
        suppressible
        lili
        (Dolezal et al., 2015)
        External Data
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        DroID - A comprehensive database of gene and protein interactions.
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3R
        Recombination map
        3-85
        Cytogenetic map
        96A23-96A23
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        96A23-96A23
        Limits computationally determined from genome sequence between P{PZ}crb07207&P{PZ}BRWD305842 and P{EP}CycB3EP3127
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        3-85

        (FlyBase, 2016)

        3-84.8

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (13)
        Genomic Clones (17)
         

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

        cDNA Clones (99)
         

        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
         
        Commercially Available Antibodies
         
        Cell Line Information
        Publicly Available Cell Lines
         
          Other Stable Cell Lines
           
            Other Comments

            Area matching Drosophila EST AA263622.

            (Davies, 2001.3.15)
            Relationship to Other Genes
            Source for database merge of

            Source for merge of: CG5807 anon-WO0118547.355

            (FlyBase, 1996-)
            Additional comments

            Source for merge of CG5807 anon-WO0118547.355 was sequence comparison ( date:051113 ).

            (FlyBase, 1996-)
            Nomenclature History
            Source for database identify of

            Source for identity of: BcDNA:GH12663 CG5807

            (Kodira, 1999.11)

            Source for identity of: lili CG5807

            (Dolezal et al., 2015)
            Nomenclature comments
            Etymology
            Synonyms and Secondary IDs (7)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            External Crossreferences and Linkouts ( 46 )
            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
            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.
            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
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            References (42)