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General Information
Symbol
Dmel\lid
Species
D. melanogaster
Name
little imaginal discs
Annotation Symbol
CG9088
Feature Type
FlyBase ID
FBgn0031759
Gene Model Status
Stock Availability
Gene Snapshot
little imaginal discs (lid) encodes a trimethyl H3K4 histone demethylase that regulates transcription through both demethylase-dependent and demethylase-independent mechanisms. It has roles in regulating cell growth, circadian rhythm, stress resistance, hematopoiesis and fertility. [Date last reviewed: 2019-03-14]
Also Known As

kdm5, l(2)10424, dKDM5/LID

Key Links
Genomic Location
Cytogenetic map
Sequence location
2L:5,989,400..5,999,501 [-]
Recombination map

2-18

RefSeq locus
NT_033779 REGION:5989400..5999501
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
Belongs to the JARID1 histone demethylase family. (Q9VMJ7)
Summaries
Gene Group (FlyBase)
JUMONJI C DOMAIN-CONTAINING LYSINE DEMETHYLASES -
The Jumonji C (JmjC) domain-containing proteins catalyze histone lysine demethylation through an oxidative reaction that requires iron Fe(II) and α-ketoglutarate as cofactors. (Adapted from FBrf0195283).
A-T RICH INTERACTION DOMAIN TRANSCRIPTION REGULATORS -
The A-T Rich Interaction Domain (ARID) transcription regulators are non-sequence specific DNA binding proteins. The ARID domain comprises a variant helix-turn-helix motif, accompanied by additional DNA-contacting loop structures. Many have roles in chromatin remodelling and regulation of general transcription. (Adapted from PMID:15922553).
HISTONE ACETYLTRANSFERASES -
Histone acetyltransferases catalyze the acetylation of conserved lysine residues on histone proteins by transferring an acetyl group from acetyl CoA to form ε-N-acetyl lysine. (Adapted from PMID:11395403).
Protein Function (UniProtKB)
Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Specifically demethylates trimethylated H3 'Lys-4'. Required for the correct regulation of homeotic genes during development. Plays a role in the regulation of the circadian rhythm and in maintaining the normal periodicity of the circadian clock. Regulates the expression of clock-controlled genes including tim, per and cry.
(UniProt, Q9VMJ7)
Summary (Interactive Fly)

trimethyl H3K4 demethylase - physically interacts with Myc to regulator Myc-induced cell growth

Gene Model and Products
Number of Transcripts
6
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\lid or the JBrowse view of Dmel\lid 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

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

Gene model reviewed during 5.45

Gene model reviewed during 5.55

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0079231
5963
1838
FBtr0079232
5831
1838
FBtr0307069
5851
1838
FBtr0307070
5841
1838
FBtr0307071
6941
1838
FBtr0345336
7004
1838
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
FBpp0078862
204.0
1838
6.61
FBpp0078863
204.0
1838
6.61
FBpp0297912
204.0
1838
6.61
FBpp0297913
204.0
1838
6.61
FBpp0297914
204.0
1838
6.61
FBpp0311492
204.0
1838
6.61
Polypeptides with Identical Sequences

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

1838 aa isoforms: lid-PA, lid-PB, lid-PC, lid-PD, lid-PE, lid-PF
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Interacts with Myc. Part of a complex containing Lid, Myc and Ash2.

(UniProt, Q9VMJ7)
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\lid using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (24 terms)
Molecular Function (7 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR001606
(assigned by InterPro )
inferred from biological aspect of ancestor with PANTHER:PTN000075014
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000075015
(assigned by GO_Central )
Biological Process (14 terms)
Terms Based on Experimental Evidence (13 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
(assigned by UniProt )
inferred from mutant phenotype
(assigned by UniProt )
inferred from expression pattern
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
(assigned by UniProt )
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000075014
(assigned by GO_Central )
Cellular Component (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000075014
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000075014
(assigned by GO_Central )
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
organism

Comment: maternally deposited

Additional Descriptive Data

lid transcript is localized to the apical tip of the adult testis.

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
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
Reporter: M{lid-HA}
Stage
Tissue/Position (including subcellular localization)
Reference
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\lid in GBrowse 2
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
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
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 13-16
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 10 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 34 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of lid
Transgenic constructs containing regulatory region of lid
Deletions and Duplications ( 4 )
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 v7.1)
Homo sapiens (Human) (7)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
12 of 15
No
Yes
12 of 15
No
Yes
11 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (7)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
12 of 15
No
Yes
11 of 15
No
Yes
11 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (5)
8 of 13
Yes
Yes
4 of 13
No
Yes
4 of 13
No
Yes
1 of 13
No
Yes
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (11)
10 of 12
Yes
Yes
6 of 12
No
Yes
4 of 12
No
Yes
2 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
Yes
1 of 12
No
Yes
1 of 12
No
Yes
1 of 12
No
Yes
1 of 12
No
Yes
Danio rerio (Zebrafish) (7)
12 of 15
Yes
Yes
11 of 15
No
Yes
11 of 15
No
Yes
3 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (3)
13 of 15
Yes
Yes
1 of 15
No
No
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (9)
5 of 9
Yes
Yes
5 of 9
Yes
Yes
5 of 9
Yes
Yes
4 of 9
No
Yes
3 of 9
No
Yes
1 of 9
No
Yes
1 of 9
No
Yes
1 of 9
No
Yes
1 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (3)
10 of 15
Yes
Yes
5 of 15
No
Yes
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (5)
7 of 12
Yes
Yes
7 of 12
Yes
Yes
6 of 12
No
Yes
1 of 12
No
No
1 of 12
No
No
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091900FM )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091500KF )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0078 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X00C7 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0RFR )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (4)
3 of 10
1 of 10
1 of 10
1 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Model Summary Ribbon
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 2 )
Potential Models Based on Orthology ( 1 )
Modifiers Based on Experimental Evidence ( 1 )
Allele
Disease
Interaction
References
Disease Associations of Human Orthologs (via DIOPT v7.1 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:
Select Layout:
Legend:
Protein
RNA
Selected Interactor(s)
Interactions Browser

Please see the Physical Interaction reports below for full details
protein-protein
Physical Interaction
Assay
References
Summary of Genetic Interactions
esyN Network Diagram
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)
Interacts with Myc. Part of a complex containing Lid, Myc and Ash2.
(UniProt, Q9VMJ7 )
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 (genetic) - An integrated Molecular Interaction Database
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
External Data
Linkouts
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2L
Recombination map

2-18

Cytogenetic map
Sequence location
2L:5,989,400..5,999,501 [-]
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
26B2-26B2
Limits computationally determined from genome sequence between P{EP}chicEP713&P{EP}chicEP1095 and P{lacW}Gef26k13720
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
26A8-26A9
(determined by in situ hybridisation)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (15)
Genomic Clones (15)
 

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

cDNA Clones (79)
 

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 sequences
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)
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
Commercially Available Antibodies
 
Other Information
Relationship to Other Genes
Source for database identify of

Source for identity of: lid CG9088

Source for database merge of

Source for merge of: lid l(2)10424

Additional comments
Other Comments

lid is required in the germ cells of the testis to regulate the levels of Stat92E, which maintains proliferation and prevents premature differentiation of germline stem cells.

lid and Su(var)3-3 have opposing functions in the establishment of euchromatin and heterochromatin boundaries; Su(var)3-3 promotes heterochromatin formation, while lid promotes euchromatin formation.

Origin and Etymology
Discoverer
Etymology

The gene is named "little imaginal discs" after the phenotype seen in mutant larvae.

Identification
External Crossreferences and Linkouts ( 63 )
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/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
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
iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
KEGG Genes - Molecular building blocks of life in the genomic space.
modMine - A data warehouse for the modENCODE project
Linkouts
ApoDroso - Functional genomic database for photoreceptor development, survival and function
BioGRID - A database of protein and genetic interactions.
DPiM - Drosophila Protein interaction map
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 (genetic) - An integrated Molecular Interaction Database
MIST (protein-protein) - An integrated Molecular Interaction Database
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
Synonyms and Secondary IDs (15)
Reported As
Symbol Synonym
Secondary FlyBase IDs
  • FBgn0010658
Datasets (0)
Study focus (0)
Experimental Role
Project
Project Type
Title
References (132)