FB2025_05 , released December 11, 2025
Gene: Dmel\Iml1
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General Information
Symbol
Dmel\Iml1
Species
D. melanogaster
Name
Increased minichromosome loss 1
Annotation Symbol
CG12090
Feature Type
protein_coding_gene
FlyBase ID
FBgn0035227
Gene Model Status
Current
Stock Availability
6 publicly available
Gene Summary
Increased minichromosome loss 1 (Iml1) encodes a component of the highly conserved GAP Activity Towards Rags 1 (GATOR1) complex, which inhibits the activity of the product of mTor in response to amino acid starvation. The product of Iml1, as well as the other GATOR1 components encoded by Nprl2 and Nprl3, regulates early meiotic progression. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)
All Summaries
Key Links
Genomic Location
Cytogenetic map
62A3-62A3
Sequence location
Recombination map
3-0.5
RefSeq locus
NT_037436 REGION:1523414..1534034
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 (12 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 GTPase activator activity
inferred from sequence or structural similarity with SGD:S000003899
(Gene Ontology Curators, 2002-)
inferred from electronic annotation with InterPro:IPR027244
(InterPro Project Members, 2004-)
Biological Process (7 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
involved_in cellular response to amino acid starvation
inferred from mutant phenotype
(Bar-Peled et al., 2013)
involved_in germarium-derived cystoblast division
inferred from mutant phenotype
(Wei et al., 2014)
involved_in germline cell cycle switching, mitotic to meiotic cell cycle
inferred from mutant phenotype
(Wei et al., 2014)
inferred from genetic interaction with UniProtKB:Q9VXA0
(Wei et al., 2014)
involved_in negative regulation of cell size
inferred from mutant phenotype
(Bar-Peled et al., 2013)
involved_in negative regulation of TOR signaling
inferred from mutant phenotype
(Bar-Peled et al., 2013)
involved_in negative regulation of TORC1 signaling
inferred from mutant phenotype
(Wei et al., 2016, Wei et al., 2014)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in cellular response to amino acid starvation
inferred from biological aspect of ancestor with PANTHER:PTN000995343
(GO Reference Genome Project, 2011-)
involved_in negative regulation of TORC1 signaling
inferred from biological aspect of ancestor with PANTHER:PTN000323637
(GO Reference Genome Project, 2011-)
involved_in positive regulation of autophagy
inferred from biological aspect of ancestor with PANTHER:PTN000323637
(GO Reference Genome Project, 2011-)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in lysosome
inferred from direct assay
(Cai et al., 2016)
part_of Seh1-associated complex
inferred from direct assay
(Cai et al., 2016)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
part_of GATOR1 complex
inferred from biological aspect of ancestor with PANTHER:PTN000323637
(GO Reference Genome Project, 2011-)
traceable author statement
(Cai et al., 2016)
is_active_in lysosomal membrane
inferred from biological aspect of ancestor with PANTHER:PTN000995343
(GO Reference Genome Project, 2011-)
part_of Seh1-associated complex
inferred from sequence or structural similarity with SGD:S000003899
(Dokudovskaya et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the IML1 family. (Q9W0E3)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Increased minichromosome loss 1 (Iml1) encodes a component of the highly conserved GAP Activity Towards Rags 1 (GATOR1) complex, which inhibits the activity of the product of mTor in response to amino acid starvation. The product of Iml1, as well as the other GATOR1 components encoded by Nprl2 and Nprl3, regulates early meiotic progression. [Date last reviewed: 2019-03-07]
Gene Group (FlyBase)
GATOR1 COMPLEX -
GATOR1 is a subcomplex of the GATOR (SEA) complex. GATOR1 possesses Rag GTPase activating protein activity and inhibits TORC1 activity in response to amino acid starvation. (Adapted from FBrf0232362 and PMID:25934700).
Protein Function (UniProtKB)
An essential component of the GATOR subcomplex GATOR1 which functions as an inhibitor of the amino acid-sensing branch of the TORC1 signaling pathway (PubMed:23723238, PubMed:25512509, PubMed:27672113). The two GATOR subcomplexes, GATOR1 and GATOR2, regulate the TORC1 pathway in order to mediate metabolic homeostasis, female gametogenesis and the response to amino acid limitation and complete starvation (PubMed:23723238, PubMed:25512509, PubMed:27672113). The function of GATOR1 in negatively regulating the TORC1 pathway is essential for maintaining baseline levels of TORC1 activity under nutrient rich conditions, and for promoting survival during amino acid or complete starvation by inhibiting TORC1-dependent cell growth and promoting catabolic metabolism and autophagy (PubMed:23723238, PubMed:25512509, PubMed:27672113). GATOR1 and GATOR2 act at different stages of oogenesis to regulate TORC1 in order to control meiotic entry and promote oocyte growth and development (PubMed:25512509, PubMed:27672113). After exactly four mitotic cyst divisions, the GATOR1 complex members (Iml1, Nprl2 and Nprl3) down-regulate TORC1 to slow cellular metabolism and promote the mitotic/meiotic transition (PubMed:25512509, PubMed:27672113). At later stages of oogenesis, the mio and Nup44A components of the GATOR2 complex inhibit GATOR1 and thus activate TORC1 to promote meiotic progression, and drive oocyte growth and development (PubMed:25512509, PubMed:27672113).
(UniProt, Q9W0E3)
Gene Model and Products
Number of Transcripts
5
Number of Unique Polypeptides
5

Please see the JBrowse view of Dmel\Iml1 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 Q9W0E3)

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.

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

Gene model reviewed during 5.46

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Iml1-RA
FBtr0072703
NM_167889
4861
1544
Iml1-RB
FBtr0072704
NM_139361
4642
1471
Iml1-RC
FBtr0072705
NM_167888
4645
1472
Iml1-RD
FBtr0333401
NM_001274330
4762
1511
Iml1-RE
FBtr0333402
NM_001274331
4738
1503
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
Iml1-PA
FBpp0072587
176.7
1544
7.38
Q9W0E3
NP_728621
AAF47505
Iml1-PB
FBpp0072588
168.9
1471
7.05
Q8IRG9
NP_647618
AAN11485
Iml1-PC
FBpp0072589
168.9
1472
7.19
Q8IRG8
NP_728620
AAN11486
Iml1-PD
FBpp0305593
173.1
1511
7.04
M9PE64
NP_001261259
AGB93954
Iml1-PE
FBpp0305594
172.4
1503
7.42
M9PDV3
NP_001261260
AGB93955
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Component of the GATOR complex consisting of mio, Nup44A/Seh1, Im11, Nplr3, Nplr2, Wdr24, Wdr59 and Sec13 (PubMed:27166823). Within the GATOR complex, probable component of the GATOR1 subcomplex which is likely composed of Iml1, Nplr2 and Nplr3 (PubMed:27166823).

(UniProt, Q9W0E3)
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\Iml1 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).

-1.03

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in lysosome
inferred from direct assay
(Cai et al., 2016)
part_of Seh1-associated complex
inferred from direct assay
(Cai et al., 2016)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Iml1 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 ( 4 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Iml1
Transgenic constructs containing regulatory region of Iml1
Aberrations (Deficiencies and Duplications) ( 3 )
Inferred from experimentation ( 3 )
Gene disrupted in
Df(3L)ED4238
(Wei et al., 2016)
Df(3L)Exel6087
(Ryder, 2004.4.26)
Gene partially disrupted in
Df(3L)Iml11
(Wei et al., 2016)
Inferred from location ( 6 )
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) (1)
Hsap\DEPDC5
13 of 14
Yes
Yes
1  
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\Depdc5
14 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Depdc5
13 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\depdc5
7 of 13
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\depdc5
14 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\T08A11.1
11 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP007010
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (0)
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\IML1
9 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\SPBC26H8.04c
8 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Iml1. 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 ( 2 )
Potential Models Based on Orthology ( 1 )
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?
DEPDC5; DEP domain containing 5, GATOR1 subcomplex subunit
13 of 14
DEP DOMAIN-CONTAINING PROTEIN 5; DEPDC5
 
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
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
Iml1
enhanceable
Nprl2
(Wei et al., 2014)
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
atos
suppressible
Iml1
(Emtenani et al., 2022)
pths
suppressible
Iml1
(Emtenani et al., 2022)
External Data
Subunit Structure (UniProtKB)
Component of the GATOR complex consisting of mio, Nup44A/Seh1, Im11, Nplr3, Nplr2, Wdr24, Wdr59 and Sec13 (PubMed:27166823). Within the GATOR complex, probable component of the GATOR1 subcomplex which is likely composed of Iml1, Nplr2 and Nplr3 (PubMed:27166823).
(UniProt, Q9W0E3 )
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
KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
Class of Gene
Genomic Location and Detailed Mapping Data
Chromosome (arm)
3L
Recombination map
3-0.5
Cytogenetic map
62A3-62A3
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
62A3-62A3
Limits computationally determined from genome sequence between P{EP}rhoEP3704&P{PZ}l(3)0622606226 and P{PZ}dlt04276
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location

3-0.5

(FlyBase, 2016)

3-2.4

(Comeron et al., 2012)
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (6)
Genomic Clones (16)
 

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

cDNA Clones (24)
 

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
      Relationship to Other Genes
      Source for database merge of
      Additional comments

      Release 4.3 annotation CG33971 corresponds to a part of release 2 annotation CG12090 which was removed from the release 3.1 version of CG12090.

      (FlyBase Genome Annotators, 2005)
      Nomenclature History
      Source for database identify of

      Source for identity of: Iml1 CG12090

      (Wei et al., 2014)
      Nomenclature comments
      Etymology

      Named 'Iml1'/'Increased minichromosome loss 1' after the S. cerevisiae homolog.

      (Wei et al., 2014)
      Synonyms and Secondary IDs (8)
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      Study result (0)
      Result
      Result Type
      Title
      External Crossreferences and Linkouts ( 48 )
      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
      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)
      KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      References (58)