FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\lt
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General Information
Symbol
Dmel\lt
Species
D. melanogaster
Name
light
Annotation Symbol
CG18028
Feature Type
protein_coding_gene
FlyBase ID
FBgn0002566
Gene Model Status
Current
Stock Availability
69 publicly available
Gene Summary
light (lt) encodes a cellular-protein trafficking protein that forms part of the homotypic fusion and vacuolar protein sorting (HOPS) and class C core vacuole/endosome tethering (CORVET) complexes. It is required for fusion of autophagosomes with lysosomes, endocytic down-regulation of Notch signaling, and eye pigment biogenesis. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Also Known As

Vps41, l(2)40Fb

Key Links
Genomic Location
Cytogenetic map
40F7-40F7
Sequence location
Recombination map
2-54
RefSeq locus
NT_033779 REGION:22924795..22943135
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 (20 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables protein-membrane adaptor activity
inferred from biological aspect of ancestor with PANTHER:PTN001759852
(GO Reference Genome Project, 2011-)
enables zinc ion binding
inferred from sequence model
(Ying et al., 2011)
Biological Process (15 terms)
Terms Based on Experimental Evidence (8 terms)
CV Term
Evidence
References
involved_in autophagosome maturation
inferred from mutant phenotype
(Takáts et al., 2014)
involved_in cellular response to starvation
inferred from mutant phenotype
(Takáts et al., 2014)
involved_in crinophagy
inferred from mutant phenotype
(Csizmadia et al., 2018)
involved_in determination of adult lifespan
inferred from mutant phenotype
(Simonsen et al., 2007)
involved_in endocytosis
inferred from mutant phenotype
(Wilkin et al., 2008)
involved_in endosomal vesicle fusion
inferred from mutant phenotype
(Lőrincz et al., 2016)
involved_in Notch receptor processing
inferred from mutant phenotype
(Wilkin et al., 2008)
involved_in symbiont entry into host cell
inferred from high throughput mutant phenotype
(Hodgson et al., 2019)
Terms Based on Predictions or Assertions (9 terms)
CV Term
Evidence
References
involved_in cellular response to starvation
inferred from biological aspect of ancestor with PANTHER:PTN000289375
(GO Reference Genome Project, 2011-)
involved_in endosomal vesicle fusion
inferred from electronic annotation with InterPro:IPR016902
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN001759852
(GO Reference Genome Project, 2011-)
involved_in intracellular protein transport
inferred from electronic annotation with InterPro:IPR000547
(InterPro Project Members, 2004-)
involved_in lysosomal transport
traceable author statement
(Luzio et al., 2000)
involved_in macroautophagy
inferred from biological aspect of ancestor with PANTHER:PTN000289375
(GO Reference Genome Project, 2011-)
involved_in protein targeting to vacuole
inferred from electronic annotation with InterPro:IPR045111
(InterPro Project Members, 2004-)
involved_in regulation of SNARE complex assembly
inferred from sequence or structural similarity with SGD:S000002487
(Solinger and Spang, 2013)
involved_in vacuolar transport
inferred from biological aspect of ancestor with PANTHER:PTN000289375
(GO Reference Genome Project, 2011-)
involved_in vesicle-mediated transport
inferred from electronic annotation with InterPro:IPR000547
(InterPro Project Members, 2004-)
inferred from sequence or structural similarity with SGD:S000002487
(Solinger and Spang, 2013)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
part_of HOPS complex
inferred from mutant phenotype
(Takáts et al., 2014)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
part_of HOPS complex
inferred from sequence or structural similarity with SGD:S000002487
(Solinger and Spang, 2013)
inferred from biological aspect of ancestor with PANTHER:PTN000289375
(GO Reference Genome Project, 2011-)
is_active_in late endosome
inferred from biological aspect of ancestor with PANTHER:PTN001759852
(GO Reference Genome Project, 2011-)
is_active_in vacuolar membrane
inferred from biological aspect of ancestor with PANTHER:PTN000289375
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the VPS41 family. (Q7PL76)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
light (lt) encodes a cellular-protein trafficking protein that forms part of the homotypic fusion and vacuolar protein sorting (HOPS) and class C core vacuole/endosome tethering (CORVET) complexes. It is required for fusion of autophagosomes with lysosomes, endocytic down-regulation of Notch signaling, and eye pigment biogenesis. [Date last reviewed: 2019-03-14]
Gene Group (FlyBase)
VPS-C COMPLEXES: HOPS AND CORVET -
The heterohexameric VPS-C complexes, HOPS and CORVET have been extensively characterised in yeast. They interact with SNAREs and Rabs to promote vesicle tethering. The CORVET complex is involved in early endosome fusion, interacting with Rab5-GTP. The HOPS complex interacts with Rab7-GTP on late endosomes (multivesicular bodies) to promote fusion with the lysosomal compartment (and vacuoles) and also autophagosome-lysosome fusion. The VPS-C complexes share common subunits and CORVET to HOPS conversion intermediates (i-CORVET and i-HOPS) have been proposed to accompany early to late endosome maturation. (Adapted from PMID:19575650 and FBrf0223135).
Protein Function (UniProtKB)
Part of the homotypic fusion and vacuole protein sorting (HOPS) tethering complex involved in endo-lysosomal vesicle trafficking and lysosome biogenesis (PubMed:24554766). The HOPS complex facilitates docking and fusion of lysosomes with late endosomes and several other types of vesicles (PubMed:24554766, PubMed:31194677). The HOPS complex is also involved in autophagy and crinophagy (the elimination of unused secretory granules through their fusion with lysosomes) (PubMed:24554766, PubMed:31194677). The HOPS complex mediates autophagocitic flux, probably by binding autophagosome-associated Syx17/syntaxin 17, promoting assembly of the trans-SNARE complex and instigating autophagosome-lysosome fusion (PubMed:24554766). Independent of Syx17/syntaxin 17, HOPS is involved in biosynthetic transport to lysosomes and lysosome-related organelles such as eye-pigment granules (PubMed:24554766, PubMed:31194677, PubMed:9644832). Required for endocytic degradation of boss/bride of sevenless and N/Notch in developing ommatidia (PubMed:24554766).
(UniProt, Q7PL76)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
lt: light
Eye color yellowish pink-lighter at high temperature, darker at low. Ocelli colorless; Drosopterins drastically reduced; no maternal effect on eye pigmentation (Nickla, 1972, Can. J. Genet. Cytol. 14: 105-11). When combined with st, eye color only slightly lighter than with lt alone; with bw it is clear yellow, pinkish in old flies (Schultz and Dobzhansky, 1934, Genetics 19: 344-64; Mainx, 1938, Z. Indukt. Abstamm. Vererbungsl. 75: 256-76). Eye color autonomous in mutant optic discs transplanted into wild-type hosts (Beadle and Ephrussi, 1936, Genetics 21: 230). Larval Malphighian tubes colorless in lt offspring of lt mothers; some color in tubes if mother is lt/+. The quantity of yellow pigment, composed primarily of riboflavin, in Malpighian tubes exhibits parallel maternal effects in larvae, pupae, and adults (Nickla, 1972, Can. J. Genet. Cytol. 14: 391-96); the amount of such pigment increases with maternal age for both lt/+ and lt/lt parental females (Nickla, 1973, Can. J. Genet. Cytol. 15: 437-42). lt stw homozygotes completely inviable (Purdom); however, lt stw3 homozygotes have good viability. car lt double mutants are also invariably lethal; the time of death varying from the third larval instar to late pupa, depending on the number of normal alleles of either gene carried by the mother (Nickla, 1977, Nature 268: 638-339). Lethal focus of the lethal interaction as measured in car/+; lt/lt, car/0; lt/lt gynandromorphs is in ventral nervous tissue (Nickla, Lilly, and Brown, 1980, Experientia 36: 402-03); larval brain histologically abnormal (McCarthy and Nickla, 1980, Experientia 36: 1361-62).
ltv: light variegated
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\lt 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 Q7PL76)

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 5.53

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

Gene model reviewed during 5.46

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

Evidence supports alternative transcription start site within flanking TE (RAMPAGE TSS data, FBrf0220331; RNA-Seq junction data). May be specific to sequenced strain; not included in gene model.

Gene model reviewed during 5.55

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
lt-RA
FBtr0111125
NM_001042951
2804
841
lt-RC
FBtr0111123
NM_001042952
2760
528
lt-RE
FBtr0333519
NM_001273766
4404
841
lt-RF
FBtr0344082
NM_001042950
5316
841
Additional Transcript Data and Comments
Reported size (kB)

3.3, 3.0 (northern blot)

(Warner et al., 1998)

3.6, 3.2 (northern blot)

(Devlin et al., 1990)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
lt-PA
FBpp0110417
96.9
841
6.88
Q7PL76
NP_001036416
EAA46034
lt-PC
FBpp0110415
61.5
528
5.96
Q8MT46
NP_001036417
EAL24548
lt-PE
FBpp0305699
96.9
841
6.88
Q7PL76
NP_001260695
AGB93230
lt-PF
FBpp0310509
96.9
841
6.88
Q7PL76
NP_001036415
EAA46035
Polypeptides with Identical Sequences

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

841 aa isoforms: lt-PA, lt-PE, lt-PF
Additional Polypeptide Data and Comments
Reported size (kDa)

841 (aa)

(Warner et al., 1998)
Comments
External Data
Subunit Structure (UniProtKB)

Part of the homotypic fusion and vacuole protein sorting (HOPS) complex, composed of Vps16A, car/Vps33A, dor/Vps18, Vps39, Vps11 and lt/Vps41.

(UniProt, Q7PL76)
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\lt 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).

-1.78

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism | ubiquitous

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)
yolk nucleus
(Fisher et al., 2012)
embryonic stage 11 -- 12
organism | faint | ubiquitous
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
yolk nucleus
(Fisher et al., 2012)
embryonic stage 13 -- 16
organism | faint | ubiquitous
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
yolk nucleus
(Fisher et al., 2012)
third instar larval stage
larval brain
(Weiler and Wakimoto, 1998)
larval circulatory system
(Weiler and Wakimoto, 1998)
larval digestive system
(Weiler and Wakimoto, 1998)
embryonic/larval fat body
(Weiler and Wakimoto, 1998)
Malpighian tubule
(Weiler and Wakimoto, 1998)
imaginal disc
(Weiler and Wakimoto, 1998)
gonad
(Weiler and Wakimoto, 1998)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage
organism | ubiquitous
(Warner et al., 1998)
(Warner et al., 1998)
embryonic stage -- adult stage
(Devlin et al., 1990)
larval stage
Malpighian tubule
(Devlin et al., 1990)
imaginal disc
(Devlin et al., 1990)
larval brain
(Devlin et al., 1990)
embryonic/larval salivary gland
(Devlin et al., 1990)
embryonic/larval fat body
(Devlin et al., 1990)
larval digestive system
(Devlin et al., 1990)
adult stage | female
ovary
(Devlin et al., 1990)
unfertilized egg stage
unfertilized egg | ubiquitous
(Warner et al., 1998)
unfertilized egg
(Warner et al., 1998)
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
part_of HOPS complex
inferred from mutant phenotype
(Takáts et al., 2014)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\lt 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
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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 44 )
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 lt
Transgenic constructs containing regulatory region of lt
Aberrations (Deficiencies and Duplications) ( 75 )
Inferred from experimentation ( 75 )
Gene duplicated in
C(2R)RM-VK2
Dp(2;Y)SD
(Temin, 1991)
Gene not disrupted in
Df(2L)061b
(Siegel, 1981)
Df(2L)D'
(Cicchetti and Loverre, 1988, Ganetzky, 1977, Hilliker, 1976, Hilliker and Holm, 1975)
Df(2L)D
(Cicchetti and Loverre, 1988, Ganetzky, 1977, Hilliker, 1976, Hilliker and Holm, 1975)
Df(2L)E55
(Wright et al., 1976)
Df(2L)E71
(Ganetzky, 1977, Wright et al., 1976)
Df(2L)F
(Ganetzky, 1977, Hilliker, 1976, Hilliker and Holm, 1975)
Df(2L)H
Df(2L)L138D-81
(Siegel, 1981)
Df(2L)L138D-C2
(Siegel, 1981)
Df(2L)L138D-C15
(Siegel, 1981)
Df(2L)L138D-FB15
(Siegel, 1981)
Df(2L)L138D-X1
(Siegel, 1981)
Df(2L)L138D-X14
(Siegel, 1981)
Df(2L)L138D-XR
(Siegel, 1981)
Df(2L)pr-A8
(Ganetzky, 1977)
Df(2L)pr-A14
(Ganetzky, 1977)
Df(2L)pr-A16
(Ganetzky, 1977)
Df(2L)pr-A20
(Ganetzky, 1977)
Df(2L)pr-B12
(Ganetzky, 1977)
Df(2L)Sd37
(Ganetzky, 1977)
Df(2L)TW1
(Wright et al., 1976)
Df(2L)TW2
(Wright et al., 1976)
Df(2L)TW3
(Wright et al., 1976)
Df(2L)TW9
(Wright et al., 1976)
Df(2L)TW12
(Siegel, 1981, Wright et al., 1976)
Df(2L)TW50
(Wright et al., 1976)
Df(2L)TW65
(Cicchetti and Loverre, 1988, Siegel, 1981, Ganetzky, 1977, Wright et al., 1976)
Df(2L)TW84
(Siegel, 1981, Wright et al., 1976)
Df(2L)TW119
(Wright et al., 1976)
Df(2L)TW130
(Wright et al., 1976)
Df(2L)TW137
(Wright et al., 1976)
Df(2L)TW150
(Wright et al., 1976)
Df(2L)TW158
(Ganetzky, 1977, Wright et al., 1976)
Df(2L)TW161
(Cicchetti and Loverre, 1988, Siegel, 1981, Ganetzky, 1977, Wright et al., 1976)
Df(2R)B
(Hilliker and Holm, 1975)
Df(2R)M41A4
(Cicchetti and Loverre, 1988, Hilliker and Holm, 1975)
Df(2R)M41A8
(Cicchetti and Loverre, 1988, Hilliker and Holm, 1975)
Df(2R)M41A10
(Cicchetti and Loverre, 1988, Hilliker and Holm, 1975)
Df(2R)rl-D
(Cicchetti and Loverre, 1988, Hilliker and Holm, 1975)
Dp(2;Y)H1
(Hodgetts, 1980)
Dp(2;Y)H2
(Hodgetts, 1980)
In(2R)bwVDe2LCyR
(Cicchetti and Loverre, 1988)
Gene not duplicated in
C(2R)RM-P4
Dp(2;Y)H
Gene disrupted in
Ab(2R)IR36
(Dimitri et al., 1997)
Df(2L)C'
(Russell and Kaiser, 1994, Dimitri, 1991, Cicchetti and Loverre, 1988, Ganetzky, 1977, Hilliker, 1976)
Df(2L)C
(Cicchetti and Loverre, 1988, Ganetzky, 1977, Hilliker, 1976, Hilliker and Holm, 1975)
Df(2L)E(SD)1
(Temin, 1991, Ganetzky, 1977)
Df(2L)E(SD)3
(Temin, 1991, Ganetzky, 1977)
Df(2L)E(SD)36
(Temin, 1991, Ganetzky, 1977)
Df(2L)lt1
(Russell and Kaiser, 1994, Dimitri, 1991, Temin, 1991)
Df(2L)lt5
(Russell and Kaiser, 1994, Dimitri, 1991, Temin, 1991)
Df(2L)lt8a
(Sharp et al., 1985)
Df(2L)lt8
(Russell and Kaiser, 1994, Dimitri, 1991, Temin, 1991)
Df(2L)lt10
(Weiler and Wakimoto, 1998, Wakimoto and Hearn, 1990)
Df(2L)lt23
(Temin, 1991)
Df(2L)lt28
(Wakimoto and Hearn, 1990)
Df(2L)lt45
(Wakimoto, 2008.11.19, Sharp et al., 1985)
Df(2L)lt47
(Sharp et al., 1985)
Df(2L)lt59
(Temin, 1991)
Df(2L)lt61
(Sharp et al., 1985)
Df(2L)lt64
(Wakimoto and Hearn, 1990)
Df(2L)lt73
(Temin, 1991)
Df(2L)lt105
(Russell and Kaiser, 1994, Wakimoto and Hearn, 1990)
Df(2L)lt109
(Wakimoto, 2008.11.19)
Df(2L)lt120
(Wakimoto and Hearn, 1990)
Df(2L)lt121
(Wakimoto, 2008.11.19)
Df(2L)lt329
(Wakimoto and Hearn, 1990)
Df(2L)lthd6
(Devlin et al., 1990)
Df(2L)ltx5
(Palopoli and Wu, 1996)
Dp(2;Y)H3
(Hodgetts, 1980)
T(2;3)ClassII
(Howe et al., 1995)
T(2;3)EHH
(Hilliker and Holm, 1975)
Inferred from location ( 2 )
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
lethal
lethal | dominant
lethal | recessive
lethal - all die before end of pupal stage | recessive
partially lethal | recessive
viable
Sterility
Allele
sterile | recessive
Other Phenotypes
Allele
abnormal eye color
abnormal eye color, with Scer\GAL4GMR.PF
abnormal eye color | adult stage, with Scer\GAL4GMR.PF
abnormal eye color | recessive
abnormal size | third instar larval stage (with Df(2L)lt45)
enhancer of variegation, with Su(var)2055/Su(var)205205
increased cell size
increased cell size | larval stage | somatic clone, with Scer\GAL4Act5C.PP
increased cell size | larval stage | somatic clone, with Scer\GAL4Act.PU
increased size | larval stage, with Scer\GAL4unspecified
short lived
short lived | male
some die during pupal stage | recessive
suppressor of variegation (with In(2L)ltX2), with E(var)3-93
suppressor of variegation | dominant (with In(2L)ltX2), with E(var)3-91
suppressor of variegation | dominant (with In(2L)ltX2), with E(var)3-92
visible
visible, with Scer\GAL4GMR.PF
visible | recessive
Phenotype manifest in
Allele
autolysosome | somatic clone | wandering third instar larval stage | nutrition conditional, with Scer\GAL4FRT.Rnor\Cd2.Act5C
autolysosome | wandering third instar larval stage | nutrition conditional (with Df(2L)lt45)
autophagosome | increased number
autophagosome | increased number | wandering third instar larval stage | nutrition conditional (with Df(2L)lt45)
embryonic/larval fat body | somatic clone | wandering third instar larval stage | nutrition conditional, with Scer\GAL4FRT.Rnor\Cd2.Act5C
embryonic/larval fat body | third instar larval stage (with Df(2L)lt45)
embryonic/larval fat body | wandering third instar larval stage | nutrition conditional (with Df(2L)lt45)
embryonic/larval garland cell | larval stage (with Df(2L)lt45)
embryonic/larval garland cell | third instar larval stage (with Df(2L)lt45)
embryonic/larval midgut cell | larval stage | somatic clone, with Scer\GAL4Act5C.PP
embryonic/larval midgut cell | larval stage | somatic clone, with Scer\GAL4Act.PU
embryonic/larval salivary gland | third instar larval stage (with Df(2L)lt45)
eye
eye, with Scer\GAL4GMR.PF
garland cell
gastric caecum | larval stage, with Scer\GAL4unspecified
larval brain | third instar larval stage (with Df(2L)lt45)
late endosome
late endosome | larval stage (with Df(2L)lt45)
late endosome | third instar larval stage (with Df(2L)lt45)
lysosome | third instar larval stage (with Df(2L)lt45)
Malpighian tubule
ocellus pigment granule
pigment cell
vacuole | larval stage (with Df(2L)lt45)
wing
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\VPS41
14 of 14
Yes
Yes
Hsap\VPS11
1 of 14
No
No
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) (2)
Rnor\Vps41
14 of 14
Yes
Yes
Rnor\Vps11
1 of 14
No
No
Mus musculus (laboratory mouse) (4)
Mmus\Vps41
13 of 14
Yes
Yes
Mmus\Vps8
1 of 14
No
No
Mmus\Vps11
1 of 14
No
No
Mmus\Vps18
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (3)
Xtro\vps41
7 of 13
Yes
Yes
Xtro\hadh
1 of 13
No
Yes
Xtro\wdr88
1 of 13
No
Yes
Danio rerio (Zebrafish) (2)
Drer\vps41
13 of 14
Yes
Yes
Drer\vps11
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\vps-41
12 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (3)
Agam\AgaP_AGAP009174
12 of 12
Yes
Yes
Agam\AgaP_AGAP002665
1 of 12
No
No
Agam\AgaP_AGAP007578
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (1)
Atha\VPS41
13 of 13
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\VPS41
11 of 13
Yes
Yes
Scer\PEP5
1 of 13
No
No
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\vps41
11 of 12
Yes
Yes
Spom\vps11
1 of 12
No
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:lt. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (2)
dor
1 of 13
Vps8
1 of 13
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 ( 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?
VPS41; VPS41 subunit of HOPS complex
14 of 14
605485
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
lt
enhanceable
Atg1
(Umargamwala et al., 2025)
lt
suppressible
Atg1
(Nicolson et al., 2024)
lt
suppressible
detr
(Nicolson et al., 2024)
lt
enhanceable
Su(var)2-1
(Clegg et al., 1998)
lt
enhanceable
Su(var)2-1|Su(var)208
(Clegg et al., 1998)
lt
enhanceable
Su(var)205|E(Pc)
(Clegg et al., 1998)
lt
enhanceable
Su(var)205|Su(var)208
(Clegg et al., 1998)
lt
enhanceable
Su(var)208|E(Pc)
(Clegg et al., 1998)
lt
enhanceable
Su(var)208|Su(var)2-1
(Clegg et al., 1998)
lt
enhanceable
w
(Lloyd et al., 2002)
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
Atg1
enhanceable
lt
(Umargamwala et al., 2025)
detr
suppressible
lt
(Nicolson et al., 2024)
FIG4
suppressible
lt
(Bharadwaj et al., 2016)
Vps8
enhanceable
lt
(Lőrincz et al., 2016)
External Data
Subunit Structure (UniProtKB)
Part of the homotypic fusion and vacuole protein sorting (HOPS) complex, composed of Vps16A, car/Vps33A, dor/Vps18, Vps39, Vps11 and lt/Vps41.
(UniProt, Q7PL76 )
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
FlyBase
External Links
External Data
Linkouts
KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
SignaLink - A signaling pathway resource with multi-layered regulatory networks.
Class of Gene
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2L
Recombination map
2-54
Cytogenetic map
40F7-40F7
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
40F7-40F7
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
40E-40F
(determined by in situ hybridisation)
(Koryakov et al., 1996)
40F-40F
(determined by in situ hybridisation)
(Devlin et al., 1990)
Relative order with respect to l(2)40Fc and l(2)40Fd is unknown.
(Hilliker, 1976)
Experimentally Determined Recombination Data
Location

2-54

(FlyBase, 2016)

2-55.3

(Comeron et al., 2012)

2-55.0

(Meyer et al., 1950)
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (69)
Genomic Clones (21)
cDNA Clones (84)
 

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
       

      polyclonal

      (Swetha et al., 2011)
      Commercially Available Antibodies
       
      Cell Line Information
      Publicly Available Cell Lines
       
        Other Stable Cell Lines
         
          Other Comments

          dsRNA made from templates generated with primers directed against lt that is transfected into S2 treated with Listeria monocytogenes reveals lt to be involved in Listeria monocytogenes intracellular growth.

          (Cheng et al., 2005)

          Variegation of lt and cta is manifest at phenotypic and gene expression levels in the adult eye, and the larval salivary glands and Malpighian tubules. The relative severity of the effect correlates with the chromosomal rearrangement. Larval imaginal discs do not display variegation, but show uniform reduction of transcription, which correlates in magnitude with the degree of variegation.

          (Weiler and Wakimoto, 1998)

          Mapping and complementation data of Class IV derivatives of the T(2;3)ltX13, P{wF} chromosome suggest that the amount of heterochromatin in cis to the lt gene is correlated with its level of activity. Chromosomes that carry the smallest deletion of heterochromatin have weaker effects on the lt+ gene when compared to those with the largest deletions.

          (Howe et al., 1995)

          Lesions in lt reduce or eliminate pigmentation in the eyes and ocelli and block pigmentation of the fat body and tubules: lt is required for normal pigmentation of all four tissues.

          (Tearle, 1991)
          Relationship to Other Genes
          Source for database merge of

          Source for merge of: lt CG18028

          (Misra, 2000.4.8)
          Additional comments

          'Light mottled' lt alleles are a series of X-ray induced light-variegated chromosome rearrangements. Some have a mixture of light and wild-type ommatidia and are classified as pale; others have a mixture of wild-type and occasional darker ommatidia and are classified as dark.

          Nomenclature History
          Source for database identify of
          Nomenclature comments
          Etymology
          Synonyms and Secondary IDs (10)
          Reported As
          Symbol Synonym
          CG18028
          (National Institute of Genetics Fly Stocks, 2022-, Caizzi et al., 2016, Yu et al., 2013, Ni et al., 2011.7.19, Ying et al., 2011, Saleh et al., 2006)
          Dm-lt(het)
          (Yasuhara et al., 2005)
          Lt
          (Takáts et al., 2014, Ying et al., 2011)
          Vps41
          (Nassari et al., 2022, Reed et al., 2022, Lakatos et al., 2021, Csizmadia and Juhász, 2020, Hodgson et al., 2019, Lőrincz et al., 2019, Csizmadia et al., 2018, Lőrincz et al., 2017, Li and Blissard, 2015, Takáts et al., 2014, Solinger and Spang, 2013)
          l(2)40Fb
          (Dimitri et al., 1997)
          light
          (Liu et al., 2020)
          lt
          (Nicolson et al., 2024, Lund et al., 2021, Csizmadia and Juhász, 2020, Cunningham et al., 2020, Meyer-Nava et al., 2020, Nakamura et al., 2020, Boda et al., 2019, Lőrincz et al., 2019, Maksimov and Koryakov, 2019, Marsano et al., 2019, Csizmadia et al., 2018, Lund et al., 2018, Miller et al., 2018, Bharadwaj et al., 2016, Lőrincz et al., 2016, Lőrincz et al., 2016, Takáts et al., 2015, Ashwal-Fluss et al., 2014, Gillingham et al., 2014, Takáts et al., 2014, Satoh et al., 2013, Lin et al., 2012, Wang et al., 2012, Du et al., 2011, Swetha et al., 2011, Ashton-Beaucage et al., 2010, Lemos et al., 2010, Chinchore et al., 2009, Lu et al., 2009, Paredes and Maggert, 2009, Venken et al., 2009, Venken et al., 2009, Wakimoto, 2008.11.19, Wilkin et al., 2008, Yasuhara and Wakimoto, 2008, de Wit et al., 2007, Falcon-Perez et al., 2007, Weiler, 2007, de Wit et al., 2005, Cherry and Perrimon, 2004)
          vps41
          (Asensio et al., 2013)
          Name Synonyms
          light
          (Casale et al., 2021, Funikov et al., 2020, Meltzer et al., 2019, Saha and Mishra, 2019, Saha et al., 2019, Branco et al., 2017, Lőrincz et al., 2016, Dönertas et al., 2013, Hilliker and Taylor-Kamall, 2013, Solinger and Spang, 2013, Yu et al., 2013, Klenov et al., 2011, Swetha et al., 2011, Zhang et al., 2011, Huang et al., 2010, Lemos et al., 2010, Roignant and Treisman, 2010, Chinchore et al., 2009, Lu et al., 2009, Paredes and Maggert, 2009, Fanti et al., 2008, Schaeffer et al., 2008, Wilkin et al., 2008, Yasuhara and Wakimoto, 2008, de Wit et al., 2007, Falcon-Perez et al., 2007, Rossi et al., 2007, Simonsen et al., 2007, Saleh et al., 2006, Yasuhara and Wakimoto, 2006, Cherry and Perrimon, 2004, Dimitri et al., 2003, Dimitri et al., 2003, Yasuhara et al., 2003, Li et al., 2002, Warner, 1997.11.13)
          pink-wing
          pinkoid
          Secondary FlyBase IDs
          • FBan0018028
          • FBgn0032992
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 57 )
          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
          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
          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 (genetic) - An integrated Molecular Interaction Database
          MIST (protein-protein) - An integrated Molecular Interaction Database
          SignaLink - A signaling pathway resource with multi-layered regulatory networks.
          References (212)