FlyBase Gene Report: Dmel\lt

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

59 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

Gene Snapshot
Alliance
Auto summary
Gene Group
Red Book
Interactive Fly

Also Known As

Vps41, l(2)40Fb

Key Links

Genomic Location

Cytogenetic map

Sequence location

2L:22,924,795..22,943,135 [+]

Recombination map

2-54

RefSeq locus

NT_033779 REGION:22924795..22943135

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

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Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (18 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 zinc ion binding

inferred from sequence model

(Ying et al., 2011)

Biological Process (15 terms)

Terms Based on Experimental Evidence (9 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 determination of adult lifespan

inferred from mutant phenotype

(Simonsen et al., 2007)

involved_in dsRNA transport

inferred from mutant phenotype

(Saleh et al., 2006)

involved_in endocytosis

inferred from mutant phenotype

(Wilkin et al., 2008)

involved_in endosomal vesicle fusion

inferred from mutant phenotype

(assigned by UniProt )

(Lőrincz et al., 2016)

involved_in Notch receptor processing

inferred from mutant phenotype

(Wilkin et al., 2008)

involved_in ommochrome biosynthetic process

inferred from mutant phenotype

(Tearle, 1991)

involved_in viral entry into host cell

inferred from high throughput mutant phenotype

(Hodgson et al., 2019)

Terms Based on Predictions or Assertions (8 terms)

CV Term

Evidence

References

involved_in cellular response to starvation

inferred from biological aspect of ancestor with PANTHER:PTN000289375

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in endosomal vesicle fusion

inferred from biological aspect of ancestor with PANTHER:PTN001759852

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in intracellular transport

traceable author statement

(Narayanan and Ramaswami, 2001)

involved_in lysosomal transport

traceable author statement

(Luzio et al., 2000)

involved_in macroautophagy

inferred from biological aspect of ancestor with PANTHER:PTN000289375

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in protein targeting to vacuole

inferred from biological aspect of ancestor with PANTHER:PTN001759852

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in regulation of SNARE complex assembly

inferred from sequence or structural similarity with SGD:S000002487

(Solinger and Spang, 2013)

involved_in vesicle-mediated transport

inferred from sequence or structural similarity with SGD:S000002487

(Solinger and Spang, 2013)

Cellular Component (2 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 (2 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:PTN001759852

(assigned by GO_Central )

(Gaudet et al., 2011)

is_active_in late endosome

inferred from biological aspect of ancestor with PANTHER:PTN001759852

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

VPS-C COMPLEXES: HOPS AND CORVET

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

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).

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

Number of Unique Polypeptides

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 New Section

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q7PL76)

If you don't see the viewer to the right, 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.

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

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

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

FBpp0110415

61.5

528

5.96

FBpp0305699

96.9

841

6.88

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

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

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.

lt_1

Linkouts

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:

low

high

Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.

Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:

low

high

as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. 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

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

embryonic/larval brain

(Weiler and Wakimoto, 1998)

embryonic/larval circulatory system

(Weiler and Wakimoto, 1998)

embryonic/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)

embryonic stage -- adult stage

(Devlin et al., 1990)

larval stage

Malpighian tubule

(Devlin et al., 1990)

imaginal disc

(Devlin et al., 1990)

embryonic/larval brain

(Devlin et al., 1990)

embryonic/larval salivary gland

(Devlin et al., 1990)

embryonic/larval fat body

(Devlin et al., 1990)

embryonic/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

• membrane

(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

GBrowse - Visual display of RNA-Seq signals

View Dmel\lt in GBrowse 2

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\lt

View exonic expression by tissue for Dmel\lt

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

FBgn0002566

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

3355130/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0002566

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0002566

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0002566

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG18028

Flygut - An atlas of the Drosophila adult midgut

FBgn0002566

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 42 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 6 )

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)

(Siegel, 1981)

(Siegel, 1981)

(Siegel, 1981)

(Siegel, 1981)

(Siegel, 1981)

(Siegel, 1981)

(Siegel, 1981)

(Ganetzky, 1977)

(Ganetzky, 1977)

(Ganetzky, 1977)

(Ganetzky, 1977)

(Ganetzky, 1977)

(Ganetzky, 1977)

(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)bw^VDe2LCy^R

(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)lt^hd6

(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)E^HH

(Hilliker and Holm, 1975)

Inferred from location ( 0 )

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal

lethal | dominant

lt¹¹

lethal | recessive

lethal - all die before end of pupal stage | recessive

partially lethal | recessive

lt²⁰

viable

Sterility

Allele

sterile | recessive

lt⁴

Other Phenotypes

Allele

abnormal eye color

abnormal eye color | recessive

abnormal size | third instar larval stage (with Df(2L)lt45)

lt¹¹

enhancer of variegation, with Su(var)205⁵/Su(var)205²⁰⁵

lt^unspecified

increased cell size

lt^LL07138

short lived

lt⁴

short lived | male

lt¹

some die during pupal stage | recessive

suppressor of variegation (with In(2L)lt^X2), with E(var)3-9³

lt¹

suppressor of variegation | dominant (with In(2L)lt^X2), with E(var)3-9¹

lt¹

suppressor of variegation | dominant (with In(2L)lt^X2), with E(var)3-9²

lt¹

visible

visible | recessive

lt^unspecified

Phenotype manifest in

Allele

autolysosome | somatic clone | wandering third instar larval stage | nutrition conditional, with Scer\GAL4^{FRT.Rnor\Cd2.Act5C}

lt^HMS00190

autolysosome | wandering third instar larval stage | nutrition conditional (with Df(2L)lt45)

lt¹¹

autophagosome | increased number

lt^LL07138

autophagosome | increased number | wandering third instar larval stage | nutrition conditional (with Df(2L)lt45)

lt¹¹

embryonic/larval brain | third instar larval stage (with Df(2L)lt45)

lt¹¹

embryonic/larval fat body | somatic clone | wandering third instar larval stage | nutrition conditional, with Scer\GAL4^{FRT.Rnor\Cd2.Act5C}

lt^HMS00190

embryonic/larval fat body | third instar larval stage (with Df(2L)lt45)

lt¹¹

embryonic/larval fat body | wandering third instar larval stage | nutrition conditional (with Df(2L)lt45)

lt¹¹

embryonic/larval garland cell | larval stage (with Df(2L)lt45)

lt^LL07138

embryonic/larval garland cell | third instar larval stage (with Df(2L)lt45)

lt¹¹

embryonic/larval salivary gland | third instar larval stage (with Df(2L)lt45)

lt¹¹

eye

lt^unspecified

garland cell

lt^LL07138

late endosome

lt^LL07138

late endosome | larval stage (with Df(2L)lt45)

lt^LL07138

late endosome | third instar larval stage (with Df(2L)lt45)

lt¹¹

lysosome | third instar larval stage (with Df(2L)lt45)

lt¹¹

Malpighian tubule

ocellus pigment granule

lt¹

pigment cell

vacuole | larval stage (with Df(2L)lt45)

lt^LL07138

wing

lt^pk

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\VPS41

14 of 15

Yes

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Vps41

14 of 15

Yes

Rattus norvegicus (Norway rat) (1)

Rnor\Vps41

7 of 13

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\vps41

9 of 12

Yes

Danio rerio (Zebrafish) (1)

Drer\vps41

8 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\vps-41

14 of 15

Yes

Arabidopsis thaliana (thale-cress) (1)

Atha\VPS41

9 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\VPS41

13 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\vps41

10 of 12

Yes

Other Organism Orthologs (via OrthoDB)

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (1)

Gene Symbol

Score

Source

Alignment

1 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

retinal degeneration, excessive endocytosis of rhodopsin

Disease Model Summary Ribbon

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v8.0 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 15

605485

SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 29; SCAR29

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

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

lt - Rab2

pull down, peptide massfingerprinting

(Gillingham et al., 2014)

lt - Vps16A

anti tag coimmunoprecipitation, western blot

(Lőrincz et al., 2019)

lt - car

anti tag coimmunoprecipitation, western blot

(Lőrincz et al., 2019)

lt - dor

anti tag coimmunoprecipitation, western blot

(Lőrincz et al., 2019)

Summary of Genetic Interactions

esyN Network Diagram

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

E(Pc)|Su(var)205

(Clegg et al., 1998)

enhanceable

E(Pc)|Su(var)208

(Clegg et al., 1998)

enhanceable

Su(var)2-1

(Clegg et al., 1998)

enhanceable

Su(var)2-1|Su(var)208

(Clegg et al., 1998)

enhanceable

Su(var)205|Su(var)208

(Clegg et al., 1998)

enhanceable

(Lloyd et al., 2002)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

FIG4

suppressible

(Bharadwaj et al., 2016)

Vps8

enhanceable

(Lőrincz et al., 2016)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

78255

DroID - A comprehensive database of gene and protein interactions.

FBgn0002566

MIST (genetic) - An integrated Molecular Interaction Database

MIST (protein-protein) - An integrated Molecular Interaction Database

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-54

Cytogenetic map

Sequence location

2L:22,924,795..22,943,135 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

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 (59)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

1592

lt³/SM5

1051

lt¹ rl¹

336

26190

26191

26192

26194

1056

103333

101540

lt¹ bw¹

106184

lt¹ rl¹

106187

lt¹ rl¹ stw³

More stocks available...

Genomic Clones (21)

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

cDNA Clones (112)

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 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.

FBgn0002566

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0002566

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

3355130

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Swetha et al., 2011)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

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.

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)lt^X13, 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)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 58 )

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.

3355130

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.

Q7PL76

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.

Q7PL76

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0002566

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0002566

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

3355130/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0002566

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

lt_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0002566

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0002566

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG18028

Flygut - An atlas of the Drosophila adult midgut

FBgn0002566

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

3355130

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC015204

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

Dmel_CG18028

MARRVEL_MODEL - MARRVEL (model organism gene)

3355130

modMine - A data warehouse for the modENCODE project

FBgn0002566

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

O76248

Linkouts

BioGRID - A database of protein and genetic interactions.

78255

DroID - A comprehensive database of gene and protein interactions.

FBgn0002566

DRSC - Results frm RNAi screens

FBgn0002566

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0002566

FlyMine - An integrated database for Drosophila genomics

FBgn0002566

MIST (genetic) - An integrated Molecular Interaction Database

MIST (protein-protein) - An integrated Molecular Interaction Database

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

CG18028

(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)

(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)

(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, Ashwal-Fluss et al., 2014, Gillingham et al., 2014, Takáts et al., 2014, Satoh et al., 2013, Lin 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

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

References (203)

The following external sites may use different assemblies or annotations than FlyBase.

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