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General Information
Symbol
Dmel\trx
Species
D. melanogaster
Name
trithorax
Annotation Symbol
CG8651
Feature Type
FlyBase ID
FBgn0003862
Gene Model Status
Stock Availability
Gene Snapshot
trithorax (trx) encodes a chromatin-modifying enzyme involved in gene regulation. It methylates the histone encoded by His3 on Lys-4, promoting its further acetylation. This activity antagonises the epigenetic silencing by Polycomb group proteins. It contributes to axon guidance, eye development and germ cell migration. [Date last reviewed: 2019-03-14]
Also Known As

trxG, l(3)j14A6, DMTRXIII, Rg-bx, l(3)s5452

Key Links
Genomic Location
Cytogenetic map
Sequence location
3R:14,263,358..14,286,903 [-]
Recombination map

3-55

RefSeq locus
NT_033777 REGION:14263358..14286903
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (26 terms)
Molecular Function (8 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
inferred from physical interaction with UniProtKB:Q94545
(assigned by UniProt )
inferred from physical interaction with UniProtKB:Q9VCH5
(assigned by UniProt )
inferred from direct assay
(assigned by UniProt )
inferred from physical interaction with FLYBASE:flw; FB:FBgn0000711
inferred from physical interaction with FLYBASE:Pp1-13C; FB:FBgn0003132
inferred from physical interaction with FLYBASE:Pp1α-96A; FB:FBgn0003134
inferred from physical interaction with FLYBASE:Pp1-87B; FB:FBgn0004103
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR001628
(assigned by InterPro )
traceable author statement
inferred from biological aspect of ancestor with PANTHER:PTN002911713
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR001628
(assigned by InterPro )
(assigned by InterPro )
inferred from sequence model
Biological Process (11 terms)
Terms Based on Experimental Evidence (11 terms)
CV Term
Evidence
References
inferred from mutant phenotype
(assigned by UniProt )
inferred from genetic interaction with UniProtKB:Q9VCH5
(assigned by UniProt )
inferred from mutant phenotype
inferred from genetic interaction with UniProtKB:Q9VCH5
(assigned by UniProt )
inferred from mutant phenotype
inferred from direct assay
inferred from mutant phenotype
inferred from direct assay
inferred from mutant phenotype
inferred from direct assay
inferred from mutant phenotype
(assigned by UniProt )
inferred from mutant phenotype
(assigned by UniProt )
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
traceable author statement
inferred by curator from GO:0044665
inferred from biological aspect of ancestor with PANTHER:PTN002911713
(assigned by GO_Central )
traceable author statement
inferred from biological aspect of ancestor with PANTHER:PTN002911713
(assigned by GO_Central )
Cellular Component (7 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002911713
(assigned by GO_Central )
Protein Family (UniProt)
Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. TRX/MLL subfamily. (P20659)
Summaries
Gene Group (FlyBase)
TRITHORAX ACETYLATION COMPLEX 1 -
The Trithorax Acetylation Complex 1 (TAC1) possesses histone H3 K4 methyltransferase and histone acetyltransferase activities. (Adapted from FBrf0192625 and FBrf0167942).
SET DOMAIN LYSINE METHYLTRANSFERASES -
SET domain lysine methyltransferases (KMTs) catalyze the addition of methyl groups to lysine residues. SET domain KMTs possess a domain that was original characterized in the D.mel KMTs Su(var)3-9, E(z) and trx. (Adapted from FBrf0216343).
TRX COMPLEX -
The Trithorax (Trx) complex is a COMPASS-like complex that mediates methylation of histone H3K4. (Adapted from FBrf0216343).
Protein Function (UniProtKB)
Histone methyltransferase that trimethylates 'Lys-9' of histone H3 (H3K9me3). H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional activation (PubMed:12408863). Functions in segment determination through interaction with genes of bithorax (BX-C) and antennapedia (ANT-C) complexes (PubMed:2107543, PubMed:7958911). Acts as an activator of BX-C (PubMed:7924996). Involved in the very early regulation of homeotic genes expressed only in the posterior region of the embryo (PubMed:7924996, PubMed:25310983).
(UniProt, P20659)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
trx: trithorax
The presence of trx+ is required throughout embryonic and larval development for the appropriate differentiation in the adult of segments in the head, thorax, and abdomen (Ingham and Whittle, 1980; Ingham, 1981), the primary effect being in the thoracic segments. Mutants show transformations of the first and the third thoracic segments to the second thoracic segment as well as transformations in the abdomen (Mozer and Dawid, 1989). The gene seems to be involved in the positive regulation of the BXC and the ANTC (Duncan and Lewis, 1982). The viable mutant combinations trx1/trx1 and trxD/+ show variable segmental transformations in adults, as do heterozygous deficiencies [Df(3R)red-P52/+, for example]. The frequency of homeotic transformations in adults and, to some extent, in larvae of such genotypes varies inversely with the dosage of the BXC (Duncan and Lewis, 1982; Sato and Denell, 1987). A similar dosage effect has been proposed for the ANTC (Sato and Denell, 1987). When the mutant allele or deficiency is maternal in origin, the frequency of transformations is higher in adults (but not in larvae). The alleles trx2, trx3, and trxD are larval or pupal lethals as homozygotes, trans-heterozygotes, or deficiency heterozygotes, and may show weak homeotic transformations in larvae or in homozygous clones in adults (Capdevila and Garcia-Bellido, 1981; Ingham, 1981, 1983, 1985b).
trx1
Flies homozygous for trx1 show a variety of partial homeotic transformations [ventral prothorax and metathorax to mesothorax and second to seventh abdominal segments to first abdominal segment (Ingham and Whittle, 1980)]. Penetrance of the transformation phenotype is stronger in hemizygotes than homozygotes and increases as the temperature is raised from 18 to 25C. At the higher temperature, the penetrance of the mutant offspring of trx1/trx1 females is almost 100%, while mutant offspring of trx1/+ females show only about 50% penetrance. The temperature-sensitive period occurs prior to hatching. Ingham (1980) noted the following abnormalities in extreme trx1 mutants: (1) Extra bristles between humerus and coxa and on the distal tibia of the first leg; (2) Similar changes on the third leg; (3) Loss or reduction of transverse bristle rows, and, in males, decrease in number of sex comb teeth on the first leg; (4) Replacement of halter disk derivatives by wing blade, notal, and scutellar structures; (5) Rotated genitalia and abnormal tergite pigmentation in male flies. 75% of heterozygotes with Df(3R)red or with the lethal allele trx3 are lethal, either as larvae or pupae (Ingham, 1981); the heterozygotes that survive show cuticular transformations of the ventral prothorax and the metathorax, an extra mesonotum developing posterior to the normal one, and anteriorly-directed abdominal transformations (Ingham, 1985a).
trx2
The recessive embryonic lethal trx2 fails to complement trx1, trx3, or trxD, either for the transformation phenotype or for lethality. Trans-heterozygotes of trx2 with another allele or with a deficiency for the locus show weak expression of the trx homeotic phenotype and about 40-50% pupal lethality. Since the lethal mutations are cell viable, trx2/trx3 clones have been induced by mitotic recombination in trx2/trx3;Dp(3;1)kar5l, trx+ flies (Ingham, 1981, 1985b). The clones produced showed transformations of the antenna, eye, head capsule, and proboscis, bristle abnormalities in the legs, vein and bristle abnormalities in the wings, and transformations of halter to wing tissue and of genital to thoracic tissue; mutant clones in abdominal segments one to seven were not found (Ingham, 1985b).
trx3
Like trx2. About 75% of the trx1/trx3 trans-heterozygotes are lethals, larval and pupal (Ingham, 1981).
trxD
Adult trxD/+ flies are viable and characterized by their "bithorax variegated" phenotype (Lewis). These mutants show no prothoracic transformations, but do show patchy transformations of halter into wing and third leg into second leg (as in bx and pbx) and variable transformations of posterior abdominal segments into more anterior ones (Capdevila and Garcia-Bellido, 1981; Duncan and Lewis, 1982). In homozygotes, deficiency heterozygotes, or trans-heterozygotes over trx1, trx2, or trx3, the trxD allele is lethal or semilethal in larvae or pupae; in clones it is cell viable. Transformed trxD/trxD clones were found in the head region (but not in the thorax or abdomen) by Capdevila and Garcia-Bellido (1981), while transformed trx2/trxD clones were found in both head and thorax (but not in the abdomen) by Ingham (1985b).
Summary (Interactive Fly)

histone methyltransferase activity (H3-K4 specific), transcription factor - zinc finger - trithorax group - maintains activity of homeotic genes - regulates systemic signaling during Drosophila imaginal disc regeneration - a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes

Gene Model and Products
Number of Transcripts
5
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\trx 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

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

Gene model reviewed during 5.48

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0082947
14052
3726
FBtr0082948
12815
3358
FBtr0082949
12366
3358
FBtr0082950
13603
3726
FBtr0100277
11066
3358
Additional Transcript Data and Comments
Reported size (kB)

14.205, 13.756, 12.968, 12.519, 10.941 (sequence analysis)

15, 12, 10 (northern blot)

12.445 (compiled cDNA)

15, 12, 10, 3 (northern blot)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0082406
400.1
3726
6.49
FBpp0082407
364.7
3358
6.11
FBpp0082408
364.7
3358
6.11
FBpp0082409
400.1
3726
6.49
FBpp0099668
364.7
3358
6.11
Polypeptides with Identical Sequences

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

3726 aa isoforms: trx-PA, trx-PD
3358 aa isoforms: trx-PB, trx-PC, trx-PE
Additional Polypeptide Data and Comments
Reported size (kDa)

405, 365 (kD predicted)

3726 (aa); 368 (kD)

Comments

trx gene product binds within an 8.4kb

regulatory region of the fkh gene that directs embryonic expression. It

also binds to ectopic sites carrying these sequences in transformed lines.

External Data
Subunit Structure (UniProtKB)

Interacts (via SET domain) with ash1 (via SET domain) (PubMed:10454589, PubMed:10656681). Interacts with Nup98 (PubMed:25310983).

(UniProt, P20659)
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\trx 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
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

antennal primordium

Comment: reported as procephalic ectoderm primordium

central brain primordium

Comment: reported as procephalic ectoderm primordium

visual primordium

Comment: reported as procephalic ectoderm primordium

dorsal head epidermis primordium

Comment: reported as procephalic ectoderm primordium

lateral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

ventral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference

Comment: reference states 11-15 hr AEL

Comment: reference states 2-4 hr AEL

Additional Descriptive Data

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

trx transcript ME is present in 0-1hr embryos and adult females suggesting that it is maternally deposited. It is also present in 2-4hr embryos where the ratio of ME to E1 to E2 is 11:3:1 . ME is also detected in 11-15hrs as a minor component. ME is detected by in situ hybridization in the syncytial blastoderm. The major site of expression is the ventral region of the posterior half of the embryo in cells fated to become mesoderm.

trx transcript E1 is detected in 2-4hr embryos. The ratio of ME to E1 to E2 at this stage is 11:3:1 . Transcript E1 is detected by in situ hybridization in the presumptive mesoderm at the syncytial blastoderm stage. It is then expressed in a broad domain that resolves into four pair-rule-like stripes in the posterior half of the embryo. Stripes 1,2 and 4 are stronger than stripe 3. By mapping relative to ftz, the stripes were located at parasegments 6, 8, 10, and 12. Stripes persist until early stage 8.

trx transcript E2 is a minor species detected in 2-4hr embryos. The ratio of ME to E1 to E2 at this stage is 11:3:1 . Transcript E2 appears to be expressed throughout the early embryo.

trx transcript L is expressed transiently in 11-15hr embryos. It becomes very abundant in early pupae, and is the major species in adult males. Transcript L is detected in late embryos by in situ hybridization. Strong staining is observed in the suboesophageal and supraoesophageal ganglia, and in the ventral nerve cord. Weaker staining is seen in the head, the clypeolabrum and the antennomaxillary complex.

Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

The trx protein accumulates in the region of the bithorax complex genes on polytene chromosomes from central and posterior regions of larval fat bodies where the homeotic genes are expressed.

trx protein strongly binds to 16 specific sites along the polytene chromosomes. Among these is the fkh gene region.

Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\trx 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) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 130 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of trx
Transgenic constructs containing regulatory region of trx
Deletions and Duplications ( 18 )
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
pupal cuticle & abdomen
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (8)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
9 of 15
Yes
Yes
8 of 15
No
Yes
 
3  
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
2  
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (13)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
8 of 15
Yes
Yes
7 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (8)
5 of 13
Yes
Yes
2 of 13
No
Yes
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (7)
7 of 12
Yes
Yes
4 of 12
No
Yes
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
Danio rerio (Zebrafish) (9)
9 of 15
Yes
Yes
9 of 15
Yes
Yes
7 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (13)
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (4)
1 of 9
Yes
Yes
1 of 9
Yes
Yes
1 of 9
Yes
No
1 of 9
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
1 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (1)
1 of 12
Yes
No
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG0919006O )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915001Q )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W001D )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch 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
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0053 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Ixodes scapularis
Black-legged tick
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G001U )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Ciona intestinalis
Vase tunicate
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (12)
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 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 )
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?
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.
Dmel gene
Ortholog showing functional complementation
Supporting References
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 (via SET domain) with ash1 (via SET domain) (PubMed:10454589, PubMed:10656681). Interacts with Nup98 (PubMed:25310983).
(UniProt, P20659 )
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
KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
Genomic Location and Detailed Mapping Data
Chromosome (arm)
3R
Recombination map

3-55

Cytogenetic map
Sequence location
3R:14,263,358..14,286,903 [-]
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
88B1-88B1
Limits computationally determined from genome sequence between P{PZ}flfl01949 and P{lacW}trxj14A6&P{PZ}trx00347
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
88B4-88B6
(determined by in situ hybridisation)
88B3-88B3
(determined by in situ hybridisation)
88B1-88B3
(determined by in situ hybridisation)
88B1-88B2
(determined by in situ hybridisation)
88B-88B
(determined by in situ hybridisation)
Location from complementation analysis with deficiency and duplication chromosomes (details unspecified).
Experimentally Determined Recombination Data
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (30)
Genomic Clones (23)
cDNA Clones (29)
 

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.

    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: trx CG8651

    Source for database merge of

    Source for merge of: trx l(3)j14A6

    Source for merge of: trx l(3)s5452

    Additional comments

    Alleles that show a recessive or dominant homeotic phenotype and fail to complement each other have been identified. All pairwise combinations of trxB14, trxB16 - trxB18 and trxE1-trxE13 are inviable except for rare survivors of the genotypes trxE11/trxB16, trxE11/trxB17, and trxB16/trxB17.

    Other Comments

    ChEST reveals this is a target of Mef2.

    trx protein is associated with the nuclear matrix.

    The SET domain of the trx protein efficiently binds to core histones and to nucleosomes. The primary target for binding is the His3 protein and binding requires the N-terminal histone tails.

    trx appears to be used in a tissue specific context at the Scr, Ubx, abd-A and Abd-B target genes. This may be due to differential regulation of trx by cell-signalling mechanisms.

    Identification: Enhancer trap expression pattern survey for loci expressed in the ring gland.

    Mutants are isolated in an EMS mutagenesis screen to identify zygotic mutations affecting germ cell migration at discrete points during embryogenesis: mutants exhibit germ cell migration defects.

    trx is required for a subset of somatic gonadal precursors (SGPs) to maintain their identity and to maintain their association with germ cells.

    The Pc and trx gene products bind to PRE target sequences by cellular blastoderm, when the bithorax complex transcription begins. At the same stage trx but not Pc gene product is strongly associated with core promoters.

    Snr1 is identified in a yeast two-hybrid screen for proteins interacting with trx. Yeast two-hybrid assays, in vitro binding assays and coimmunoprecipitation of proteins from cultured cells and transgenic flies demonstrates the trx and Snr1 proteins interact.

    Lack of E(z) protein activity disrupts chromosome binding by trx protein.

    Maintenance but not initiation of en gene expression in the embryo requires trx, which is also required to maintain stable long-term expression of the homeotic genes throughout development. trx is required for normal en expression in the wing imaginal disc. trx-dependent loss of en expression in the dorsal fat body is correlated with female sterility.

    Proper regulation of both trx and Pc can be established by transient assays with a haploid cell line expressing Ubx promoters fused to a Ecol\lacZ reporter gene. This system has been used to map the regulatory sequences in the Ubx promoter to a 440bp region. The Ubx proximal promoter is essential for trx-dependent activation.

    trx exerts its effect by binding directly or indirectly to specific DNA sequences in its target genes.

    Phenotypic studies and genetic interactions suggest that Snr1 and brm act together, and with trx, to regulate homeotic gene transcription.

    The negative autoregulation of ph-p starts at the blastoderm stage and is partly mediated by a transvection effect. As the number of functional copies of ph-p increases a concomitant reduction of the transcription in each copy is observed. This regulation is ensured positively by the trx group and negatively by the Pc group gene products.

    Sections of the Scr regulatory region may be important for regulation of Scr by Polycomb- and trithorax-group genes.

    Mutations of trx interact with Dfd to reduce the viability of the Dfd3/Dfd13 combination.

    The trx and fs(1)h proteins can function independently as activators of the Ubx locus.

    The anterior and posterior boundaries of trx expression are set up by hb and tll. trx expression is altered in Kr and kni mutant embryos but not in gt or pair rule mutant embryos. dl is involved in the activation of trx and sna activity is required after cellularization to maintain trx expression in the ventral domain.

    trx gene structure and the two predicted trx protein isoforms are characterised. trx mutations identify functionally important domains of the protein. trx RNAs encoding the larger isoform exhibit a transient spatially restricted expression pattern.

    Dvir\trx is cloned and the gene structure and expression pattern are determined. Many aspects of trx structure and expression are conserved between D.melanogaster and D.virilis. In particular a distinct expression pattern in early embryos previously implicated in maintenance of BX-C expression is also found in D.virilis, suggesting that it is an important feature of trx function.

    Mutations cannot rescue the lethality of the Df(1)ph-2-Psc1 interaction, demonstrating that trx group mutations cannot suppress Pc group phenotypes.

    Alleles of trx lighten the eye colour of some pairing sensitive allele of w, whereas alleles of Pcl darken their eye colour.

    trx gene product binds to at least 16 sites on larval salivary gland polytene chromosomes. The intensity of binding is strongly decreased in larvae carrying mutations in ash1 and E(z). trx gene product binds within an 8.4kb regulatory region that directs fkh expression in several embryonic tissues. These results demonstrate that trx maintains expression of target genes by interaction with their regulatory regions and this interaction depends on the presence of at least some trx and Pc group proteins.

    Proper expression of genes in the Bithorax and Antennapedia complexes is maintained by products of different trx RNAs at different times in embryogenesis.

    trx exerts its effects by positively regulating homeotic gene expression, but Ubx, Antp, abd-A, Abd-B, Scr and Dfd all have different tissue-specific, parasegment-specific and promoter-specific reductions in expression in a trx mutant background.

    Zygotic reduction or loss of trx+ fails to suppress the E(z) maternal effect to viability, total loss of zygotic trx+ activity dramatically suppresses maternal effect homeotic transformations.

    trx is required for the activation of the homeotic genes within the BXC and ANTC, mutations in trx suppress Pc and Pcl mutations.

    trx is required for normal expression of homeotic genes within the BXC and ANTC. trx is necessary for normal levels of Antp, Ubx and abd-A protein accumulation.

    The frequency of the trx mutant bithorax-variegated phenotype is increased in combination with Ubx mutations in cis regulatory regions not involved in the Ubx coding region, especially the abx and pbx region.

    trx cDNA has been cloned and sequenced.

    Genetic tests were used to confirm that ash1 and ash2 belong a functionally related class of genes, mutations in which cause a wide variety of homeotic transformations that are similar to the transformations caused by trx. Homozygous clones of lethal alleles do not express the transformation of posterior abdominal segments to anterior abdominal segments.

    trx is one of the 18 loci identified in a screen for dominant modifiers of Pc and/or Antp phenotypes. Alleles of Pc, Pcl, Scm, Dll, brm, kto, Scr and trx show clear dominant enhancement or suppression of AntpScx, whereas alleles of vtd, Vha55, Su(Pc)37D, urd, mor, skd and osa do not.

    22-52% of double heterozygotes involving a null allele of Ash-1 and the trx deficiency, Df(3R)red-P93, show partial transformations of halteres to wings and/or partial transformations of third (and sometimes first) legs to second legs, whereas in single heterozygotes no transformations are shown (Shearn, 1989). Heterozygosis for null alleles of trx suppresses the extra sex combs phenotype of +/Df(3L)Pc-MK, and increases penetrance of the maternal-effect homeotic phenotype of fs(1)h. trx function seems to be necessary for optimal expression of Scr- (Sato, 1988).

    The presence of trx+ is required throughout embryonic and larval development for the appropriate differentiation in the adult of segments in the head, thorax, and abdomen (Ingham and Whittle, 1980; Ingham, 1981), the primary effect being in the thoracic segments. Mutants show transformations of the first and the third thoracic segments to the second thoracic segment as well as transformations in the abdomen (Mozer and Dawid, 1989). The gene seems to be involved in the positive regulation of the BXC and the ANTC (Duncan and Lewis, 1982). The viable mutant combinations trx1/trx1 and trxD/+ show variable segmental transformations in adults, as do heterozygous deficiencies <up>Df(3R)red-P52/+, for example</up>. The frequency of homeotic transformations in adults and, to some extent, in larvae of such genotypes varies inversely with the dosage of the BXC (Duncan and Lewis, 1982; Sato and Denell, 1987). A similar dosage effect has been proposed for the ANTC (Sato and Denell, 1987). When the mutant allele or deficiency is maternal in origin, the frequency of transformations is higher in adults (but not in larvae). The alleles trx2, trx3 and trxD are larval or pupal lethals as homozygotes, transheterozygotes, or deficiency heterozygotes and may show weak homeotic transformations in larvae or in homozygous clones in adults (Capdevila and Garcia-Bellido, 1981; Ingham, 1981; Ingham, 1983; Ingham, 1985b).

    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 101 )
    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 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
    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
    SignaLink - A signaling pathway resource with multi-layered regulatory networks.
    Linkouts
    ApoDroso - Functional genomic database for photoreceptor development, survival and function
    BioGRID - A database of protein and genetic interactions.
    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.
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Synonyms and Secondary IDs (25)
    Reported As
    Symbol Synonym
    R-bx
    l(3)bxv
    l(3)j3A2
    trx
    (Delandre and Marshall, 2019, Gervais et al., 2019, Haberle et al., 2019, Leatham-Jensen et al., 2019, Sang Cho et al., 2019, Tiwari et al., 2019, Umer et al., 2019, Billmann et al., 2018, Ma et al., 2018, Sadasivam and Huang, 2018, Song et al., 2018, Janssens et al., 2017, Ables et al., 2016, Brewer-Jensen et al., 2016, Du et al., 2016, Hirano et al., 2016, Liu and Bossing, 2016, McCracken and Locke, 2016, Morimoto et al., 2016, Shih et al., 2016, Bieli et al., 2015, Chen et al., 2015, Dietz et al., 2015, Dupont et al., 2015, Ghasemi et al., 2015, Kim et al., 2015, Fereres et al., 2014, Gonzalez et al., 2014, Herrera and Morata, 2014, Komori et al., 2014, Oh et al., 2014, Pascual-Garcia et al., 2014, Stern et al., 2014, Tie et al., 2014, Kanda et al., 2013, Rougeot et al., 2013, Smith et al., 2013, Cuddapah et al., 2012, Follmer et al., 2012, Hallson et al., 2012, Izutsu et al., 2012, Ji et al., 2012, Popkova et al., 2012, Rincon-Arano et al., 2012, Abruzzi et al., 2011, Avery et al., 2011, Du et al., 2011, Islam et al., 2011, Mohan et al., 2011, Pérez et al., 2011, Pruteanu-Malinici et al., 2011, Rodriguez-Jato et al., 2011, Arancio et al., 2010, Baig et al., 2010, Bhatia et al., 2010, Frise et al., 2010, Gan et al., 2010, Lamiable et al., 2010, Reis et al., 2010, Siebold et al., 2010, Smulders-Srinivasan et al., 2010, Bejarano and Milán, 2009, Fang et al., 2009, González and Busturia, 2009, Hartmann et al., 2009, Khan et al., 2009, Tie et al., 2009, Blanco et al., 2008, Cukier et al., 2008, Estella et al., 2008, Florence and Faller, 2008, Fujioka et al., 2008, Garaulet et al., 2008, González et al., 2008, Lagarou et al., 2008, Melicharek et al., 2008, Ohno et al., 2008, Pauli et al., 2008, Petruk et al., 2008, Ranade et al., 2008, Srinivasan et al., 2008, Vázquez et al., 2008, Zhang et al., 2008, Baeg et al., 2007, Buszczak et al., 2007, Chang et al., 2007, Haigh and Lloyd, 2007, Ogasawara et al., 2007, Secombe et al., 2007, Bennett et al., 2006, Buszczak and Spradling, 2006, de Navas et al., 2006, Kavi et al., 2006, Petruk et al., 2006, Ringrose, 2006, Bejarano et al., 2005, Chen et al., 2005, Chen et al., 2005, Coffman et al., 2005, Möller et al., 2005, Muyrers-Chen et al., 2004, Rudenko et al., 2004, Marenda et al., 2003, Rudenko et al., 2003, Joanis and Lloyd, 2002, Fair et al., 2001, Gim et al., 2001, Hirose et al., 2001)
    trxI and trxII
    Secondary FlyBase IDs
    • FBgn0011040
    • FBgn0011340
    • FBgn0011443
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    Study focus (0)
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    References (539)