Gene Dmel\trx

General Information
Symbol	Dmel\trx	Species	D. melanogaster
Name	trithorax	Annotation symbol	CG8651
Feature type	protein_coding_gene	FlyBase ID	FBgn0003862
Created / Updated	2005-01-10/2005-01-10
Genomic Location
Chromosome (arm)	3R	Recombination map	3-54.2
Cytogenetic map	88B1-88B1	Sequence location	3R:10,089,080..10,112,623 [-]
Map ( GBrowse )
Summary Information
Automatically generated summary See sections below for more information	The gene trithorax is referred to in FlyBase by the symbol trx (CG8651, FBgn0003862). It has the cytological map location 88B1. Its sequence location is 3R:10089080..10112623. Its molecular function is described as: DNA binding; histone lysine N-methyltransferase activity (H3-K4 specific); sequence-specific DNA binding; protein binding; zinc ion binding; transcription factor activity. It is involved in the biological processes: germ cell migration; chromatin-mediated maintenance of transcription; histone methylation; regulation of transcription, DNA-dependent. 121 alleles are reported. The phenotypes of these alleles are annotated with 45 unique terms, many of which group under: adult segment; adult; organ system; peripheral nervous system; nervous system; thoracic segment; midgut constriction; mouthpart; abdominal segment 7; primordium. It has 5 annotated transcripts and 5 annotated polypeptides.
External Summaries

Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	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).
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 88B1-88B1 Limits computationally determined from genome sequence between P{PZ}flfl⁰¹⁹⁴⁹ and P{lacW}trx^j14A6&P{PZ}trx⁰⁰³⁴⁷
Experimentally Determined Cytological Location
Cytogenetic map Notes References 88B4-88B6 (determined by in situ hybridisation) (Ranz et al., 2001) 88B3-88B3 (determined by in situ hybridisation) (Lukacsovich et al., 2001) 88B1-88B3 (determined by in situ hybridisation) (Spradling et al., 1999) 88B1-88B2 88B3--4 (BDGP Project Members, 1994-1999) 88B1-88B2 (determined by in situ hybridisation) (Breen and Harte, 1991) 88B-88B (determined by in situ hybridisation) (Mozer and Dawid, 1989) 88B1-88B3 Location from complementation analysis with deficiency and duplication chromosomes (details unspecified). (Kennison and Tamkun, 1988)
Experimentally Determined Recombination Data
Location	3-54.2 (Kennison and Tamkun, 1988) 3- (Moore et al., 1998)
Left of (cM)	e (Moore et al., 1998)
Right of (cM)	st (Moore et al., 1998)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology) References Gene Order (overall orientation not stated) References
Gene Model & Products
Please see the GBrowse view of Dmel\trx for information on other features
Comments on Gene Model
	DGC clone LD39445 appears problematic: incomplete CDS
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) trx-RA FBtr0082947 NM_134282 14050 3726 trx-RB FBtr0082948 NM_057422 12813 3358 trx-RC FBtr0082949 NM_134281 12364 3358 trx-RD FBtr0082950 NM_057421 13601 3726 trx-RE FBtr0100277 NM_001014621 11064 3358
Additional Transcript Data & Comments
Reported size (kB)	14.205, 13.756, 12.968, 12.519, 10.941 (sequence analysis) (Sedkov et al., 1994) 15, 12, 10 (northern blot) (Breen and Harte, 1991) 15, 12, 10, 3 (northern blot) (Mozer and Dawid, 1989) 12.445 (compiled cDNA) (Mazo et al., 1990)
Comments	trx transcripts appear to use one major transcription start site and two major polyadenylation sites. Alternative splicing and polyadenylation is used to generate multiple transcripts. (Stassen et al., 1995)
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein trx-PA FBpp0082406 400.1 3726 6.49 NP_599109 AAF55041 trx-PB FBpp0082407 364.7 3358 6.11 NP_476770 AAN13600 trx-PC FBpp0082408 364.7 3358 6.11 NP_599108 AAN13601 trx-PD FBpp0082409 400.1 3726 6.49 NP_476769 AAN13599 trx-PE FBpp0099668 364.7 3358 6.11 NP_001014621 AAX52951
Additional Polypeptide Data & Comments
Reported size (kD)	3759 (aa) (Mazo et al., 1990) 405, 365 (kD predicted) (Stassen et al., 1995) 3726 (aa); 368 (kD) (Sedkov et al., 1994)
Comments	Two antibodies were prepared against trx protein. One recognizes both isoforms. The other is specific to the larger trx protein isoform. trx protein binds reproducibly at at least 63 sites along the polytene chromosomes. They are in euchromatic regions in the first, second and third chromosomes. Many of the sites coincide with sites of Pc protein binding. One of the sites of trx protein binding is within the Ubx promoter region. (Chinwalla et al., 1995, Chinwalla et al., 1995) Cysteine-rich regions of trx protein expressed in E. coli from a cDNA are capable of zinc binding in vitro, suggesting that trx encodes a metal-dependent DNA-binding protein. (Mazo et al., 1990) Antibodies were prepared which specifically recognize the larger trx protein. Antibodies that recognize both proteins were also made. (Kuzin et al., 1994) 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. (Kuzin et al., 1994)
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0003862
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Zinc finger, RING/FYVE/PHD-type (IPR013083) SET (IPR001214) Zinc finger, nuclear hormone receptor-type (IPR001628) Zinc finger, PHD-type (IPR001965) Post-SET zinc-binding region (IPR003616) FY-rich, N-terminal (IPR003888) FY-rich, C-terminal (IPR003889) Zinc finger, RING-type (IPR001841) Zinc finger, FYVE/PHD-type (IPR011011) MLL Transcription Factor (IPR015722) Methyltransferase, trithorax (IPR016569) TRANSFAC - Eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles • T00850
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA246802 AA392946 AA697691 AA802571 AA803610 AC007904 AE003704 AAF55041 AE003704 AAN13599 AE003704 AAN13600 AE003704 AAN13601 AI107179 AI109051 AI519730 AQ025177 AQ026397 AQ034083 AQ073004 AQ073881 AY051904 AAK93328 BF491509 BG632318 BG632382 BG640274 BH615002 BH901058 BH901059 BP541117 BP541118 CL868557 CL943588 CO267679 CO268755 CO271202 CO285140 CO312534 CO315525 CO325296 CO330212 CO342167 CO342802 CZ466647 CZ471163 CZ471164 CZ471670 CZ471897 CZ472227 CZ472676 CZ475703 CZ475704 CZ476503 CZ477168 CZ477170 CZ477171 CZ477231 CZ478873 CZ479080 EC051735 EC051741 EC052229 EC056535 EC057473 EC067429 EC074356 EC080466 EC082951 EC086366 EC088864 EC088949 EC197174 EC197564 EC212152 EC215171 EC217389 EC236979 EC242895 EC249724 EC256093 EL874460 EL874461 EL874533 EL874534 EL874604 EL874605 EL874676 EL874677 EL884872 G00467 GH06495 GH07557 M31617 AAA29025 U23446 Z31725 CAA83515 Z31725 CAA83516 Z50152 CAA90513 Z50152 CAA90514

UniProtKB/Swiss-Prot	P20659
UniProtKB/TrEMBL

Maps to	FBcl0298057 (FlyBase, 1992-, Lukacsovich et al., 2001)
Does NOT map to
Identified with	GH06495 (Spradling et al., 1999, Lukacsovich et al., 2001) LD39445 (BDGP Project Members, 2000-) Dm0096 (BDGP Project Members, 1994-1999, Spradling et al., 1999)
Mapped Features & Mutations
Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here Type Symbol & Location Additional Notes References aberration junction Df(3R)red-P6 3R:10,103,265..10,104,814 comment=breakpoint maps within the intron evidence=experimental (Breen, 1999, Breen and Harte, 1991) aberration junction trx[B14]-mutation-28 3R:10,095,105..10,097,493 comment=proximal breakpoint of 11kb deletion evidence=experimental linked_to=HindIII-HindIII_rfrag (Breen and Harte, 1991) aberration junction Df(3R)JY19 3R:10,085,815..10,086,021 comment=aberration breakpoint localized to a restriction fragment; position of restriction fragment on reference sequence inferred by FlyBase curator evidence=experimental linked_to=EcoRI-EcoRI_rfrag (Breen and Harte, 1991) aberration junction Df(3R)JY28 3R:10,125,490..10,129,589 comment=aberration breakpoint localized to a restriction fragment; position of restriction fragment on reference sequence inferred by FlyBase curator evidence=experimental linked_to=HindIII-HindIII_rfrag (Breen and Harte, 1991) aberration junction T(Y;3)red[P4].bk2 3R:10,126,907..10,127,159 comment=aberration breakpoint localized to a restriction fragment; position of restriction fragment on reference sequence inferred by FlyBase curator evidence=experimental linked_to=EcoRI-EcoRI_rfrag (Breen and Harte, 1991) aberration junction trx[B14]-mutation-13 3R:10,107,480..10,110,509 comment=distal breakpoint of 11kb deletion evidence=experimental linked_to=EcoRI-EcoRI_rfrag (Breen and Harte, 1991) complex substitution trx[E3] 3R:10,094,816..10,095,647 comment=Deletion of 832 nucleotides and insertion of 19 nucleotides leads to an in frame deletion of 271 amino acids. evidence=experimental (Mazo et al., 1990) deletion trx[B11] 3R:10,099,235..10,100,201 comment=Reported as a deletion of 833 nucleotides (2817-3649 in GB:M31617) leading to a frameshift and early translation termination. In the reference sequence, the span between the deletion endpoints is 967 bases. evidence=experimental (Mazo et al., 1990) deletion red[C1] 3R:10,125,309..10,126,912 evidence=experimental comment=red[C1] is a 600bp deletion which maps entirely within a 1.6kb EcoRI fragment. linked_to=EcoRI-EcoRI_rfrag (Breen and Harte, 1991) insertion site trx[A] 3R:10,105,003..10,107,485 evidence=experimental comment=position of restriction fragment on reference sequence inferred by FlyBase curator linked_to=EcoRI-EcoRI_rfrag (Breen and Harte, 1991) insertion site trx[1] 3R:10,105,003..10,107,485 evidence=experimental linked_to=EcoRI-EcoRI_rfrag comment=position of restriction fragment on reference sequence inferred by FlyBase curator (Breen and Harte, 1991) point mutation trx[Z16] 3R:10,096,786..10,096,786 pr_change=R1753W\|trx-PD,R1385W\|trx-PC,R1385W\|trx-PB,R175 3W\|trx-PA,R1385W\|trx-PE na_change=C10096786T evidence=experimental (Stassen et al., 1995) point mutation trx[Z11] 3R:10,091,173..10,091,173 na_change=G10091173A pr_change=G3601S\|trx-PD,G3233S\|trx-PC,G3233S\|trx-PB,G360 1S\|trx-PA,G3233S\|trx-PE evidence=experimental (Stassen et al., 1995) rescue fragment trx[+t34] 3R:10,086,016..10,120,779 comment=The boundaries of the 34kb genomic DNA fragment contained in the cosmid used for rescue lie close to EcoRI sites. There are several internal EcoRI sites within this genomic region. evidence=experimental linked_to=EcoRI-EcoRI_rfrag comment=The boundaries of the 34kb genomic DNA fragment contained in the cosmid used for rescue lie close to EcoRI sites. There are several internal EcoRI sites within this genomic region. (Breen and Harte, 1991) uncharacterized change in nucleotide sequence trx[JY16] 3R:10,102,286..10,102,600 comment=Breakpoint lies within the region encoding amino acids 172-276 evidence=experimental (Breen, 1999)
External Data
Linkouts	DEDB - Drosophila exon database: splicing graphs • 9419
Crossreferences
Expression Data
FlyBase-Curated Data
Transcript and Protein data	Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
Summary of Transcript Expression
Stage Tissue/Position Reference embryonic stage \| early (Sedkov et al., 1994) embryonic stage embryonic central nervous system (Sedkov et al., 1994) embryonic stage,larval stage,pupal stage (Mozer and Dawid, 1989) larval stage \| third instar dorsal mesothoracic disc \| posterior (Kuzin et al., 1994) adult stage \| female (Sedkov et al., 1994) embryonic stage \| early (Mozer and Dawid, 1989) embryonic stage head (Sedkov et al., 1994) embryonic stage \| stage 7-9 (Stassen et al., 1995) embryonic stage \| 11-15 hr (Sedkov et al., 1994) larval stage \| third instar imaginal disc (Kuzin et al., 1994) adult stage \| male (Sedkov et al., 1994) embryonic stage,larval stage,pupal stage (Breen and Harte, 1991) larval stage \| third instar dorsal metathoracic disc \| posterior (Kuzin et al., 1994) embryonic stage \| early mesoderm \| presumptive (Sedkov et al., 1994) embryonic stage \| stage 5 mesoderm anlagen (Stassen et al., 1995) embryonic stage embryonic central nervous system (Kuzin et al., 1994) embryonic stage supraoesophageal ganglion (Sedkov et al., 1994) larval stage \| third instar eye-antennal disc (Kuzin et al., 1994) larval stage \| third instar ventral mesothoracic disc \| posterior (Kuzin et al., 1994) embryonic stage \| 2-4hr (Sedkov et al., 1994) embryonic stage \| stage 4 (Stassen et al., 1995) embryonic stage suboesophageal ganglion (Sedkov et al., 1994) embryonic stage \| early mesoderm \| presumptive (Sedkov et al., 1994) embryonic stage antenno-maxillary complex (Sedkov et al., 1994) embryonic stage-adult stage (Mozer and Dawid, 1989) embryonic stage \| early (Mozer and Dawid, 1989) embryonic stage ventral nerve cord (Mozer and Dawid, 1989) embryonic stage \| early (Sedkov et al., 1994) embryonic stage ventral nerve cord (Sedkov et al., 1994) adult stage \| female (Sedkov et al., 1994) embryonic stage (Breen and Harte, 1991)