Gene Dmel\Ubx

General Information
Symbol	Dmel\Ubx	Species	D. melanogaster
Name	Ultrabithorax	Annotation symbol	CG10388
Feature type	protein_coding_gene	FlyBase ID	FBgn0003944
Created / Updated	2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)	3R	Recombination map	3-58.8
Cytogenetic map	89D6-89D9	Sequence location	3R:12,482,098..12,560,348 [-]
Map ( GBrowse )
Summary Information
Automatically generated summary See sections below for more information	The gene Ultrabithorax is referred to in FlyBase by the symbol Ubx (CG10388, FBgn0003944). It has the cytological map location 89D6-89D9. Its sequence location is 3R:12482098..12560348. Its molecular function is described as: protein binding; DNA binding; specific RNA polymerase II transcription factor activity; transcription factor activity; sequence-specific DNA binding. It is involved in the biological processes described with 15 unique terms, many of which group under: anatomical structure development; organ development; regulation of metabolic process; segment specification; trunk segmentation; regulation of biological process; transcription, DNA-dependent; organ morphogenesis; embryonic pattern specification; mesodermal cell fate specification; transcription from RNA polymerase II promoter; leg morphogenesis; regulation of developmental process; embryonic heart tube development; open tracheal system development; gut development. 463 alleles are reported. The phenotypes of these alleles are annotated with 154 unique terms, many of which group under: adult segment; thoracic segment; adult mesothoracic segment; peripheral nervous system; nervous system; organ system; larval abdominal segment; embryonic nervous system; blastoderm embryo; embryonic segment. It has 6 annotated transcripts and 6 annotated polypeptides.
External Summaries

Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	abx: anterobithorax (E.B. Lewis) Homozygotes show variable tranformations of the anteriormost portion of the third thoracic segment (T3) toward the corresponding part of T2. Homozygotes also show variable tranformations of posterior T2 to posterior T1. The latter effect is enhanced by low temperature. Partially complements and shows transvection with bx1, bx3, and bx34e. abx/pbx has the posterior portion of the distal segment of the haltere very slightly transformed into wing tissue; abx/pbx2 is similar if heterozygous for a rearrangement that suppresses transvection. bx: bithorax (E.B. Lewis) bx: bithorax From Bridges and Morgan, 1923, Carnegie Inst. Washington Publ. No. 327: 152. Homozygote has anterior portion of third thoracic segment (T3) transformed toward corresponding region of second (T2). The extent of this transformation is allele dependent and is most extreme in bx3 and weakest in bx4. Although the transformations caused by most bx alleles are uniform, those caused by bx1 and bx34eprv are highly variable. At 17C several bx alleles show weak and variable transformations of posterior T2 to posterior T1. bx3, bx8, and bxG over pbx show a very slight pbx effect (as described for abx) if heterozygous for a rearrangement that suppresses transvection. bxd: bithoraxoid (E.B. Lewis) bxd: bithoraxoid From Bridges and Morgan, 1923, Carnegie Inst. Washington Publ. No. 327: 225. Homozygotes show transformation of the anterior first abdominal segment (A1) to the corresponding region of the third thoracic segment (T3). In addition, bxd homozygotes have posterior T3 and posterior A1 transformed toward posterior T2. Hemizygotes for the stronger bxd alleles show (with variable expression) formation of one or a pair of well-developed thoracic legs and, rarely, an extra haltere on A1; the frequency of these abdominal halteres is greatly enhanced in hemizygotes for bxd9 iab2K. The A1 legs in bxd hemizygotes contain underdeveloped posterior compartments, indicating that posterior A1 is partially transformed toward thorax. Cbx: Contrabithorax (E.B. Lewis) Cbx1/+ has a strong transformation of the posterior region of the second thoracic segment (T2) toward the corresponding region of the third (T3), and a weak and variable transformation of anterior T2 toward anterior T3. The Cbx1 homozygote differs in having a stronger, but still variable, transformation of anterior T2 toward T3. Cbx1/Ubx has a slight enhancement of the Ubx phenotype (see also su-Cbx). Cbx2 has both anterior and posterior regions of T2 moderately transformed toward T3. CbxHm affects only the wing, which is strongly transformed to haltere. Flies carrying two doses of CbxHm plus a normal allele have a virtually complete transformation of wing to haltere (as figured in Lewis, 1982). Cbx2 and CbxHm have inseparable recessive bxd effects. Cbx3/+ transforms anterior portions of T2 variably toward anterior T3. It has no effect in posterior T2. For an overview of the effects of Cbx mutants on specific structures see Table 1: Lewis, 1982. pbx: postbithorax Adult homozygotes and hemizygotes have posterior region of third thoracic segment (T3) transformed toward corresponding region of the second (T2). Uab: Ultraabdominal (E.B. Lewis) Uab1, Uab2, and Uab4 cause A1 to transform toward A2. Uab5 causes A1 and A2 to transform toward A3. Uab1 is an intra-complex inversion with a breakpoint in the bxd region, Uab2 is associated with a Uab mutation, the Uab4 breakpoint is an iab-3 mutation, and the Uab5 breakpoint is a weak bxd mutation. Reversion studies show that Uab1, Uab4, and Uab5 cause abnormal expression of abd-A domain functions in A1. Ubx: Ultrabithorax (E.B. Lewis) Larvae homozygous and hemizygous for strong Ubx mutants, such as the Ubx1-type, have the ventral setal bands or "hooklets" of the first abdominal segment (A1) and T3 transformed toward those of T2; dorsally, the hair patterns of posterior T2 and posterior T3 are transformed toward posterior T1; Keilin organs with 2 hairs appear on A1; ventral pits appear on segments A1 thru A7; two extra sets of anterior spiracles appear, one on T3 and one on A1. Homozygotes die, usually as tiny third-instar larvae, but occasionally grow to a normal-sized third-instar larvae and may pupate. Homozygotes of some weaker alleles, such as Ubx61d, survive to adult stage and show weak bx, bxd, and pbx effects, especially in the haltere, and A1 is generally reduced.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 89D6-89D9 Limits computationally determined from genome sequence between P{lacW}CSN5^L4032 and P{EP}MESK4^EP1015
Experimentally Determined Cytological Location
Cytogenetic map Notes References 89E1-89E2 (determined by in situ hybridisation) (Ranz et al., 1997) 89E1-89E2 (determined by in situ hybridisation) (Qian et al., 1991) 89E1-89E2 (determined by in situ hybridisation) (Thali et al., 1988) 89E-89E (determined by in situ hybridisation) (Akam, 1983)
Experimentally Determined Recombination Data
Location	3-58.8
Left of (cM)	Abd-B (Kuhn et al., 1984) Sgs9 (Hoshizaki et al., 1987)
Right of (cM)
Notes	Ubx^bx-8 maps 0.0018 map units distal to Ubx^bx-34e. (Babu et al., 1987)
Molecular Map Data
Gene Order (in direction of increasing cytology) References In direction of increasing cytology: Fas1+ nonA-l+ Cctγ+ CG14906- CG31217- CG31217- Ubx- bxd- Glut3+ abd-A- iab-4+ CG10349+ Abd-B- Actn3- Ahcy89E- (Martin et al., 1995) In direction of increasing cytology: Fas1? nonA-l? Cctγ? Ubx? (Walkley and Malik, 1996) In direction of increasing cytology: Ubx- abd-A- Abd-B- (Tillib et al., 1999) Gene Order (overall orientation not stated) References
Gene Model & Products
Please see the GBrowse view of Dmel\Ubx for information on other features
Comments on Gene Model

Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Ubx-RA FBtr0083347 NM_080504 4729 389 Ubx-RB FBtr0083348 NM_080500 4600 346 Ubx-RC FBtr0083349 NM_169730 4678 372 Ubx-RD FBtr0083350 NM_169728 4651 363 Ubx-RE FBtr0083351 NM_169729 4702 380 Ubx-RF FBtr0083352 NM_206497 4627 355
Additional Transcript Data & Comments
Reported size (kB)	4.3, 3.2 (northern blot) (Rowe and Akam, 1988)
Comments	Microexons 1 and 2 correspond to Ubx exons 2 and 3. (Artero et al., 1992, Artero et al., 1992) The "class IV" splice variants don\\'t contain either of the microexons (exons 2 and 3). (Artero et al., 1992) Two Ubx transcripts are detected by the genomic probe used in this paper, one at 3.2 kb and one at 4.3 kb. (Rowe and Akam, 1988, Rowe and Akam, 1988)
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein Ubx-PA FBpp0082793 40.0 389 9.07 NP_536752 AAF55355 Ubx-PB FBpp0082794 35.4 346 9.55 NP_536748 AAF55356 Ubx-PC FBpp0082795 38.2 372 9.09 NP_732173 AAN13719 Ubx-PD FBpp0082796 37.2 363 9.52 NP_732171 AAN13717 Ubx-PE FBpp0082797 39.1 380 9.49 NP_732172 AAN13718 Ubx-PF FBpp0089155 36.3 355 9.11 NP_996219 AAS65158
Additional Polypeptide Data & Comments
Reported size (kD)
Comments	Gel-shift analysis shows specific binding of Ubx protein to fragments from the Pc gene region. (Chan et al., 1994)
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0003944
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Homeobox (IPR001356) Homeobox protein, antennapedia type (IPR001827) Homeodomain-like (IPR009057) Homeodomain-related (IPR012287) PDB - Protein Data Bank. An information portal to biological macromolecular structures • 1B8I TRANSFAC - Eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles • R01516 R01517 R01518 R01519 R01520 R01521 R01522 R01523 R01524 R01525 R01526 R01527 R01528 R01529 R01530 R01888 R02554 R02555 R02556 R02622 R04948 R04949 R04950 T00863 T02101 T02102
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA390393 AE003714 AAF55355 AE003714 AAF55356 AE003714 AAN13717 AE003714 AAN13718 AE003714 AAN13719 AE003714 AAS65158 AI516075 BI357303 BI362075 BI578023 BP556359 BT010241 AAQ23559 CK658289 CO179010 CO186487 CO190745 CO262084 CO272734 CO275373 CO281006 CO281387 CO286782 CO296509 CO297719 CO315069 CO323008 CO339204 CO339498 CZ471499 CZ471573 CZ489950 CZ489951 EC057363 EC057364 EC059148 EC059851 EC073122 EC085593 EC087188 EC196645 EC205165 EC209244 EC210775 EC217449 EC218331 EC218715 EC219396 EC221926 EC229591 EC230741 EC237517 EC242544 EC244033 EC246544 EC250459 EC253187 EC258935 EC260006 EC265391 K01959 AAA28615 K01963 AAA29008 L32205 L32750 L48177 M23335 M23336 M23337 M24609 U31961 AAA84408 U31961 AAA84409 U31961 AAA84410 U31961 AAA84411 U31961 AAA84412 X05427 CAA29008 X05427 CAA29009 X05723 CAA29194 X05724 CAA29194 X05725 CAA29194 X05726 X05727 CAA29194 X67586 X76210 CAA53803

UniProtKB/Swiss-Prot	P83949
UniProtKB/TrEMBL

Maps to	DS03126 (Gemkow et al., 1998, Hittinger et al., 2005)
Does NOT map to
Identified with	RE43738 (BDGP Project Members, 2000-) D1308 Dm0116 Dm0119 Dm0151 (BDGP Project Members, 1994-1999)
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 T(2;3)Hm.bk4 3R:12,563,229..12,563,229 comment=Position of mutation on reference sequence inferred by FlyBase curator based on author statement. Breakpoint is at position -3077 of sequence from FBrf0046101. evidence=experimental (Saari and Bienz, 1987, Bienz et al., 1988) aberration junction In(3R)Ubx[80].bk2 3R:12,482,098..12,560,348 evidence=experimental (Minana and Garcia-Bellido, 1982, Sanchez-Herrero and Morata, 1983) deletion Ubx[849] 3R:12,558,420..12,559,185 comment=Position of mutation on reference sequence inferred by FlyBase curator based on author statement. Mutation is a deletion of 110 bp in the 5' protein coding region. evidence=experimental (Weinzierl et al., 1987) deletion Ubx[6.28] 3R:12,559,074..12,559,105 comment=Mutation is a deletion evidence=experimental (Weinzierl et al., 1987) deletion Ubx[9.22] 3R:12,484,640..12,486,220 comment=Position of mutation on reference sequence inferred by FlyBase curator based on author's statement. See Figure 2 of FBrf0046283. Mutation is a deletion of 1580bp which removes the splice acceptor site and much of the homeobox. evidence=experimental (Weinzierl et al., 1987) point mutation Ubx[195] 3R:12,536,289..12,536,289 comment=Position of mutation on reference sequence inferred by FlyBase curator based on author statement. See Figure 2c of FBrf0046283. Nonsense codon only causes termination in transcripts which use this exon. These transcripts should terminate 7 amino acids before the start of the homeobox. evidence=experimental na_change=G12536289A pr_change=W288\|Ubx-PA,W271\|Ubx-PC,W262\|Ubx-PD,W279\|U bx-PE reported_na_change=TGG?TAG reported_pr_change=W?@ (Weinzierl et al., 1987) protein binding site Ubx-protein_bind-1 3R:12,527,016..12,527,028 bound_moiety=ftz-XP evidence=experimental (Qian et al., 1993, Bergman et al., 2004) protein binding site Ubx-protein_bind-10 3R:12,527,089..12,527,106 bound_moiety=tll-XP evidence=experimental (Qian et al., 1993, Bergman et al., 2004) protein binding site Ubx-protein_bind-100 3R:12,599,841..12,599,849 bound_moiety=kni-XP evidence=experimental (Bergman et al., 2004, Zhang et al., 1991) protein binding site Ubx-protein_bind-101 3R:12,590,088..12,590,103 bound_moiety=z-XP evidence=experimental (Mahmoudi et al., 2003, Bergman et al., 2004) protein binding site Ubx-protein_bind-102 3R:12,560,212..12,560,230 bound_moiety=z-XP evidence=experimental (Bergman et al., 2004, Biggin et al., 1988) protein binding site Ubx-protein_bind-103 3R:12,599,161..12,599,179 bound_moiety=ftz-XP evidence=experimental (Bergman et al., 2004, Pirrotta et al., 1995) protein binding site Ubx-protein_bind-104 3R:12,590,374..12,590,398 bound_moiety=z-XP evidence=experimental (Mahmoudi et al., 2003, Bergman et al., 2004) protein binding site Ubx-protein_bind-105 3R:12,590,026..12,590,042 bound_moiety=pho-XP evidence=experimental (Mahmoudi et al., 2003, Bergman et al., 2004) protein binding site Ubx-protein_bind-106 3R:12,560,246..12,560,260 bound_moiety=z-XP evidence=experimental (Bergman et al., 2004, Biggin et al., 1988) protein binding site Ubx-protein_bind-107 3R:12,599,313..12,599,325 bound_moiety=ftz-XP evidence=experimental (Bergman et al., 2004, Muller and Bienz, 1992) protein binding site Ubx-protein_bind-108 3R:12,526,648..12,526,665 bound_moiety=hb-XP evidence=experimental (Qian et al., 1993, Bergman et al., 2004) protein binding site Ubx-protein_bind-109 3R:12,589,546..12,589,563 bound_moiety=hb-XP evidence=experimental (Bergman et al., 2004, Mahmoudi et al., 2003) protein binding site Ubx-protein_bind-11 3R:12,560,061..12,560,108 bound_moiety=Ubx-XP evidence=experimental (Beachy et al., 1988, Bergman et al., 2004) protein binding site Ubx-protein_bind-110 3R:12,589,906..12,589,918 bound_moiety=Trl-XP evidence=experimental (Bergman et al., 2004, Mahmoudi et al., 2003) protein binding site Ubx-protein_bind-111 3R:12,590,301..12,590,332 bound_moiety=z-XP evidence=experimental (Bergman et al., 2004, Mahmoudi et al., 2003) protein binding site Ubx-protein_bind-112 3R:12,560,269..12,560,283 bound_moiety=z-XP evidence=experimental (Biggin et al., 1988, Bergman et al., 2004) protein binding site Ubx-protein_bind-113 3R:12,527,019..12,527,037 bound_moiety=twi-XP evidence=experimental (Bergman et al., 2004, Qian et al., 1993) protein binding site Ubx-protein_bind-114 3R:12,481,511..12,481,516 bound_moiety=z-XP evidence=experimental (Benson and Pirrotta, 1988, Bergman et al., 2004) protein binding site Ubx-protein_bind-115 3R:12,590,719..12,590,752 bound_moiety=Trl-XP evidence=experimental (Mahmoudi et al., 2003, Bergman et al., 2004) protein binding site Ubx-protein_bind-116 3R:12,526,900..12,526,909 bound_moiety=twi-XP evidence=experimental (Qian et al., 1993, Bergman et al., 2004) protein binding site Ubx-protein_bind-12 3R:12,599,167..12,599,180 bound_moiety=en-XP evidence=experimental (Pirrotta et al., 1995, Bergman et al., 2004) protein binding site Ubx-protein_bind-13 3R:12,560,330..12,560,344 bound_moiety=Trl-XP evidence=experimental (Biggin and Tjian, 1988, Bergman et al., 2004) protein binding site Ubx-protein_bind-14 3R:12,526,804..12,526,815 bound_moiety=en-XP evidence=experimental (Bergman et al., 2004, Qian et al., 1993) protein binding site Ubx-protein_bind-15 3R:12,599,333..12,599,346 bound_moiety=ftz-XP evidence=experimental (Muller and Bienz, 1992, Bergman et al., 2004) protein binding site Ubx-protein_bind-16 3R:12,590,108..12,590,125 bound_moiety=z-XP evidence=experimental (Mahmoudi et al., 2003, Bergman et al., 2004) protein binding site Ubx-protein_bind-17 3R:12,590,056..12,590,072 bound_moiety=Trl-XP evidence=experimental (Mahmoudi et al., 2003, Bergman et al., 2004) protein binding site Ubx-protein_bind-18 3R:12,589,921..12,589,943 bound_moiety=pho-XP evidence=experimental (Mahmoudi et al., 2003, Bergman et al., 2004) protein binding site Ubx-protein_bind-19 3R:12,589,585..12,589,605 bound_moiety=Trl-XP evidence=experimental (Mahmoudi et al., 2003, Bergman et al., 2004) protein binding site Ubx-protein_bind-2 3R:12,599,333..12,599,351 bound_moiety=kni-XP evidence=experimental (Bergman et al., 2004, Zhang et al., 1991) protein binding site Ubx-protein_bind-20 3R:12,590,251..12,590,278 bound_moiety=hb-XP evidence=experimental (Mahmoudi et al., 2003, Bergman et al., 2004) protein binding site Ubx-protein_bind-21 3R:12,599,326..12,599,345 bound_moiety=en-XP evidence=experimental (Bergman et al., 2004, Pirrotta et al., 1995) protein binding site Ubx-protein_bind-22 3R:12,562,948..12,562,960 evidence=experimental (Eresh et al., 1997, Bergman et al., 2004) protein binding site Ubx-protein_bind-23 3R:12,560,253..12,560,271 evidence=experimental (Bergman et al., 2004, Biggin and Tjian, 1988) protein binding site Ubx-protein_bind-24 3R:12,560,027..12,560,046 evidence=experimental (Biggin and Tjian, 1988, Bergman et al., 2004) protein binding site Ubx-protein_bind-25 3R:12,527,001..12,527,023 bound_moiety=hb-XP evidence=experimental (Qian et al., 1991, Bergman et al., 2004) protein binding site Ubx-protein_bind-26 3R:12,562,924..12,562,942 evidence=experimental (Eresh et al., 1997, Bergman et al., 2004) protein binding site Ubx-protein_bind-27 3R:12,526,966..12,526,992 bound_moiety=tll-XP evidence=experimental (Qian et al., 1993, Bergman et al., 2004) protein binding site Ubx-protein_bind-28 3R:12,599,167..12,599,184 bound_moiety=hb-XP evidence=experimental (Zhang et al., 1991, Bergman et al., 2004) protein binding site Ubx-protein_bind-29 3R:12,599,116..12,599,134 bound_moiety=twi-XP evidence=experimental (Pirrotta et al., 1995, Bergman et al., 2004) protein binding site Ubx-protein_bind-3 3R:12,589,580..12,589,595 bound_moiety=hb-XP evidence=experimental (Mahmoudi et al., 2003, Bergman et al., 2004) protein binding site Ubx-protein_bind-30 3R:12,560,289..12,560,304 bound_moiety=z-XP evidence=experimental (Bergman et al., 2004, Biggin et al., 1988) protein binding site Ubx-protein_bind-31 3R:12,589,526..12,589,545 bound_moiety=Trl-XP evidence=experimental (Mahmoudi et al., 2003, Bergman et al., 2004) protein binding site Ubx-protein_bind-32 3R:12,600,037..12,600,045 bound_moiety=kni-XP evidence=experimental (Zhang et al., 1991, Bergman et al., 2004) protein binding site Ubx-protein_bind-33 3R:12,589,860..12,589,903 bound_moiety=Trl-XP evidence=experimental (Mahmoudi et al., 2003, Bergman et al., 2004) protein binding site Ubx-protein_bind-34 3R:12,526,987..12,527,005 bound_moiety=twi-XP evidence=experimental (Bergman et al., 2004, Qian et al., 1993) protein binding site Ubx-protein_bind-35 3R:12,590,048..12,590,066 bound_moiety=pho-XP evidence=experimental