Table 1. Assessing phenotypes associated with third chromosome balancer breakpoints.

Inversiona	Balancer	Breakpointb	Genes disrupted	Deletion or mutation tested	Phenotypes	Related observations
In(3LR)P88	TM6	61A6	Between CG13485 & CG12483	Df(3L)ED50002, Df(3L)ED4079	Viable, female fertile	Df(3L)ED50002 & Df(3L)ED4079 are homozygous viable
		61B3	Tudor-SN	Df(3L)BSC125, Df(3L)Exel6084	Viable, female fertile
		89B14	ss	ss1	Viable, female fertile, bristle loss	ss mutation associated with In(3LR)P88 (Lindsley and Grell 1967; Morata and Lawrence 1978; Struhl 1982)
In(3LR)HR33	TM6B	61B2	Between CG34453 & E(bx)	Df(3L)ED201, Df(3L)Exel6084	Viable, female fertile	In(3LR)HR33 is homozygous viable (Ashburner 1972)
		87B3	Between CG12256 & CG3916	Df(3R)Exel7313, Df(3R)Exel6162	Viable, female fertile
In(3L)P	TM6, TM6B	63B9	CG14964	Df(3L)BSC671, Df(3L)BSC672c	Viable, weak female fertility	In(3L)P is homozygous viable and fertile (Payne 1918, 1924).
		72E1	Between CG13042 & CR32160	Df(3L)BSC560, Df(3L)BSC579	Viable, female fertile
In(3LR)sep	TM3	65D3	Between Prat2 & CG45413	Df(3L)Exel6109, vvlsep	Viable, female fertile, vein defects	In(3LR)sep homozygotes and other vvl mutants show vein defects (Diaz-Benjumea and García-Bellido 1990)
		85F2	Glut4EF	Df(3R)Exel6155, Df(3R)Exel6154, Glut4EFsep	Viable, female fertile, outheld wings	Glut4EF mutants have outheld wings (Yazdani et al. 2008)
In(3LR)TM3-3	TM3	71B6	FucTA	Df(3L)ED218, Df(3L)BSC837	Viable, weakly female fertile	FucTA mutants viable (Yamamoto-Hino et al. 2010)
		94D10	p53	Df(3R)BSC803, Df(3R)ED6103	Viable, female fertile	p53 mutants viable and fertile (Rong et al. 2002; Sogame et al. 2003; Xie and Golic 2004)
In(3LR)M6	TM6, TM6B	75D6	CR43987	Df(3L)BSC832, Df(3L)BSC416	Viable, female fertile	Some TM6C chromosomes, which carry In(3LR)M6, are homozygous viable and fertile
		94A11	CG13857	Df(3R)BSC511, Df(3R)BSC685	Viable, female fertile
In(3LR)TM3-2	TM3	76B1–2	CG32206 & possibly ms(3)76Ba	Df(3L)ED228	Viable, female fertile, male fertile
		92F4	Lrrk	Df(3R)BSC141, Df(3R)BSC488	Viable, female fertile, normal locomotion	Locomotory and female fertility loss in aging Lrrk mutants (Lee et al. 2007). We saw no overt phenotypes in young flies.
In(3LR)TM3-1	TM3	79F3	CG14459	Df(3L)BSC451, Df(3L)ED230	Viable, female fertile
		100D1	kek6	Df(3R)ED6361, Df(3R)BSC505	Viable, female fertile
In(3R)Hu	TM6B	84B2	Between CR44933 & Sodh-1	Df(3R)Antp17	Viable, female fertile, malformed tergites	In(3R)Hu is homozygous viable (Bridges and Brehme 1944). TkR86C mutations are homozygous viable and fertile (Asahina et al. 2014)
		84F8	CR44318	Df(3R)Exel6147	Viable, female fertile
		86C5	TkR86C	Df(3R)BSC529, Df(3R)Exel6159	Viable, female fertile
In(3R)C	TM3, TM6, TM6B	92E2	Between CG4362 & CG42668	Df(3R)ED6025, Df(3R)ED6027	Viable, female fertile	In(3R)C is homozygous viable and fertile (Dexter 1914; Muller 1918; Bridges and Morgan 1923; Sturtevant 1926)
		100F2–3	Distal to genes	Df(3R)ED50003, Df(3R)ED6361, Df(3R)ED6362d	Viable, female fertile

^aThe In(3LR)TM3-1, In(3LR)TM3-2 and In(3LR)TM3-3 inversions are named here for the first time.

^bCytological bands predicted from sequence coordinates (Table S2) using FlyBase reference table except 100F2–3, where we cite polytene analysis (Morgan et al. 1937)

^cFertility higher in TM6B crosses than TM6 crosses with both deletions.

^dP{RS3}CB-0686-3, the FRT-bearing progenitor of the distal Df(3R)ED6361 and Df(3R)ED6362 breakpoints, lies within the subtelomeric region (Phalke et al. 2009) at a position that may not be distal to the In(3R)C breakpoint.