Markup | Genome Research

Table 1.

Genes Identified or Predicted in the 1A–3C Interval

Cytology	Gene symbol	Gene	HMMER	EST	Matching gene(s)	EDGP vs. joint sequence
	EG:23E12.1		PF01019: G_glu_transpept	GH10105	CG17636	0
	EG:23E12.5			GH15984	CG17617	0
	EG:23E12.2		PF00169: PH	LD22360	CG17960	B−
			PF00620: RhoGAP
			PF00621: RhoGEF
	EG:23E12.3				CG17707	0
	EG:BACR37P7.1		PF01762: Galactosyl_T	CK01556	CG3038	0
	EG:BACR37P7.2		PF00856: SET	LD10743	CG2995	0
			PF00023: ank
1A8	^† EG:BACR37P7.3	^† cin	PF00994: MoCF_biosynth	GH09380	CG2945	0
	EG:BACR37P7.9		PF00106: adh_short		CG13377	A−
1A8	EG:BACR37P7.7	ewg		AF171732	CG3114	B+
	EG:BACR37P7.8		PF00071: ras		CG13375	B−
	EG:BACR37P7.5			bs28b06	CG12470	0
	EG:125H10.1			LP06894	CG3777	0
1B1	EG:125H10.2	y			CG3757	0
1B1	EG:125H10.3	ac	PF00010: HLH		CG3796	0
1B2	EG:198A6.1	sc	PF00010: HLH		CG3827	0
1B3	EG:198A6.2	l(1)sc	PF00010: HLH		CG3839	0
1B4	EG:EG0001.1	pcl	PF00026: asp		CG13374	0
1B4	EG:165H7.2	ase	PF00010: HLH		CG3258	0
	EG:165H7.1	Cyp4g1	PF00067: p450	GH20504	CG3972	0
1B4	EG:165H7.3	l(1)Bb		LD14543	CG3923	D+^*
	EG:171D11.6			LD04586	CG13372	D^*
					CG18166
					CG18273
	EG:171D11.2		PF00664: ABC_membrane	LD18126	CG3156	A−
			PF00005: ABC_tran
	^† EG:171D11.1		PF00171: aldedh	GM07535	CG17896	0
	EG:171D11.5				CG17778	0
1B7	^† EG:171D11.3	^† svr	PF00246: Zn_carbOpept	LD28490	CG4122	D^*
					CG18503
	EG:171D11.4; EG:65F1.3	arginase	PF00491: arginase	GH02581	CG18104	C+
1B8	^† EG:65F1.2	^† elav	PF00076: rrm	HL03451	CG4262	0
	EG:65F1.1			GH24496	CG4293	0
1B8	EG:65F1.5	Appl	PF02177: A4_EXTRA	HL03850	CG7727	A+
1B9	EG:118B3.1	vnd	PF00046: homeobox		CG6172	0
	EG:118B3.2		PF00307: CH	GH04661	CG13366	0
1B13	EG:115C2.5	mod(r)		LP01383	CG17828	0
	EG:115C2.1		PF00294: pfkB	LP11157	CG13369	0
	EG:115C2.12			LP11709	CG18451	0
	EG:115C2.6		PF00096: zf-C2H2	LD23988	CG17829	0
1B13	EG:115C2.7	RpL36	PF01158: Ribosomal_L36e	LD01128	CG7622	0
1B13	EG:115C2.2	l(1)lBi		LD09823	CG6189	0
1B13	EG:115C2.9	Dredd	PF00655: ICE_p10	LD14339	CG7486	B−
			PF00656: ICE_p20
1B13	EG:115C2.3	su(s)		LD06838	CG6222	0
	EG:115C2.8			GH16756	CG13367	A−
	EG:115C2.11			GH22310	CG16982	B+
	EG:115C2.10		PF00856: SET	LD03312	CG13363	C−
1B13	EG:115C2.4	skpA	PF01466: Skp1	LD03188	CG16983	0
1B14-C1	EG:BACR19J1.1	sdk	PF00041: fn3	GM02010	CG5227	B+
			PF00047: ig
	EG:BACR19J1.2		PF00153: mito_carr	LD09021	CG5254	0
	EG:BACR19J1.3			GH28702	CG5273	0
	EG:BACR19J1.4	RpL22	PF01776: Ribosomal_L22e	LP05628	CG7434	0
	EG:34F3.2		PF00784: MyTH4	LD11354	CG12467	D
			PF00169: PH
	EG:34F3.1			LD26268	CG12467	D
	EG:34F3.8		PF00957: synaptobrevin	LD05791	CG7359	0
	EG:34F3.10				CG13358	A+
	EG:34F3.9				CG13359	B−
1B14-C1	EG:34F3.3	Rbf	PF01858: RB_A	LP07395	CG7413	0
			PF01857: RB_B
	EG:34F3.4			LD26306	CG16989	0
	EG:34F3.5			LP04844	CG13360	0
	EG:34F3.7		PF02366: PMT	LP01681	CG12311	A− C−
	EG:34F3.6	fz3	PF01534: Frizzled		CG16785	A−
			PF01392: Fz
	EG:BACR7A4.2			bs33b10	CG3713	0
	EG:BACR7A4.3		PF00089: trypsin		CG11664	0
	EG:BACR7A4.19		PF00651: BTB	LP01394	CG3711	0
			PF01344: Kelch
	EG:BACR7A4.6			1.82	CG3034	0
	EG:BACR7A4.18		PF00956: NAP_family	GH17085	CG3708	A+
	EG:BAC7A4.20			LP11534	CG3706	0
	EG:BACR7A4.5			LP07093	CG11642	0
	EG:BACR7A4.17			LD33276	CG3704	0
	EG:BACR7A4.16			LD03548	CG3026	0
	EG:BACR7A4.15			GH12139	CG3703	A−
	EG:BACR7A4.14		PF00106: adh_short	LP06734	CG3699	D−^*
			PF00678: adh_short_C2
	EG:BACR7A4.13		PF00083: sugar_tr	GH13765	CG3690	0
	EG:BACR7A4.7		PF02268: TFIIA_gamma	GM03032	CG11639	0
	EG:BACR7A4.12		PF00036: efhand	bs03d05	CG11638	A++
1E1-4	EG:BACR7A4.8	anon-1Ed		LD29918	CG3021	C−
	EG:BACR7A4.11	CDC45L		LD08729	CG3658	0
1E1-4	EG:BACR7A4.9	anon-1Eb		GH11273	CG14630	A−
1E1-4	EG:BACR7A4.10	su(w[a])	PF01805: Surp	SD01276	CG3019	B−
	EG:103E12.2			GH24974	CG14629	0
	EG:103E12.3			LD08339	CG3655	0
	EG:BACR42I17.12		PF00076: rrm		CG14628	0
	EG:BACR42I17.1		PF01652: IF4E	bs10b09	CG11392	B+
	EG:BACR42I17.2			LP03214	CG11378	0
	EG:BACR42I17.3				CG11384	0
	EG:BACR42I17.4			bs31h12	CG11379	0
	EG:BACR42I17.5				CG14627	A++
	EG:BACR42I17.6				CG14626	A−
	EG:BACR42I17.7				CG11380	A++
	EG:BACR42I17.8				CG14625	A+
	EG:BACR42I17.9				CG11381	D
					CG14624
	EG:BACR42I17.10			LP08751	CG11382	0
	EG:BACR42I17.11		PF00096: zf-C2H2		CG11398	0
	EG:33C11.3			LP06890	CG3638	A+ C−−
	EG:33C11.2			GM08856	CG11403	0
	EG:33C11.1	A3-3	PF00170: bZIP	GH24653	CG11405	0
	EG:114D9.1		PF00036: efhand		CG11408	0
	EG:114D9.2		PF02181: FH2	LD26058	CG14622	A−−
	EG:190E7.1				CG18091	0
	EG:8D8.1			GM13066	CG11411	0
	EG:8D8.2			LD34263	CG11409	0
	EG:8D8.6		PF00583: Acetyltransf	LD06467	CG11412	B+
	EG:8D8.8			GM12784	CG11418	0
	EG:8D8.7		PF00335: transmembrane4	LP04678	CT11415	0
	EG:8D8.3		PF00324: aa_permeases	LD15480	CG12773	0
	EG:8D8.4			LD08351	CG11417	0
	EG:8D8.5	png	PF00069: pkinase		CG11420	0
	EG:132E8.1		PF00076: rrm	LD09340	CG3056	0
1F	EG:132E8.2	SNF1A	PF00069: pkinase	GH05909	CG3051	0
	EG:132E8.3		PF00085: thiored	LD03613	CG3719	0
	EG:132E8.4				CG11448	0
	EG:49E4.1	futsch		GH21135	CG3064	D^*
	EG:BACN32G11.1				CG18531	0
	EG:BACN32G11.2			GH10964	CG14785	0
	EG:BACN32G11.3		PF01535: PPR	LD01992	CG14786	0
	EG:BACN32G11.4		PF00378: ECH	LP07530	CG14787	A−
	EG:BACN32G11.5		PF01926: MMR_HSR1	HL05876	CG14788	0
	EG:BACN32G11.6			GH07929	CG14789	A−
	EG:80H7.10			GH22272	CG14777	0
	EG:80H7.1		PF00089: trypsin		—
	EG:80H7.2			LD18706	CG14779	0
	EG:80H7.3		PF00089: trypsin		CG14780	0
	EG:80H7.4		PF00071: ras	GM10914	CG14791	B−
	EG:80H7.11			LD02045	CG14781	B+
	EG:80H7.5		PF01363: FYVE	GM03532	CG14782	0
			PF00169: PH
2B1-2	EG:80H7.6	sta	PF00318: Ribosomal_S2	LD27557	CG14792	A− B C+
	EG:80H7.7		PF00060: lig_chan		CG14793	D^*
	EG:196F3.1				—
	EG:196F3.3				CG14795	A+
	EG:196F3.2		PF02214: K_tetra	LD05656	CG14783	C+
	EG:56G7.1		PF01607: Chitin_bind_2		CG14796	0
2B5	^† EG:123F11.1; EG:17A9.1; EG:25D2.1	^† br	PF00651: BTB PF00096: zf-C2H2	LP05017	CG11491	0
2B6	EG:171E4.1	dor		LD12589	CG3093	0
	EG:171E4.4			CK00326	CG3740	D^*
	EG:171E4.2		PF00560: LRR		CG3095	A+ C+
	EG:171E4.3				CG3737	0
	EG:73D1.1			LD24507	CG3791	0
2B6-7	EG:9D2.1	b6		HL05401	CG3100	0
	EG:9D2.2			GH23439	CG3783	D^*
2B6-8	EG:9D2.3	a6		LD13641	CG3771	C−
	EG:9D2.4		PF00089: trypsin		CG3795	0
	EG:4F1.1			GH21860	CG14808	0
	EG:BACN35H14.1	Adar	PF02137: A_deamin	LD31451	CG12598	A+
			PF00035: dsrm
	EG:137E7.1			LD19625	CG17968	0
	EG:131F2.2		PF00929: Exonuclease		CG14801	A−
	EG:131F2.3			LP07325	CG14812	0
	EG:63B12.10	δCOP		LD30910	CG14813	0
	EG:63B12.6			GM12676	CG14814	A−
	EG:63B12.13			GH20211	CG14802	0
	EG:63B12.5		PF00515: TPR	GH08708	CG14815	0
	EG:63B12.9			LD13889	CG14803	B+
	EG:63B12.4		PF00300: PGAM	LD30851	CG14816	0
	EG:63B12.8			LD10891	CG14804	0
	EG:63B12.11			GH01621	CG14817	0
	EG:63B12.7		PF00400: WD40	LD02447	CG14805	B+
	EG:63B12.12			LP05103	CG14818	0
2B15	EG:63B12.3	trr	PF00856: SET	GM10003	CG3848	B++
2B15	EG:63B12.2	anon-2Bd	PF00252: Ribosomal_L16	GH05976	CG3109	B+
2B15	EG:86E4.6	arm	PF00514: Armadillo_seg	LD10209	CG11579	A+
	EG:86E4.2		PF01532: Glyco_hydro_47	LD21416	CG3810	C+
	EG:86E4.3		PF00400: WD40		CG17766	A−
	EG:86E4.4			LD27573	CG3480	0
2B15	EG:86E4.1	eIF-2bε	PF02020: W2	LD26247	CG3806	0
			PF00132: hexapep
	EG:86E4.5		PF00783: IPPc	GH18456	CG3573	0
	EG:39E1.1			LD22420	CG11596	0
	EG:39E1.3			LP09039	CG3857	0
	EG:39E1.2			LD09945	CG3587	0
	EG:BACH61I5.1				CG3600	0
	EG:133E12.2		PF00104: hormone_rec		CG16902	D^*
			PF00105: zf-C4
	EG:133E12.3		PF01650: Peptidase_C13		CG4406	A+
	EG:133E12.4	east		LD33602	CG4399	0
2C3	^† EG:133E12.1	^† Actn	PF00307: CH	HL01581	CG4376	0
			PF00036: efhand
			PF00435: spectrin
2C3	EG:22E5.1	usp	PF00104: hormone_rec	LD09973	CG4380	0
			PF00105: zf-C4
	EG:22E5.12		PF00097: zf-C3HC4		CG4325	0
	EG:22E5.11		PF00001: 7tm_1		CG4322	C+
	EG:22E5.10		PF00001: 7tm_1	GM02327	CG4313	0
	EG:22E5.8		PF00069: pkinase	GH06888	CG4290	0
	EG:22E5.7			LD08665	CG4281	D^*
	EG:22E5.5		PF00355: Rieske	GH11732	CG4199	A+
			PF00070: pyr_redox
	EG:22E5.6			LD31238	CG4194	0
	EG:22E5.3		PF01137: RCT	GH07716	CG4061	0
	EG:22E5.4		PF02390: Methyltransf_4	GM01339	CG4045	C+
	EG:22E5.9			LP10820	CG4025	0
	EG:67A9.2			LD01561	CG16903	C−−
	EG:67A9.1			CK00561	CG3981	A−
2D3	^† EG:BACN25G24.2	^† csw	PF00017: SH2	HL03192	CG3954	0
			PF00102: Y_phosphatase
2D3	EG:BACN25G24.3	ph-d	PF00536: SAM	GH08934	CG3895	A−− B+ C+
2D3	EG:87B1.5	ph-p	PF00536: SAM	GH19743		D^*
	EG:87B1.3		PF01565: FAD_binding_4	GH17284	CG3835	0
2D6	EG:87B1.4	Pgd	PF00393: 6PGD	GH13486	CG3724	0
2D6	EG:87B1.6	bcn92			CG3717	0
2D6	EG:87B1.2	wapl		LD29979	CG3707	A+
2D6	EG:87B1.1	Cyp4d1	PF00067: p450	GH01333	CG3656	0
	EG:152A3.3			HL02445	CG3630	0
	EG:152A3.7	anon-2Db			CG3621	0
	EG:152A3.2	Cyp4d14	PF00067: p450	HL05508	CG3540	0
2E1	EG:152A3.4	Cyp4d2	PF00067: p450	GH09810	CG3466	A−
2E1	EG:152A3.6	Cyp4ae1	PF00067: p450	GH24265	CG10755	0
2E1	EG:152A3.5	pn		GM10090	CG3461	0
2E3	EG:152A3.1	Nmd3		LD13746	CG3460	0
	EG:17E2.1			LD17911	CG3457	B−
2E3	EG:103B4.3	Mct1	PF01587: MCT	LP01643	CG3456	A−
	EG:103B4.2			LP02712	CG18031	D
2E3	EG:103B4.4	msta		GH20239	CG18033	0
2E3	EG:103B4.1	Vinc	PF01044: Vinculin	LD16157	CG3299	0
2E3	EG:30B8.4	pcx		LD27929	CG3443	B−−
2F1	EG:30B8.2	kz		GH21962	CG3228	0
2F1	EG:30B8.5	fs(1)K10		LD08992	CG3218	0
2F1	EG:30B8.7	Or2a			CG3206	C
2F1	EG:30B8.1	crn	PF02184: HAT	LP05055	CG3193	0
	EG:30B8.3		PF00650: CRAL_TRIO	GM01086	CG3191	0
	EG:30B8.6			GH06335	CG3078	D
	EG:25E8.3		PF00400: WD40	LD29959	CG3071	B+
	EG:25E8.2		PF00179: UQ_con	LD09991	CG2924	A+ C−
	EG:25E8.1		PF00012: HSP70	GH11566	CG2918	0
	EG:25E8.6				CG2879	D
	EG:25E8.4			GH04956	CG2865	0
	EG:BACH48C10.1				CG14050	0
	EG:BACH48C10.2			GH19593	CG2854	C−
2F6	EG:BACH48C10.3	phl	PF00130: DAG_PE-bind	GH03557	CG2845	B+
			PF02196: RBD
			PF00069: pkinase
	EG:BACH48C10.6				CG14048	0
2F6	EG:BACH48C10.5	ptr		GH02860	CG2841	A+
	EG:BACH48C10.4			GH27724	CG14047	D
	EG:BACH7M4.1			SD05785	CG14045	A−−
	EG:BACH7M4.2		PF00168: C2	CK01827	CG14045	A− C−
			PF00505: PDZ
	EG:BACH7M4.4				CG12496	C−
3A2	EG:BACH7M4.5	gt			CG7952	0
3A3	^† EG:BACH59J11.1	^† tko	PF00164: Ribosomal_S12	GM03810	CG7925	0
	EG:BACH59J11.2		PF00041: fn3	SD01373	CG13756	B+
3A3	EG:BACH59J11.3	z			CG7803	0
	EG:BACR25B3.11	pcan	PF0008: EGF	GM03359	CG7981	D^*
			PF00047: ig
			PF00054: laminin_G
			PF00057: ldl_recept_a
	EG:BACR25B3.10		PF00047: ig	GM02481	CG7981	D^*
	EG:BACR25B3.1		PF00047: ig	GM06086	CG7981	A++ C−
			PF00052: laminin_B
			PF00053: laminin_EGF
			PF00057: ldl_recept_a
	EG:BACR25B3.2		PF00057: ldl_recept_a		CG12497	A+ B+
	EG:BACR25B3.3		PF00002: 7tm_2		CG13758	D
	EG:BACR25B3.4		PF01813: ATP-synt_D	GH28048	CG8310	D
	EG:BACR25B3.5			GH02552	CG13759	B+
	EG:BACR25B3.6			LD41675	CG13760	A−−
	EG:BACR25B3.7	wds	PF00400: WD40	LD30385	CG17437	0
3A8	EG:BACR25B3.8	egh			CG9659	0
3A8	EG:BACR25B3.9	Klp3A	PF00225: kinesin 14	LD21815	CG8590	0
3A9	EG:BACR7C10.3	mit(1)15		LD31038	CG9900	0
	EG:BACR7C10.4	Bzd	PF01753: zf-MYND		CG13761	C+
	EG:BACR7C10.6		PF00335: transmembrane4	GH15125	CG10742	0
	EG:BACR7C10.1			LD08769	CG9904	0
	EG:BACR7C10.7				CG13762	B−
	EG:BACR7C10.2		PF00613: PI3Ka	GH26308	CG10260	D
			PF00454: PI3_PI4_kinase
3B1	EG:155E2.3	sgg	PF00069: pkinas3	GM02018	CG2621	A+
3B2	EG:155E2.2	HLH3B	PF00010: HLH		CG2655	0
	EG:155E2.5			GH07966	CG2652	0
3B2	^† EG:155E2.4	^† per	PF00989: PAS	GH01975	CG2647	A− B+
3B2	EG:155E2.1	anon-3B1.2			CG2650	B−
	EG:100G10.7	anon-3Ba	PF0004: AAA	GH01006	CG2658	0
			PF01434: Peptidase_M41
	EG:100G10.6		PF00628: PHD	HL01595	CG2662	0
	EG:100G10.5	anon-3Bb		LD37122	CG2675	A+
	EG:100G10.3		PF01008: IF-2B		CG2677	0
	EG:100G10.4			GH11163	CG2680	B+
	EG:100G10.2			GH02982	CG2681	B−
	EG:100G10.1			LD25954	CG2685	0
	EG:100G10.8; EG:95B7.10			LD34251	CG2695	0
3B4	EG:95B7.9	anon-3Bd		GH08386	CG2701	0
3C1	EG:95B7.8	fs(1)Yb			CG2706	0
3C1	EG:95B7.4	fs(1)Ya		LD47547	CG2707	A−
	EG:95B7.5				CG2709	0
3C1	EG:95B7.6	dwg	PF00096: zf-C2H2	LD08032	CG2711	0
	EG:95B7.3			LD05179	CG2713	0
	EG:95B7.7	anon-3Be	PF00096: zf-C2H2	LD39664	CG2712	0
3C2	EG:95B7.2	crm	PF00249: myb_DNA-	LD09365	CG2714	0
			binding
	EG:95B7.1		PF00804: Syntaxin		CG2715	0
	EG:BACN33B1.2			HL08104	CG2766	D^*
					CG2716
3C2	EG:BACN33B1.1	w	PF00005: ABC_tran	GH06126	CG2759	0
	EG:BACR43E12.1				CG12498	0
	EG:BACR43E12.7			GM07661	CG14416	0
	EG:BACR43E12.6				CG14417	0
	EG:BACR43E12.5				CG14417	0
	EG:BACR43E12.4		PF00569: ZZ	GH01442	CG3526	A++
	EG:100G7.6				CG3588	A−− C+
	EG:100G7.5				CG14424	0
3C5	EG:100G7.1	anon-3Ca			CG18089	0
3C5	EG:100G7.2	anon-3Cb			CG3591	0
	EG:100G7.3				CG3598	0

[i] All known or predicted genes have a symbol in the formEG:#, where the # indicates the clones on which they were first discovered followed by a dot and integer. Genes previously known are also shown with their FlyBase symbols and, if determined, cytological locations. The EST column indicates a matching EST sequence from either the BDGP collection or B. Oliver's testes-derived EST collection (as submitted to GenBank; see Andrews et al. 2000). Only one cDNA clone name is listed for each gene. The column headed “Matching Gene(s)” indicates the matching gene from the Joint Sequence. The column headed “EDGP vs. Joint Sequence” indicates the result of comparing the EDGP and Joint Sequence at the predicted protein level. In this column, 0 indicates identity or <1% difference in sequence; A, that the sequences differ in their predicted start sites; B, that they differ in their predicted termination sites; and C, that they differ by a predicted exon or intron. A ‘D’ indicates that the gene models predicted by us and by the Joint Sequence differ very markedly; an accompanying asterisk indicates that we have evidence that the EDGP model is the more correct (see text). A plus sign indicates the EDGP sequence is longer than the CG sequence; a minus sign indicates that it is shorter. For more details see the supplementary data. Only positive hits of known or predicted proteins to PFAM are shown (see text). A dagger before a gene symbol indicates a gene with alternatively spliced messages.