TABLE S2

Genes, known and predicted, that have been determined on the sequence of the Adh region. All genes are protein coding, unless indicated tscan in the prediction column, these are tRNAs

symbol

alleles(1)

EST(2)

cDNA(3)

prediction(4)
    gf,gs

BLAST(5)

B4

P

AA263884(2)

AF022364

48,153

-

BG:BACR48E02.1

-

-

-

21,-

-

BG:BACR48E02.2

-

-

-

-,60

-

BG:BACR48E02.3

-

-

-

23,54

-

kuz

P

AA201945 (3)

U60591

77,286

HRW

BG:DS07660.1

-

AI294232 (1)

-

-,101

HRDWAO

BG:BACR48E02.4

-

AA438735 (4)

LD13077*

42,68

HRWYAO

BG:DS01368.1

-

AA142254 (1)

CK00026*

80,153

W

BG:DS08249.1

-

-

-

36,139

HRDWO

BG:DS08249.2

-

-

-

73,163

HRWYO

BG:DS08249.3

-

-

-

50,91

HRWO

BG:DS08249.4

-

-

-

38,97

-

BG:DS08249.5

-

-

-

-,50

-

BG:DS00797.1

P

AA699136 (3)

LD32761*

59,185

HWYA

BG:DS00797.2

-

AA697797 (1)

HL03175*

39,77

YO

p38b

-

AA567041 (5)

GM01004*

71,173

HRWYAO

BG:DS00797.4

-

-

-

30,69

WA

BG:DS00797.5

-

AA140924 (2)

CK01017*; LD33192*

87,296

HRW

BG:DS00797.6

-

-

-

71,170

WO

BG:DS00797.7

-

AA391258 (3)

LD29171*

218,632

HRWYAO

BG:DS00941.1

-

AI110179 (6)

GH09688*

56,122

HRWO

BG:DS00941.2

-

-

-

55,54

HRWY

BG:DS00941.3

-

-

-

44,99

H

Sos

P

AI062565 (1)

M83931; M77501

230,573

HRWYO

b

+

AA699258 (2)

U01239

109,259

HRYO

tamas

+

AA263336 (3)

U60298; U62547

143,337

HRYAO

Sop2

+

AA140648 (1)

pers. comm.

75,199

HRWY

Orc5

+

-

U43505

59,166

HRO

MtPolB

+

AA695573 (1)

U94702

26,86

HR

RpII33

P

AA391035 (3)

LD09978*

53,161

HRWYAO

BG:DS00941.11

-

-

-

47,98

-

BG:DS00941.12

-

-

-

58,139

-

BG:DS00941.13

-

AI257133 (3)

LP05416*

50,113

-

BG:DS00941.14

-

AI257386 (1)

LP05733*

65,145

-

BG:DS00941.15

-

AI260810 (1)

LP04791*

32,-

-

BG:DS08220.1

P

AA390942 (2)

LD11783*

127,298

HRDWYAO

anon-34Ea

-

AA202382 (6)

LD02558*

175,505

-

Ance

+

AA392405 (6)

U25344

107,296

HRWO

Acyp

-

-

-

20,296

HRO

BG:DS00180.2

-

-

-

69,184

-

BG:DS00180.3

-

AA697312 (1)

HL02234*

66,145

-

BG:DS00180.5

-

-

-

35,201

HRO

BG:DS00180.12

-

AI108572 (2)

GH07762*

32,201

HRWO

BG:DS00180.7

-

AA567553 (1)

HL01444*

67,100

HRDWO

BG:DS00180.8

-

AA140891 (2)

CK00536*; CK00194*

62,128

HRDWO

BG:DS00180.9

-

-

-

30,85

HRDO

BG:DS00180.10

-

AI257173 (1)

LP05465*

21,120

HRWO

BG:DS00180.11

-

-

-

91,54

HRWYO

BG:DS00180.14

-

-

-

91,56

HRWO

rk

P

-

pers. comm.

87,207

HRDWYAO

BG:DS01514.1

-

-

-

tscan,69

-

BG:DS01514.3

-

-

-

-,49

-

BG:DS01514.2

P

AA391612 (8)

pers. comm; LD10778*

93,230

HRWYAO

l(2)34Fa

P

-

-

37,84

-

BG:DS05899.1

-

AA949294 (1)

pers. comm.

87,252

HRWYAO

BG:DS05899.7

-

-

-

-,55

HRDWYAO

BG:DS05899.6

-

-

-

-,46

-

BG:DS05899.3

-

-

-

42,106

HRDWO

BG:DS05899.5

-

-

-

-,94

-

BG:DS05899.4

-

-

-

-,64

HRDWO

BG:DS01759.1

-

-

-

77,192

-

BG:DS01759.2

-

AA697929 (1)

HL03474*

-,45

-

BG:DS01523.1

-

-

-

112,230

-

BG:DS01523.2

-

-

-

153,510

HRDO

smi35A

P

AA141561 (8)

LD10161*

48,217

HRDWYAO

wb

P

AA140697; AA140696 (3)

AF135118; CK00390*; CK02229*

150,565

HRDWO

BG:DS03792.2

-

-

-

-,109

-

BG:DS01068.1

-

-

-

100,397

-

BG:DS01068.11

-

-

GH05919*

172,487

HRDW

BG:DS01068.2

-

-

-

172,487

WO

BG:DS01068.10

-

-

-

38,30

HRDWO

BG:DS01068.4

-

AA979161 (2)

LD33443*

41,92

-

BG:DS01068.5

-

-

-

35,382

RO

BG:DS01068.6

+

AA264787 (6)

LD09509*

112,382

WYO

Rab14

P

AA202923 (4)

D84316; LD03340*

39,55

HRWYO

l(2)35Aa

+

AA941044 (1)

pers. comm.; LD24449*

107,263

HRWO

spel1

-

AA979275 (3)

U17893

83,211

HRWYAO

ppk

-

-

AF043263; Y16225

28,132

HRWO

elB

P

-

-

74,199

HD

BG:DS06238.4

-

-

-

30,63

DO

elA

-

AI35185 (5)

GH12842*

-,-

-

noc

P

AA696574 (3)

L14009

88,179

HR

BG:DS04641.2

-

-

-

tscan,57

-

tRNA:G3:35Ba

-

-

-

tscan,72

-

tRNA:G3:35Bb

-

-

-

tscan,72

-

tRNA:G3:35Bc

-

-

-

tscan,72

-

tRNA:G3:35Bd

-

-

-

tscan,72

-

tRNA:G3:35Be

-

-

-

tscan,68

-

BG:DS04641.8

-

-

-

-,95

-

BG:DS01486.1

-

-

-

-,-

HRDWYAO

BG:DS01486.2

-

-

-

tscan,57

-

BG:DS01486.3

-

-

-

tscan,57

-

BG:DS01486.4

-

-

-

tscan,57

-

osp

P

AA439528; AA441103 (5)

Z0030; LD14119*; LD15891*

94,431

HRW

Adh

+

AA567713 (3)

J01066

-,132

HRWYAO

Adhr

-

AA695692 (1)

X98338

-,132

HRYO

BG:DS09219.1

-

-

-

-,41

-

BG:DS07721.1

-

AA141849 (1)

CK02594*

-,-

-

BG:DS07721.3

-

-

-

21,47

-

BG:DS07721.6

-

-

-

-, 271

-

BG:DS00810.1

-

-

-

25,97

W

BG:DS00810.2

-

AI259984 (6)

LP03565*

-,-

-

BG:DS00810.3

-

AI135814 (4)

GH13704*

16,14

-

BG:DS06874.1

-

-

-

27,59

-

BG:DS06874.2

-

-

-

-, 111

HRA

BG:DS06874.3

-

-

-

44,127

HRDWYAO

BG:DS06874.4

-

-

-

-,103

HRDWO

BG:DS06874.6

-

-

-

-,-

HRDWO

BG:DS06874.7

-

-

-

-,119

-

BG:DS03431.1

-

-

-

55,111

HRDWO

Mst35Ba

-

-

Z46783; Z46790

-,-

O

Mst35Bb

-

-

Z46784; Z46785

-,-

O

BG:DS03144.1

-

-

-

49,123

HRDWO

BG:DS03323.1

-

-

-

102,405

HRDWAO

BG:DS01219.3

-

-

-

-,99

OD

BG:DS01219.1

-

AA441153 (5)

LD16050*

40,53

W

BG:DS00929.16

-

-

-

-,71

-

BG:DS00929.1

-

-

-

21,49

O

BG:DS00929.2

-

AA539145 (1)

LD17234*

43,75

HRDWYAO

BG:DS00929.3

-

-

-

44,70

HRWYAO

BG:DS00929.4

-

-

-

29,62

YO

l(2)35Bd

P

AA391413 (14)

LD09819*; LD22017*

49,684

HYO

BG:DS00929.6

-

-

-

31,684

HRDWO

BG:DS00929.7

-

-

-

-,-

HRDWO

BG:DS00929.8

-

-

-

66,684

D

l(2)35Bg

P

AA696894 (4)

LD32407*

41,46

HWYO

Su(H)

P

AA539138 (4)

M94383; X58393

80,188

HRWO

ck

P

AA391840 (3)

pers. comm.

179,630

HRDWYAO

TfIIS

+

AA951789 (9)

L26091; Z53670

69,128

HRWYO

vas

P

AA246989 (3)

M23560

27,285

HRWYO

vig

-

AA263918 (3)

pers. comm.; LD07162*

81,248

HW

BG:DS00929.15

-

-

-

-,285

-

BG:DS04929.1

-

-

-

68,302

WO

BG:DS04929.3

-

-

-

54,461

HRDWYO

stc

P

AA390501 (10)

U09306

114,461

HRWYO

BG:DS03192.1

-

-

-

tscan,66

-

BG:DS03192.3

-

AA801485 (1)

HL02392*

-,-

-

BG:DS03192.2

-

-

-

82,301

HRDWYO

BG:DS03192.4

-

AA140990 (1)

CK01083*

-,-

-

BG:DS07295.1

-

AA567110 (6)

GM01103*

35,66

HRWYAO

BG:DS07295.4

-

-

-

-,76

-

BG:DS07295.2

-

-

-

128,261

-

BG:DS07295.3

-

AA390953 (3)

LD09767*

60,139

-

BG:DS07295.5

-

-

-

26,96

HRWO

BG:DS05639.1

-

AI238048 (1)

GH14032*

59,205

HRDWYO

BG:DS07851.11

-

-

GH14032*

32,349

-

gft

P

AA391453 (5)

pers. comm.; LD10516*

79,349

HDWYO

BG:DS07851.3

-

AA567164 (1)

GM01181*

22,-

HRWYO

BG:DS07851.4

-

-

-

22,65

-

BG:DS07851.8

-

-

-

22,59

-

ms(2)35Ci

P

-

-

-,35

-

BG:DS07851.5

-

-

-

31,108

-

BG:DS07851.6

-

-

-

20,60

D

esg

P

-

M83207

65,158

HRWYO

BG:DS03023.4

-

-

-

-,193

-

wor

+

-

pers. comm.

73,147

HRDWYO

BG:DS03023.2

-

-

-

30,127

WY

sna

+

-

Y00288

73,136

HRWYO

Tim17

-

-

-

-,77

HRWYO

lace

P

AA539354 (1)

LD17449*

67,147

HRDWYAO

BG:DS04862.2

-

-

-

-,66

-

kek3

-

AI1346684 (2)

GH12215*

110,252

HRDWO

BG:BACR44L22.1

-

-

-

25,64

HRWO

BG:BACR44L22.8

-

-

-

-,110

HRWO

BG:BACR44L22.2

-

-

-

23,110

HRWO

BG:BACR44L22.3

-

-

-

-,53

HRWO

BG:BACR44L22.4

-

-

-

-,-

HRWO

BG:BACR44L22.5

-

-

-

-,51

-

BG:BACR44L22.6

-

-

-

25,64

HRWO

BG:DS07108.4

-

AI296913 (2)

LP11031*

46,155

HRDWO

BG:DS07108.2

-

-

-

128,309

HRWO

BG:DS07108.1

-

-

-

-,75

HRDWO

BG:DS07108.5

P?

-

-

-,25

HRDWO

CycE

P

AA539450 (13)

X75026; X75027

94,193

HRWYO

BG:DS09217.1

-

AA568016 (2)

GH01660*

36,60

W

l(2)35Df

P

AA391849 (9)

LD10786*

161,404

HRDWYAO

Gli

P

-

L39083

100,216

HRWO

BG:DS09217.4

-

AA264587 (1)

LD08227*

64,105

HWYA

l(2)35Ea

P

AA202739 (2)

LD02957*

67,137

HRDWYO

BG:DS09217.6

-

-

-

97,262

HR

BG:DS02252.3

-

-

-

-,376

HYO

BG:DS02252.4

-

-

-

-,71

-

BG:DS02252.1

-

-

-

48,129

-

BG:DS02252.2

-

-

-

61,189

HDWO

BG:DS00365.1

-

-

-

-,83

HRWYO

BG:DS00365.2

-

-

-

38,251

HRWO

BG:DS00365.3

-

-

-

51,170

HRWYAO

beat-B

-

-

pers. comm.

-,127

D

BG:DS07486.3

-

AI258377 (1)

LP01559*

-,300

HRDWO

BG:DS07486.4

-

-

-

-,70

-

BG:DS07486.5

-

-

-

-,63

-

BG:DS07486.2

-

-

-

24,54

WO

beat-C

-

-

pers. comm.

26,157

D

BicC

+

AA263958 (7)

U15928

130,270

W

beat

+

-

U67057

-,106

-

BG:DS04095.1

-

AI110040 (1)

GH09478*

-,64

-

BG:DS04095.2

-

-

-

-,53

D

BG:DS04095.3

-

-

GH12581*

-,-

-

Ca-_1D

+

AI062722 (3)

U00690

74,626

HRWYO

BG:DS02795.3

-

-

-

-,108

-

BG:DS07473.1

-

-

-

104,506

HRWO

PRL-1

P

AA392622 (13)

AF063902; LD12894*

-,-

HRWY

BG:DS07473.2

-

AA941281 (2)

LD25338*

48,146

-

twe

P

AA201276 (8)

M94158; X69018

45,123

HRWY

BG:DS02740.2

-

-

LH*

20,60

HRDWYAO

crp

P

AA392052 (17)

LH*

94,223

HWO

BG:DS02740.4

-

AA697365 (1)

LH*

70,236

HW

BG:DS02740.5

-

-

-

23,-

-

l(2)35Fb

+

-

-

53,142

HRDWYAO

heix

P

AA264681 (13)

LH*

43,103

O

BG:DS02740.8

-

-

LH*

-,70

HRDWYO

BG:DS02740.9

-

-

LH*

-,-

HRYO

BG:DS02740.10

-

AA695616 (2)

LH*

-,54

-

anon-35Fa

-

AA803126 (3)

LH*

26,-

HW

Sed5

+

AA202437 (4)

X78219

53,117

HRWYAO

cni

+

-

U28069

-,-

RWY

fzy

P

AA264915 (25)

U22419

65,114

HRWYO

cact

P

AA391908 (31)

L04964; L03368; L03367

51,143

HRWYO

anon-35F/36A

P

AA949980 (2)

LH*

25,50

YO

l(2)35Fe

P

AA979191 (1)

LH*

35,-

WO

BG:DS02740.18

-

-

-

-,336

-

BG:DS02740.19

-

-

-

-,205

-

BG:DS09218.1

-

-

-

23,52

-

chif

P

AA439734 (7)

pers. comm.

44,570

O

BG:DS09218.3

-

AA392115 (3)

LD12474*

39,-

-

BG:DS09218.4

-

AA246605 (18)

LD05503*

86,179

HRDWYAO

BG:DS09218.5

-

-

-

22,78

O

BG:DS02780.1

-

AA141295 (1)

CK01518*

38,125

HRDWAO

Idgf1

-

AA735713 (5)

GM09616*

31,81

HRWYAO

Idgf2

-

AA134980 (11)

GH12581*

45,101

HRWYAO

Idgf3

-

AA140749 (5)

CK00436*

45,125

HRWYAO

dac

P

-

U19269

50,123

HR

1. Whether mutant alleles are known; + indicates alleles are known, - that they are not and P that there is at least one P-element allele (see Table 2).

2. The accession number of the most 5'-extended EST sequence is given. This normally corresponds to the longest cDNA. In the cases of wb and osp the accession numbers of two, non-overlapping, cDNAs are given. The number in parentheses indicates the number of independent cDNAs. The accession numbers of these other cDNAs can be found on FlyBase.

3. Complete cDNA sequences were from this study (see MATERIALS and METHODS, marked with an asterisk) or were from the work of others (pers. comm.), in which case see footnote 2 to TABLE 1. Clones marked LH were isolated by library screening, and thus do not have corresponding ESTs. They were sequenced by L. H. as part of this study.

4. gf = GENEFINDER; gs = GENSCAN; tscan = tRNAscan-SE; the numbers represent the scores of the GENEFINDER and GENSCAN prediction programs for the CDS regions. Sometimes there will be multiple scores for one gene, representing more than one scan or exon (for example if a gene crosses between two P1 clones); if so, only the largest of these is given here. A - indicates that the program did not predict the gene, at least not at or above the cutoff used here (a score of 20 for GENEFINDER and 45 for GENSCAN, see text). An exception is made for BG:DS09219.1 which spans two P1 clones with independent GENSCAN predictions of 41 and 35.

5. A summary of the species to which there was a significant match (expect P = <e-7 or less). H = human; R = rodent (rat, mouse); D = Drosophila; W = C. elegans; A = A. thaliana; Y = S. cerevisiae; O = other. True Drosophila matches are excluded from this table. The BLASTP matches for dac are from searches with the complete protein (SPTREMBL:Q24027), since that on this contig is truncated. See text for further details of these matches and http://www.genetics.org/supplemental/ and FlyBase for more complete information.