Table 3

Summary of 24 S. cerevisiae ribosomal protein paralogs with largely nonhomologous intronic sequences despite relatively low levels of synonymous divergence

I1 (bp)

I2 (bp)



Duplicate pair

KS

5' homology (bp)

3' homology (bp)

E1 (bp)

5' H

NH

3' H

E2 (bp)

5' H

NH

3' H

E3 (bp)


YDL075W/YLR406C

0.3363

3

2

57

6

415/343

0

285

-

-

YMR230W/YOR293W

0.3132

15

1

52

8

400/427

2

266

-

-

YLR448W/YML073C

0.2992

10

2

15

6

375/406

3

516

-

-

YDL082W/YMR142C

0.2970

3

2

8

2

358/395

5

592

-

-

YGR034W/YLR344W

0.2841

0

1

19

6

68/438

3

365

-

-

YDL083C/YMR143W

0.2838

4

4

24

7

423/535

2

408

-

-

YBL027W/YBR084C

0.2698

3

0

2

6

370/492

8

568

-

-

YBR191W/YPL079W

0.2508

5

1

11

7

377/410

4

472

-

-

YMR242C/YOR312C

0.2504

5

0

1

2

467/416

8

518

-

-

YDR450W/YML026C

0.2491

4

1

47

8

424/390

3

394

-

-

YNL302C/YOL121C

0.2076

5

0

20

10

539/378

2

415

-

-

YLR287C-A/YOR182C

0.2022

5

0

3

6

420/401

4

189

-

-

YBR048W/YDR025W

0.1987

3

0

45

7

502/330

2

426

-

-

YNL301C/YOL120C

0.1955

1

0

112

6

424/439

2

449

-

-

YDR447C/YML024W

0.1896

3

0

3

6

298/382

10

408

-

-

YGR118W/YPR132W

0.1546

4

3

65

6

312/357

2

373

-

-

YIL018W/YFR031C-A

0.1523

2

0

4

6

391/138

3

761

-

-

YIL001W/YKL006W

0.1429

1

2

129

7

318/318

74

288

-

-

YER074W/YIL069C

0.1333

2

1

3

6

458/401

2

405

-

-

YGL076C/YPL198W

0.1196

5

0

11

6

451/400

12

94

7

456/395

5

630

YHR141C/YNL162W

0.0918

10

0

4

5

433/504

2

317

-

-

YJR145C/YHR203C

0.0854

6

1

14

7

247/260

2

772

-

-

YDL136W/YDL191W

0.0395

2

2

3

4

387/473

12

360

-

-

YBR181C/YPL090C

0.0388

4

0

6

4

336/378

10

705

-

-


Column 3 and 4 list the length of the extent of discernible homology between the two paralogs upstream of the initiation codon and downstream of the termination codon, respectively. Columns 5, 9 and 13 (E1, E2 and E3) list the length of exons 1, 2 and 3 (where applicable), respectively. Columns 6 to 8 provide details about the extent of homology between the two paralogs across intron 1. Columns 6 and 8 list the length of the short tracts of homology in the 5' and 3' ends of intron 1 near the splice junctions. Column 7 lists the length of the nonhomologous tracts of intron 1 for both paralogs. Columns 10 to 12 list similar details for intron 2, where present.

Katju et al. Genome Biology 2009 10:R75   doi:10.1186/gb-2009-10-7-r75

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