Table 4

Nucleotide substitution analysis of a subset of genes in the duplication of chromosomes 11 and 12. A high confidence gene set has been selected for the calculation of synonymous (Ks) and non-synonymous (Ka) nucleotide substitutions. The genes are presented with their Ks/Ka values according to their chromosomal positions.

Gene Number

gene putative function

chrom11 start

chrom11 stop

chrom12 start

chrom12 stop

Ks

se of Ks

Ka

se of Ka

my


1

WRKY family transcription factor

749015

750212

788607

789687

0.16

0.037

0.055

0.013

12.30769

2

WRKY family transcription factor

758715

762245

801426

804997

0.04

0.017

0.015

0.006

3.076923

3

WRKY family transcription factor

781473

782513

816140

817037

0.023

0.017

0.007

0.004

1.769231

4

WRKY family transcription factor

786625

787866

823302

824540

0.077

0.02

0.04

0.007

5.923077

5

alpha-hydroxynitrile lyase

811241

812335

851943

854138

0.0196

0.034

0.0118

0.007

1.507692

6

polyneuridine aldehyde esterase-like

812960

814118

855275

856433

0.025

0.0147

0.009

0.0065

1.923077

7

glycosyl hydrolase family

819185

821808

857627

859498

0.02567

0.009

0.02

0.0053

1.974615

8

scarecrow

1119113

1121579

1042889

1045809

0.0865

0.03

0.0087

0.0026

6.653846

9

glutathione S = transferase T3

1165521

1166165

1096622

1097382

0.327

0.116

0.155

0.04

25.15385

10

apyrase GS52

1174941

1177791

1106432

1109216

0.027

0.01

0.019

0.005

2.076923

11

apyrase S-type

1221864

1225463

1129908

1132441

0.084

0.04

0.027

0.016

6.461538

12

no apical meristem

1233158

1234682

1138382

1139934

0.094

0.026

0.017

0.004

7.230769

13

no apical meristem

1240175

1241314

1146147

1147453

0.32

0.15

0.073

0.0155

24.61538

14

40S robosomal protein S16

1284724

1285173

1168928

1169349

0.093

0

0.003

0

7.153846

15

exostosin family

1288082

1291244

1172080

1174695

0.098

0.02

0.0135

0.004

7.538462

16

cdc45-like protein

1305369

1307183

1188143

1189957

0.068

0.02

0.0037

0.0017

5.230769

17

myb protein homolog

1316546

1317575

1199788

1200856

0.0535

0

0.0115

0

4.115385

18

homoserine dehydrogenase-like protein

1328599

1332331

1215892

1219509

0.0339

0.01

0.01

0.0037

2.607692

19

receptor-like protein kinase

1537568

1540056

1472686

1475196

0.1

0.036

0.02

0.0054

7.692308

20

receptor-loke protein kinase

1545094

1547508

1490358

1492844

0.081

0.021

0.011

0.0027

6.230769

21

60S acidic ribosomal protein

1645643

1647855

1601129

1603328

0.071

0.019

0.0054

0.0027

5.461538

22

calcium dependent protein kinase

1691610

1693844

1647299

1649413

0.0279

0.01

0.00077

0.00078

2.146154

23

YVH 1 protein-tyrosine phosphatase

1696442

1698793

1651813

1654064

0.034

0.012

0.012

0.00436

2.615385

24

hydroxymethylglutaryl-CoA lyase

1715582

1718088

1671209

1673936

0.0757

0.016

0.022

0.0053

5.823077

25

cytochrome P450-like protein

1766039

1767592

1715187

1716737

0.176

0.039

0.0138

0.003

13.53846

26

zinc finger protein-like

1791802

1794503

1731264

1733959

0.1596

0.0386

0.0132

0.0039

12.27692

27

cell death associated protein

1802302

1804168

1744300

1746170

0.1235

0.036

0.0204

0.00572

9.5

28

steroid sulfotransferase

1911460

1912476

1836949

1837788

0.1936

0.078

0.202

0.049

14.89231

29

cyt p450 protein

1997769

2000557

1905242

1908061

0.02

0.015

0.0088

0.0006

1.538462


The Rice Chromosomes 11 and 12 Sequencing Consortia* BMC Biology 2005 3:20   doi:10.1186/1741-7007-3-20

Open Data