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Table 1 Summary of identified genes homologous to glycosyl hydrolase family 35 galactosidase

From: Genomic and expression analysis of glycosyl hydrolase family 35 genes from rice (Oryza sativa L.)

Gene name

BGI entries (AAAA...)a

Genomic Contig.

Chr.b

UniGene

Gene Locus (NCBI, RGP)

Gene Locus (TIGR)

Corresponding cDNAc

Numberd

Tissue libraryse

Expression profile (TPM) Transcript per millonf

GEO profileg

        

mRNA

ESTs

 

Cl.

Fw.

Lf.

P

Rt.

Sd.

St.

Vm

 

OsBgal1

1002951

AP008209.1

3

Os.13559

Os03g0165400

LOC_Os03g06940

AF499737

5

99

Fw, Cl, P, Mx, Wp, UnT, Vm, Sd, St, Rt

121

241

46

120

14

92

23

217

Up: CKl, AB&GBd, AnX, Dw: AB&GB, NaCl, Na3AsO4, CKrl

OsBgal2

1003471

AP004729.3, AP008212.1

6

Os.87715

Os06g0573600

LOC_Os06g37560

AK102756

4

201

P, Lf, Mx, St, Rt, Cl, Fw, Wp, UnT

66

80

291

391

205

0

118

0

Up: CKl, AB&GBd, NaCl Dw: AnX, AB&GB, Na3AsO4, CKrl

OsBgal3

01012445, 01022298

AP008207.1, AP003546.4

1

Os.18562

Os01g0580200

LOC_Os01g39830

AK103045

2

44

Cl, Wp, P, St, Fw, Mx, UnT, Vm

115

43

0

37

0

30

47

217

Up: CKl, AB&GBd, AB&GB, Na3AsO4, NaCl Dw: AnX, CKrl

OsBgal4

ND

AP003297.3, AP008207.1

1

Os.9892

Os01g0875500

LOC_Os01g65460

AK101399

3

107

Cl, Fw, Mx, P, Rt, UnT, St, Wp

279

263

0

45

29

30

0

0

Up: CKl, AnX, AB&GBd, Na3AsO4, NaCl Dw: AB&GB

OsBgal5

1000473.1

AP003447.2, AP008207.1, AP003445.2

1

Os.41043

Os01g0533400

LOC_Os01g34920

AK119447

2

3

Mx, St

ND

ND

ND

ND

ND

ND

ND

ND

Up: Na3AsO4, CKrl Dw: CKl, AnX, NaCl

OsBgal6

101013714.1

AC135419.2, AC135429.2

5

Os.82841

P0636F09.15

LOC_Os05g35360

EU602310

ND

1

UnT

ND

ND

ND

ND

ND

ND

ND

ND

-

OsBgal7

01011567, 01017443

AP008208.1

2

Os.14358

Os02g0219200

LOC_Os02g12730

AK059059

7

57

P, Mx, St, Cl, UnT, Fw, Wp, Rt

24

21

0

135

14

92

78

0

Up: AnX, CKl, AB&GB, AB&GBd, NaCl, Na3AsO4 Dw: CKrl

OsBgal8

1001024

AP008209.1, DP000009.2

3

Os.22360

Os03g0255100

LOC_Os03g15020

AK067479

3

253

Fw, Mx, St, Lf, P, Rt, Cl, UnT, Sd, Wp

42

761

133

120

190

216

228

0

Up: AnX, CKl, AB&GBd, NaCl Dw: Na3AsO4

OsBgal9

ND

AP008211.1

5

Os.14570

Os05g0539400

LOC_Os05g46200

AK068572

2

66

Lf, St, P, Mx, Cl, UnT, Wp, Sd, Rt

12

0

122

52

14

247

110

0

Up: CKl, AB&GBd, AB&GB, NaCl Dw: AnX, Na3AsO4

OsBgal10

1005991

AP008214.1, AP003912.3

8

Os.18310

Os08g0549200

LOC_Os08g43570

AK069066

3

137

Mx, Fw, P, St, UnT

0

249

0

158

0

0

0

0

Up: AB&GBd, AB&GB, AnX Dw: Na3AsO4, CKrl

OsBgal11

1013958

AP008215.1

9

Os.49945

Os09g0539200

LOC_Os09g36810

EU603286

2

7

Mx, Sd

0

0

0

0

0

61

0

0

Up: AnX, Na3AsO4, NaCl Dw: CKl

OsBgal12

10005757.1

AP008216.1, DP000086.1

10

Os.46702

Os10g0330600

LOC_Os10g18400

AK119350

3

3

Mx, Fw

0

7

0

0

0

0

0

0

Up: AnX

OsBgal13

ND

AP008218.1

12

Os.52193

Os12g0429200

LOC_Os12g24170

AK065546

2

36

Mx, St, Lf, Fw, UnT, P, Wp, Cl

6

21

34

15

0

0

55

0

Up: CKl, AB&GBd, AB&GB Dw: AnX, Na3AsO4, NaCl

OsBgal14

10006090

ND

10

Os.22528

J090043H02

LOC_Os10g19960

AK242960

2

58

Fw, P, UnT, Sd, Wp

0

358

0

7

0

61

0

0

-

OsBgal15

1003798.1

AP004733

6

NF

AP004733

LOC_Os06g42310

EU051629

ND

 

ND

ND

ND

ND

ND

ND

ND

ND

ND

-

  1. aContig number in Beijing Genome Institute (the numbers given are the Genbank Accession without the initial 'AAAA').
  2. bChromosome locations from mapping of the corresponding genes on the 12 rice chromosomes in GenBank.
  3. cAccessions of full-length cDNA clones of japonica rice databases [64] or indica clones from this study (OsBgal6, OsBgal11 and OsBgal15).
  4. dThe number of mRNA and EST identified by UniGene from the NCBI Genbank database.
  5. eTissue libraries means the source tissue from which the corresponding ESTs were isolated. Tissue abbreviations are: Cl: callus, Fw: Flower, Lf: leaf, P: Panicle, Rt: root, Sd: Seed, St: Stem, Mx: Mixed Tissues, Vm: Vegetative meristem, Wp: whole plant, UnT: unspecified tissue.
  6. fExpression profile means transcript frequency per million calculated from the number of ESTs in a certain library. ND: not determined.
  7. gGEO (Gene Expression Omnibus public repository of microarray and other forms of high-throughput data submitted by the scientific community). Abbreviations are: Up: up-regulated, Dw:down-regulate, CKrl: Cytokinin effect on rice roots and leaves: time course, CKl: Cytokinin-inducible type-A response regulator OsRR6 overexpression effect on rice leaves, AB&GB: Abscisic acid and gibberellin effect on calluses, gene expression array-based, log ratio, AB&GBd: Abscisic acid and gibberellin effect on calluses (dye-swap), AnX: Anoxia effect on rice coleoptiles, NaCl: Salinity stress response, Na3AsO4: Sodium arsenate effect on Azucena and Bala varieties.
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BMC Plant Biology

ISSN: 1471-2229

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