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Table 2 The IQD gene family of Oryza sativa

From: Genome-wide comparative analysis of the IQD gene families in Arabidopsis thaliana and Oryza sativa

Gene Identifiera

Clone IDb

Positionc

Protein ID Coded

cDNA Accessione

Expressionf

Protein Nameg

Size (aa)

Mass (kD)

IP

Predicted Locationh

          

PSORT

TargetP

Os01m00895

AP002743

02000445

70239–72382

NP_914546

AK119868

B

OsIQD22

465

49.7

10.5

N

M 0.69/3

Os01m00929

AP002746

02000453

152586–155207

NP_914588

AK073282

B

OsIQD5

442

48.9

10.3

?

?

Os01m04963

AP002901

02003727

7612–9986

NP_916574

AK102451

A

OsIQD9

441

48.2

11.0

?

M 0.55/5

Os01m05025

AP003288

02003743

38561–44222

9629.m05025i

AK062106

A B

OsIQD24

574

63.1

9.8

N

C 0.44/5

Os01m05259

AP003768

02003803

95943–99625

NP_916047j

-

A B

OsIQD20

378

42.4

10.7

?

?

Os01m06082

AP004366

02004199

106290–110032

BAD73780

AK072219

A B

OsIQD2

500

56.1

10.2

N

?

Os01m06368

AP003611

02004332

27187–28795

BAB63799k

AK120019*

-

 

n.d.

n.d.

n.d.

n.d.

n.d.

Os01m06663

AP003349

02004466

15479–17371

NP_915152

AK105622*

A

OsIQD11

563

61.7

11.5

?

?

Os02m01875

AP005534

02005830

59894–65564

XP_465098

AK105486

B

OsIQD13

485

52.0

10.4

?

?

Os03m00334

AC099399

02007792

57690–58691

XP_470188

-

B

OsIQD26

303

32.3

11.2

N

M 0.47/4

Os03m00584

AC105729

02029613

135566–136967

AAN06867

-

B

OsIQD17

417

44.3

10.2

?

M 0.61/4

Os03m04199

AC120505

02010452

144176–145684

XP_468989

-

-

OsIQD16

447

48.2

10.4

?

M 0.83/3

Os03m04309

AL731878

02014260

118442–126461

AK067192l

AAU89191

A B

OsIQD3

440

48.7

9.6

N

?

Os03m05627

AC084296

02011159

48853–52578

AAT75259

AK103438

A B

OsIQD4

422

47.0

9.8

?

?

Os04m04570

Chr.4m

02014535

27592940–27594955

9632.m04570

-

-

OsIQD27

368

41.6

11.4

N

?

Os04m04664

AL607001

02017716

151253–153796

XP_473550

AK100392

A B

OsIQD15

464

50.1

10.4

N

M 0.42/5

Os04m05532

AL606999

02015015

85710–91604

XP_474230

AK066310

A B

OsIQD25

893

98.5

4.8

N

?

Os05m00240

AC093089

02015233

81361–85365

AAV33309

AK065809

A B

OsIQD1

474

52.0

10.2

?

?

Os05m00863

AC093954

02015642

45436–47015

XP_476075

-

-

OsIQD21

497

52.6

10.4

?

M 0.57/4

Os05m03604

AC108500

02017442

23568–26042

AAU90174

-

-

OsIQD6

538

57.8

9.6

N

?

Os05m04170

Chr.5n

02017671

24971333–24973284

-

-

-

OsIQD19

367

40.5

10.8

N

?

Os05m04307

AC097112

02017716

54441–58756

XP_475770

AK101555

A B

OsIQD23

574

63.8

9.8

N

C 0.38/5

Os05m04352

AC104713

02017731

37570–40338

XP_475808

AK107193

B

OsIQD10

408

44.6

10.6

?

C 0.36/5

Os06m00539

AP004844

02018243

90441–94332

BAD69297

AK099462

A B

OsIQD7

353

39.4

10.4

N

?

Os06m02303

AP003572

02019223

18921–22322

BAD61625

-

-

OsIQD12

470

50.0

10.6

N

?

Os06m03925

AP0039440

2020217

329–2234

9634.m03925

AK109238*

-

OsIQD28

432

46.1

8.3

N

M 0.55/4

Os08m00125

AP005657

02022817

88345–90355

XP_479772

AK100461

A B

OsIQD14

543

59.0

11.0

?

?

Os10m02409

AC027662

02029613

17834–19903

NP_921513

AK110922

B

OsIQD18

485

52.2

10.3

N

M 0.73/3

Os12m04168

AL732532

02035326

133867–139274

9640.m04168

AK102525

A

OsIQD8

442

48.2

10.1

N

?

  1. a TIGR V2 pseudo-molecules annotation.
  2. b Upper line: nucleotide accession of a BAC clone coding for a rice IQD gene from O. sativa ssp. japonica [93]. Lower line: alternative rice BAC clone from O. sativa ssp. indica (the prefix, AAAA, is omitted).
  3. c Position of the IQD gene on the BAC clone from O. sativa ssp. japonica.
  4. d For four IQD genes, protein identification numbers are only available from the TIGR Rice Genome Project database [74].
  5. e cDNAs clones are full-length if not otherwise indicated. Asterisks denote cDNA sequences that are likely 5'-truncated by comparison with predicted mRNAs and encoded OsIQD proteins.
  6. f Additional evidence for expression provided by (A) EST clones and (B) Massively Parallel Signature Sequencing (MPSS, [106]).
  7. g Nomenclature of OsIQD genes is arbitrary. Levy et al. [37] cloned AtIQD1 and reported closely related rice genes OsIQD1-OsIQD5. The designation of OsIQD6-OsIQD29 is based on the phylogenetic analysis presented in Figure 1c.
  8. h PSORT predictions: N (nucleus), C (chloroplast), M (mitochondrion). TargetP predictions: values indicate score (0.00 – 1.00) and reliability class (1–5; best class is 1).
  9. i Region of Os01m05025 is not annotated on BAC clone AP003288 as indicated for AK062106 full-length cDNA sequence on KOME website [98]. Therefore, no Protein ID is available and the TIGR gene model accession is given instead.
  10. j Predicted gene model shows an N-terminal extension by 11 amino acids (possibly incorrect start codon), which was removed to meet consensus of IQD protein N-termini for computational analysis of protein properties.
  11. k Predicted protein of this gene locus is shorter for both O. sativa subspecies than the predicted polypeptide encoded by the partial cDNA clone that is truncated in the coding region N-terminal to the predicted IQ67 domain. Therefore, theoretical physico-chemical parameters of the predicted full-length protein could not be determined (n.d.).
  12. l Protein coding region is misannotated when compared with the predicted protein encoded by the full-length cDNA sequence.
  13. m BAC clone OJ1087C03 cannot be retrieved from GenBank.
  14. n Incorrect hyperlink from gene locus to BAC clone on RiceGE website.