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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.