Plant Transcription factor database - Universität Potsdam
version: 3.0

Oryza sativa subsp. indica MADS Family

Description

Riechmann & Meyerowitz. 1997: The MADS domain (MCM1, AGAMOUS, DEFICIENS, and SRF, serum response factor) is a conserved DNA-binding/dimerization region present in a variety of transcription factors from different kingdoms. MADS box genes represent a large multigene family in vascular plants. In angiosperms, many of the genes of the MADS family are involved in different steps of flower development, most notably in the determination of floral meristem and organ identity. The roles that MADS box genes play, however, are not restricted to control the development of the plant reproductive structures. The genetic, molecular, and biochemical basis of the action of the MADS domain proteins in the plant life cycle are reviewed here.

Members of this family
  SHOULD possess SRF-TF domain

Domain alignments

Benchmark against A. thaliana

The Sensitivity and Positive Predictive Value (PPV) were assessed for this family. The data reported by Parenicova et al. 2003 for A. thaliana were taken as gold standard.

The gold standard reported 108 members for this family, 99 of which are present in ArabTFDB, giving a PPV of 0.95. Nine additional members not present in ArabTFDB might be false negatives, giving a Sensitivity of 0.92.

This family is also present in:

References

There are 73 gene models in this family



Gene modelDescriptionDomains
OsIBCD000653 Chr01_976,420,,,1,420, SRF-TF
OsIBCD002219 Chr01_3544,1083,,,1,1083, SRF-TF
OsIBCD003179 Chr01_4965,585,,,1,585, K-box SRF-TF
OsIBCD004085 Chr01_6288,630,,,1,630, K-box SRF-TF
OsIBCD004104 Chr01_6311,798,,,1,798, K-box SRF-TF
OsIBCD004330 Chr01_6626,213,,,1,213, SRF-TF
OsIBCD004730 Chr02_37,777,,,1,777, K-box SRF-TF
OsIBCD005171 Chr02_675,693,,,1,693, SRF-TF
OsIBCD005208 Chr02_735,783,,,1,783, K-box SRF-TF
OsIBCD006987 Chr02_3678,708,,,1,708, K-box SRF-TF
OsIBCD007572 Chr02_4547,657,,,1,657, K-box SRF-TF
OsIBCD007862 Chr02_4972,282,,,1,282, SRF-TF
OsIBCD008046 Chr02_5228,669,,,1,669, K-box SRF-TF
OsIBCD009095 Chr03_789,747,,,1,747, K-box SRF-TF
OsIBCD009286 Chr03_1035,264,,,1,264, SRF-TF
OsIBCD009497 Chr03_1343,558,,,1,558, SRF-TF
OsIBCD012008 Chr03_5416,741,,,1,741, K-box SRF-TF
OsIBCD012009 Chr03_5417,720,,,1,720, K-box SRF-TF
OsIBCD013716 Chr04_1766,720,,,1,720, K-box SRF-TF
OsIBCD013717 Chr04_1768,279,,,1,279, SRF-TF
OsIBCD013773 Chr04_1866,1035,,,1,1035, SRF-TF
OsIBCD014116 Chr04_2486,222,,,1,222, SRF-TF
OsIBCD014451 Chr04_2974,540,,,1,540, K-box SRF-TF
OsIBCD014455 Chr04_2978,789,,,1,789, K-box SRF-TF
OsIBCD014574 Chr04_3146,300,,,1,300, SRF-TF
OsIBCD015350 Chr04_4257,906,,,1,906, K-box SRF-TF
OsIBCD015572 Chr04_4571,729,,,1,729, K-box SRF-TF
OsIBCD016769 Chr05_982,303,,,1,303, SRF-TF
OsIBCD016773 Chr05_989,417,,,1,417, SRF-TF
OsIBCD018064 Chr05_3275,765,,,1,765, K-box SRF-TF
OsIBCD019154 Chr06_80,1281,,,1,1281, K-box SRF-TF
OsIBCD019516 Chr06_639,678,,,1,678, K-box SRF-TF
OsIBCD019839 Chr06_1109,936,,,1,936, K-box SRF-TF
OsIBCD020504 Chr06_2239,234,,,1,234, SRF-TF
OsIBCD020815 Chr06_2863,1779,,,1,1779, SRF-TF zf-CCCH
OsIBCD021720 Chr06_4333,849,,,1,849, K-box SRF-TF
OsIBCD021996 Chr06_4734,588,,,1,588, K-box SRF-TF
OsIBCD022142 Chr07_69,804,,,1,804, K-box SRF-TF
OsIBCD022271 Chr07_287,1077,,,1,1077, SRF-TF
OsIBCD024147 Chr07_3478,1044,,,1,1044, K-box SRF-TF
OsIBCD024798 Chr08_126,627,,,1,627, SRF-TF
OsIBCD026603 Chr08_3295,291,,,1,291, SRF-TF
OsIBCD026947 Chr08_3863,1014,,,1,1014, SRF-TF
OsIBCD027200 Chr08_4242,828,,,1,828, K-box SRF-TF
OsIBCD027202 Chr08_4244,612,,,1,612, SRF-TF
OsIBCD029060 Chr09_2765,591,,,1,591, K-box SRF-TF
OsIBCD031321 Chr10_3064,201,,,1,201, SRF-TF
OsIBCD033567 Chr11_3272,1128,,,1,1128, SRF-TF
OsIBCD034344 Chr12_904,606,,,1,606, K-box SRF-TF
OsIBCD034658 Chr12_1450,426,,,1,426, SRF-TF
OsIBCD035052 Chr12_2250,279,,,1,279, SRF-TF
OsIBCD036055 Chr01_1075,1815,,,1,1815, SRF-TF
OsIBCD036194 Chr01_1808,723,,,1,723, SRF-TF
OsIBCD036195 Chr01_1810,834,,,1,834, SRF-TF
OsIBCD036289 Chr01_2300,1224,,,1,1224, SRF-TF
OsIBCD036290 Chr01_2301,348,,,1,348, SRF-TF
OsIBCD037124 Chr01_6468,1110,,,1,1110, SRF-TF
OsIBCD037141 Chr01_6533,1440,,,1,1440, SRF-TF
OsIBCD037264 Chr01_7117,627,,,1,627, SRF-TF
OsIBCD037278 Chr02_42,312,,,1,312, SRF-TF
OsIBCD037606 Chr02_1788,585,,,1,585, SRF-TF
OsIBCD039100 Chr03_3651,414,,,1,414, SRF-TF
OsIBCD039115 Chr03_3722,804,,,1,804, SRF-TF
OsIBCD039954 Chr04_1878,630,,,1,630, SRF-TF
OsIBCD039955 Chr04_1879,630,,,1,630, SRF-TF
OsIBCD040940 Chr05_1577,585,,,1,585, SRF-TF
OsIBCD041011 Chr05_2181,657,,,1,657, SRF-TF
OsIBCD042003 Chr06_2101,717,,,1,717, SRF-TF
OsIBCD043762 Chr08_2045,555,,,1,555, SRF-TF
OsIBCD043955 Chr08_3258,426,,,1,426, SRF-TF
OsIBCD044258 Chr09_140,558,,,1,558, SRF-TF
OsIBCD044260 Chr09_150,633,,,1,633, SRF-TF
OsIBCD045861 Chr11_1018,555,,,1,555, SRF-TF

General references

Jack, T. 2001. Plant development going MADS. Plant Mol. Biol. 46(5):515-20 PUBMEDID:11516144
Nam, J; dePamphilis, CW; Ma, H; Nei, M. 2003. Antiquity and evolution of the MADS-box gene family controlling flower development in plants. Mol. Biol. Evol. 20(9):1435-47 PUBMEDID:12777513
Nam, J; Kim, J; Lee, S; An, G; Ma, H; Nei, M. 2004. Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proc. Natl. Acad. Sci. U.S.A. 101(7):1910-5 PUBMEDID:14764899
Ng, M; Yanofsky, MF. 2001. Function and evolution of the plant MADS-box gene family. Nat. Rev. Genet. 2(3):186-95 PUBMEDID:11256070
Riechmann, JL; Meyerowitz, EM. 1997. MADS domain proteins in plant development. Biol. Chem. 378(10):1079-101 PUBMEDID:9372178
Shore, P; Sharrocks, AD. 1995. The MADS-box family of transcription factors. Eur. J. Biochem. 229(1):1-13 PUBMEDID:7744019
West, AG; Sharrocks, AD. 1999. MADS-box transcription factors adopt alternative mechanisms for bending DNA. J. Mol. Biol. 286(5):1311-23 PUBMEDID:10064699