Plant Transcription factor database - Universität Potsdam
version: 3.0

Physcomitrella patens 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 22 gene models in this family



Gene modelDescriptionDomains
104526 estExt_fgenesh1_pm.C_80015 SRF-TF
109598 estExt_fgenesh1_kg.C_260002 K-box SRF-TF
109826 estExt_fgenesh1_kg.C_550007 SRF-TF
125581 e_gw1.55.5.1 SRF-TF
125652 e_gw1.55.13.1 K-box SRF-TF
128084 e_gw1.68.221.1 SRF-TF
140819 e_gw1.171.4.1 K-box SRF-TF
143861 e_gw1.209.37.1 K-box SRF-TF
148211 e_gw1.273.6.1 SRF-TF
166549 estExt_fgenesh1_pg.C_1180093 SRF-TF
179228 estExt_gwp_gw1.C_340302 SRF-TF
186168 estExt_gwp_gw1.C_900087 SRF-TF
191533 estExt_gwp_gw1.C_1630046 SRF-TF
202186 estExt_Genewise1.C_80073 SRF-TF
231108 fgenesh2_pg.scaffold_122000045 SRF-TF
39538 gw1.81.151.1 SRF-TF
49593 gw1.88.220.1 SRF-TF
83991 fgenesh1_pg.scaffold_118000119 K-box SRF-TF
87956 fgenesh1_pg.scaffold_163000049 SRF-TF
90569 fgenesh1_pg.scaffold_198000079 SRF-TF
90570 fgenesh1_pg.scaffold_198000080 SRF-TF
94754 fgenesh1_pg.scaffold_267000029 K-box 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