Plant Transcription factor database - Universität Potsdam
version: 3.0

Arabidopsis lyrata 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 79 gene models in this family



Gene modelDescriptionDomains
314222 fgenesh1_pm.C_scaffold_1003002 SRF-TF
317287 fgenesh1_pm.C_scaffold_3000303 SRF-TF
320100 fgenesh1_pm.C_scaffold_4000157 K-box SRF-TF
320424 fgenesh1_pm.C_scaffold_4000481 SRF-TF
321962 fgenesh1_pm.C_scaffold_4002019 K-box SRF-TF
328110 fgenesh1_pm.C_scaffold_7000337 SRF-TF
336095 fgenesh1_pg.C_scaffold_1002660 SRF-TF
338390 fgenesh1_pg.C_scaffold_2000489 SRF-TF
357809 fgenesh1_pg.C_scaffold_8001596 SRF-TF
358254 fgenesh1_pg.C_scaffold_8002041 SRF-TF
471935 fgenesh2_kg.1__1889__AT1G17310.1 SRF-TF
472101 fgenesh2_kg.1__2055__AT1G18750.1 SRF-TF
472923 fgenesh2_kg.1__2877__AT1G24260.1 K-box SRF-TF
475240 fgenesh2_kg.2__370__AT1G60920.1 SRF-TF
475244 fgenesh2_kg.2__374__AT1G60880.1 SRF-TF
476039 fgenesh2_kg.2__1169__AT1G69120.1 K-box SRF-TF
476289 fgenesh2_kg.2__1419__AT1G71692.1 K-box SRF-TF
476870 fgenesh2_kg.2__2000__AT1G77080.2 SRF-TF
476959 fgenesh2_kg.2__2089__AT1G77950.1 SRF-TF
476961 fgenesh2_kg.2__2091__AT1G77980.1 SRF-TF
477299 fgenesh2_kg.2__2429__AT1G77950.2 SRF-TF
477978 fgenesh2_kg.3__679__AT3G66656.1 SRF-TF
479371 fgenesh2_kg.3__2072__AT3G18650.1 SRF-TF
481114 fgenesh2_kg.4__174__AT2G22540.1 K-box SRF-TF
482404 fgenesh2_kg.4__1464__AT2G34440.1 SRF-TF
483701 fgenesh2_kg.4__2761__AT2G45650.1 K-box SRF-TF
485833 fgenesh2_kg.5__1825__AT3G54340.1 K-box SRF-TF
486166 fgenesh2_kg.5__2158__AT3G57230.1 K-box SRF-TF
486333 fgenesh2_kg.5__2325__AT3G58780.1 K-box SRF-TF
486583 fgenesh2_kg.5__2575__AT3G61120.1 K-box SRF-TF
488202 fgenesh2_kg.6__1336__AT5G13790.1 K-box SRF-TF
488929 fgenesh2_kg.6__2063__AT5G20240.1 K-box SRF-TF
489185 fgenesh2_kg.6__2319__AT5G23260.2 K-box SRF-TF
489614 fgenesh2_kg.6__2748__AT5G27944.1 SRF-TF
489617 fgenesh2_kg.6__2751__AT5G27070.1 SRF-TF
489841 fgenesh2_kg.6__2975__AT4G09960.3 K-box SRF-TF
490004 fgenesh2_kg.6__3138__AT4G11880.1 K-box SRF-TF
490820 fgenesh2_kg.7__253__AT4G37940.1 K-box SRF-TF
492389 fgenesh2_kg.7__1822__AT4G24540.1 K-box SRF-TF
492570 fgenesh2_kg.7__2003__AT4G22950.1 K-box SRF-TF
493979 fgenesh2_kg.7__3412__AT5G41200.1 SRF-TF
496727 fgenesh2_kg.8__2543__AT5G65050.2 K-box SRF-TF
496768 fgenesh2_kg.8__2584__AT5G65330.1 SRF-TF
497339 fgenesh2_kg.233__4__AT5G65050.3 K-box SRF-TF
859602 Al_scaffold_0007_3101 SRF-TF
860242 Al_scaffold_0007_3741 SRF-TF
864749 Al_scaffold_0005_228 SRF-TF
864830 Al_scaffold_0005_309 K-box SRF-TF
865435 Al_scaffold_0005_914 K-box SRF-TF
868378 Al_scaffold_0004_541 SRF-TF
871928 Al_scaffold_0003_569 SRF-TF
876002 Al_scaffold_0002_596 SRF-TF
876627 Al_scaffold_0002_1221 SRF-TF
877021 Al_scaffold_0002_1615 SRF-TF
878307 Al_scaffold_0001_74 SRF-TF
880553 Al_scaffold_0001_2320 SRF-TF
885294 Al_scaffold_0008_1558 K-box SRF-TF
886791 Al_scaffold_0008_3055 SRF-TF
890115 scaffold_102909.1 K-box SRF-TF
891573 scaffold_104367.1 SRF-TF
891578 scaffold_104372.1 SRF-TF
893571 scaffold_200645.1 SRF-TF
895087 scaffold_202161.1 SRF-TF
896196 scaffold_300166.1 K-box SRF-TF
898356 scaffold_302326.1 SRF-TF
901071 scaffold_400572.1 SRF-TF
901108 scaffold_400609.1 SRF-TF
904011 scaffold_403512.1 K-box SRF-TF
905471 scaffold_501175.1 SRF-TF
905731 scaffold_501435.1 SRF-TF
908971 scaffold_601028.1 K-box SRF-TF
909555 scaffold_601612.1 K-box SRF-TF
910778 scaffold_602835.1 SRF-TF
912597 scaffold_700339.1 SRF-TF
914774 scaffold_702516.1 K-box SRF-TF
916318 scaffold_704060.1 SRF-TF
918221 scaffold_801621.1 K-box SRF-TF
919101 scaffold_802501.1 SRF-TF
919330 scaffold_802730.1 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