Plant Transcription factor database - Universität Potsdam
version: 3.0

Populus trichocarpa 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 111 gene models in this family



Gene modelDescriptionDomains
172304 gw1.I.904.1 SRF-TF
174544 gw1.I.3144.1 SRF-TF
175744 gw1.I.4344.1 K-box SRF-TF
175758 gw1.I.4358.1 SRF-TF
179173 gw1.I.7773.1 SRF-TF
195109 gw1.IV.198.1 K-box SRF-TF
202997 gw1.IX.3462.1 K-box SRF-TF
203294 gw1.IX.3759.1 SRF-TF
206188 gw1.V.1589.1 SRF-TF
207877 gw1.V.3278.1 K-box SRF-TF
209623 gw1.V.5024.1 SRF-TF
216811 gw1.VII.1116.1 SRF-TF
216909 gw1.VII.1214.1 K-box SRF-TF
216929 gw1.VII.1234.1 SRF-TF
216934 gw1.VII.1239.1 SRF-TF
217646 gw1.VII.1951.1 SRF-TF
218145 gw1.VII.2450.1 K-box SRF-TF
240188 gw1.XIII.437.1 SRF-TF
244188 gw1.XIV.931.1 K-box SRF-TF
244198 gw1.XIV.941.1 K-box SRF-TF
249483 gw1.XIX.1883.1 K-box SRF-TF
249497 gw1.XIX.1897.1 K-box SRF-TF
253402 gw1.XV.2838.1 K-box SRF-TF
253673 gw1.XV.3109.1 K-box SRF-TF
257800 gw1.XVI.3739.1 SRF-TF
258177 gw1.XVII.168.1 K-box SRF-TF
265533 gw1.12122.1.1 SRF-TF
265566 gw1.1217.2.1 SRF-TF
268072 gw1.131.74.1 SRF-TF
276576 gw1.185.8.1 SRF-TF
278303 gw1.205.32.1 SRF-TF
286013 gw1.3897.5.1 SRF-TF
287971 gw1.41.456.1 K-box SRF-TF
288710 gw1.4342.4.1 SRF-TF
292381 gw1.64.33.1 SRF-TF
292424 gw1.64.76.1 SRF-TF
294451 gw1.690.3.1 SRF-TF
296154 gw1.7800.4.1 SRF-TF
410976 gw1.II.2311.1 K-box SRF-TF
411196 gw1.II.2531.1 SRF-TF
420382 gw1.VIII.1810.1 K-box SRF-TF
421688 gw1.XII.148.1 K-box SRF-TF
422533 gw1.XII.993.1 K-box SRF-TF
548040 eugene3.00010481 K-box SRF-TF
553018 eugene3.00002333 SRF-TF
557553 eugene3.00090813 SRF-TF
557554 eugene3.00090814 SRF-TF
557926 eugene3.00091186 SRF-TF
561938 eugene3.00061897 SRF-TF
563759 eugene3.00080354 SRF-TF
567029 eugene3.00101587 SRF-TF
570376 eugene3.00121029 SRF-TF
570801 eugene3.00130165 SRF-TF
575173 eugene3.00150568 SRF-TF
575376 eugene3.00150771 K-box SRF-TF
578016 eugene3.00180240 SRF-TF
584741 eugene3.01660058 SRF-TF
588539 eugene3.02510007 SRF-TF
588572 eugene3.02520011 SRF-TF
591180 eugene3.36680001 SRF-TF
591593 eugene3.40490001 SRF-TF
594233 eugene3.62880001 SRF-TF
596719 eugene3.00860010 SRF-TF
640573 grail3.0008056401 K-box SRF-TF
643714 grail3.0003079001 SRF-TF
643871 grail3.0003092401 K-box SRF-TF
644373 grail3.0033033502 K-box SRF-TF
646538 grail3.0018023503 K-box SRF-TF
647036 grail3.0047013501 K-box SRF-TF
647039 grail3.0047013603 K-box SRF-TF
647042 grail3.0047013701 SRF-TF
648506 grail3.0139000303 K-box SRF-TF
651191 grail3.0083000102 K-box SRF-TF
651468 grail3.0002017601 K-box SRF-TF
654586 grail3.0058021901 K-box SRF-TF
659188 grail3.0006057701 K-box SRF-TF
660583 grail3.0081005702 K-box SRF-TF
661810 grail3.0042013901 K-box SRF-TF
673070 grail3.0155001701 K-box SRF-TF
678188 grail3.0041013401 K-box SRF-TF
680171 grail3.0690000103 K-box SRF-TF
709904 estExt_Genewise1_v1.C_LG_II0440 K-box SRF-TF
719775 estExt_Genewise1_v1.C_LG_VII4001 K-box SRF-TF
719996 estExt_Genewise1_v1.C_LG_VIII0399 K-box SRF-TF
745710 estExt_Genewise1_v1.C_1550090 K-box SRF-TF
751926 fgenesh4_pg.C_LG_I001529 SRF-TF
752730 fgenesh4_pg.C_LG_I002333 SRF-TF
753148 fgenesh4_pg.C_LG_I002751 K-box SRF-TF
754832 fgenesh4_pg.C_LG_II001012 K-box SRF-TF
756379 fgenesh4_pg.C_LG_II002559 SRF-TF
758707 fgenesh4_pg.C_LG_IV000335 K-box SRF-TF
759391 fgenesh4_pg.C_LG_IV001019 SRF-TF
762094 fgenesh4_pg.C_LG_VI000404 K-box SRF-TF
762746 fgenesh4_pg.C_LG_VI001056 SRF-TF
763951 fgenesh4_pg.C_LG_VII000296 K-box SRF-TF
765155 fgenesh4_pg.C_LG_VIII000169 SRF-TF
770139 fgenesh4_pg.C_LG_X001629 SRF-TF
770799 fgenesh4_pg.C_LG_X002289 SRF-TF
773289 fgenesh4_pg.C_LG_XII001064 SRF-TF
773512 fgenesh4_pg.C_LG_XII001287 K-box SRF-TF
777314 fgenesh4_pg.C_LG_XVI000556 SRF-TF
778182 fgenesh4_pg.C_LG_XVII000061 K-box SRF-TF
778208 fgenesh4_pg.C_LG_XVII000087 SRF-TF
781757 fgenesh4_pg.C_scaffold_41000125 SRF-TF
800675 fgenesh4_pm.C_LG_IV000362 SRF-TF
801173 fgenesh4_pm.C_LG_V000265 K-box SRF-TF
804358 fgenesh4_pm.C_LG_IX000405 K-box SRF-TF
820484 estExt_fgenesh4_pg.C_LG_VIII0760 SRF-TF
823509 estExt_fgenesh4_pg.C_LG_XII1207 K-box SRF-TF
827076 estExt_fgenesh4_pg.C_570124 K-box SRF-TF
832404 estExt_fgenesh4_pm.C_LG_VII0453 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