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About SoybeanTFDB

SoybeanTFDB hosted by the RIKEN Plant Science Center is a public database that provides predicted transcription factor (TF) encoding genes annotated in the soybean genome sequence Glyma1.0 model provided by Phytozome. The current version (ver. 1.0) of SoybeanTFDB contains 4342 gene loci encoding 5035 TF models which are classified into 61 families based on their DNA binding domains. 51 HMMs of Pfam and those of 11 HMMs, which were originally created using HMMbuild of HMMER package (http://hmmer.janelia.org/) were used to search against the proteome dataset of Glyma1. The search results for each TF family were then analyzed to retrieve discovered regions as conserved DBDs and relevant annotation information.


Reference

In silico Analysis of Transcription Factor Repertoire and Prediction of Stress Responsive Transcription Factors in Soybean.
Keiichi Mochida, Takuhiro Yoshida, Tetsuya Sakurai, Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki and Lam-Son Phan Tran
DNA Res. 2009 Nov 2 PubMed Logo


  TF families  
  • ABI3VP1 (163)
  • AP2_EREBP (405)
  • ARF (75)
  • ARID (22)
  • Alfin-like (27)
  • Aux_IAA (126)
  • BBR-BPC (21)
  • BES1 (21)
  • C2C2_Zn-CO-like (101)
  • C2C2_Zn-Dof (87)
  • C2C2_Zn-GATA (65)
  • C2C2_Zn-YABBY (28)
  • C2H2_Zn (270)
  • C3H-TypeI (178)
  • CAMTA (14)
  • CCAAT_Dr1 (23)
  • CCAAT_HAP2 (42)
  • CCAAT_HAP3 (47)
  • CCAAT_HAP5 (26)
  • CPP (22)
  • E2F_DP (23)
  • EIL (14)
  • GARP_ARRB (21)
  • GARP_G2-like (104)
  • GRAS (127)
  • GRF (10)
  • GeBP (17)
  • HB (283)
  • HMG-box (50)
  • HRT (1)
  • HSF (65)
  • JUMONJI (54)
  • LFY (3)
  • LIM (41)
  • LUG (10)
  • MADS (220)
  • MBF1 (3)
  • (R1)R2R3_MYB (333)
  • MYB_related (168)
  • atypical_MYB (89)
  • NAC (205)
  • Nin-like (23)
  • PHD (333)
  • PLATZ (40)
  • PcG (94)
  • S1Fa-like (4)
  • SAP (2)
  • SBP (58)
  • SRS (24)
  • TCP (61)
  • TUB (37)
  • Trihelix (34)
  • ULT (32)
  • VOZ (8)
  • WRKY_Zn (219)
  • Whirly (11)
  • ZIM (57)
  • bHLH (390)
  • bZIP (205)
  • zf-HD (57)
  • zf-TAZ (8)