DRTF - The Database of Rice Transcription Factor
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HMM profiles used || BLAST conditions || Glossary || Download
Percentage of putative TFs in DRTF annotated by various tools and databases   back to top..
To provide comprehensive information for the putative TFs, we made extensive annotations using a number of bioinformatics tools and databases.
Tools/Databases Indica(%) Japonica(%)
InterPro 98.9 98.4
GO 77.5 77.1
EMBL 99.8 100.0
UniProt 96.0 96.1
PDBSelect 58.9 59.2
TRANSFAC 61.1 65.9
RefSeq 86.3 90.4
RIKEN 74.2 78.3
UniGene 86.1 88.9
GEO 70.4 74.9
HMM profiles used   back to top..
All these HMM profiles were selected form Pfam except for the Trihelix family. Unless expressly noted, the e-value cut-off 0.01 was used.
Family Pfam Query HMM InterProID Note
ABI3/VP1 PF02362 B3 DNA binding domain IPR003340  
AP2/EREBP PF00847 AP2 domain IPR001471  
ARF PF06507 Auxin response factor IPR010525  
ARID PF01388 ARID/BRIGHT DNA binding domain IPR001606  
AS2 PF03195 Protein of unknown function DUF260 IPR004883  
AUX/IAA PF02309 AUX/IAA family IPR003311  
BES1 PF05687 Plant protein of unknown function (DUF822) IPR008540  
bHLH PF00010 Helix-loop-helix DNA-binding domain IPR001092 Max e-value<0.46
bZIP PF00170 bZIP transcription factor IPR011616  
C2C2-CO-like PF06203 CCT motif IPR010402  
C2C2-Dof PF02701 Dof domain, zinc finger IPR003851  
C2C2-Gata PF00320 GATA zinc finger IPR000679  
C2C2-YABBY PF04690 YABBY protein IPR006780  
C2H2 PF00096 Zinc finger, C2H2 type IPR007087  
C3H PF00642 Zinc finger C-x8-C-x5-C-x3-H type (and similar) IPR000571  
CAMTA PF03859 CG-1 domain IPR005559  
CCAAT-HAP2 PF02045 CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B IPR001289  
CPP PF03638 Tesmin/TSO1-like CXC domain IPR005172  
E2F/DP PF02319 E2F/DP family winged-helix DNA-binding domain IPR003316  
EIL PF04873 Ethylene insensitive 3 IPR006957  
FHA PF00498 FHA domain IPR000253  
GARP-ARR-B PF00072 Response regulator receiver domain IPR001789 Required: 1) a MYB-like domain, 2) and a response regulator receiver domain with the conservative DDK sites
GARP-G2-like PF00249 Myb-like DNA-binding domain IPR001005  
GeBP? PF04504 Protein of unknown function, DUF573 IPR007592  
GIF PF05030 SSXT protein (N-terminal region) IPR007726  
GRAS PF03514 GRAS family transcription factor IPR005202  
HB PF00046 Homeobox domain IPR001356  
HMG PF00505 HMG (high mobility group) box IPR000910  
HSF PF00447 HSF-type DNA-binding IPR000232?  
JUMONJI-TF_JmjC? PF02373 JmjC domain IPR003347  
JUMONJI-TF_JmjN? PF02375 jmjN domain IPR003349  
LFY PF01698 Floricaula / Leafy protein IPR002910  
LIM PF00412 LIM domain IPR001781  
MADS PF00319 SRF-type transcription factor (DNA-binding and dimerisation domain) IPR002100  
MYB PF00249 Myb-like DNA-binding domain IPR001005 Myb domain number >=2
MYB-related กก กก กก Myb domain number <2
NAC PF02365 No apical meristem (NAM) protein IPR003441  
Nin-like PF02042 RWP-RK IPR003035  
PcG PF00856 SET domain IPR001214  
PHD PF00628 PHD-finger IPR006565  
PLATZ PF04640 Protein of unknown function, DUF597 IPR006734  
S1Fa-like PF04689 DNA binding protein S1FA IPR006779  
SBP PF03110 SBP domain IPR004333  
SRS PF05142 Domain of unknown function (DUF702) IPR007818  
TAZ PF02135 TAZ zinc finger IPR000197  
TCP PF03634 TCP family transcription factor IPR005333  
Trihelix       self- built HMM profile
TUB PF01167 Tub family IPR000007  
WRKY PF03106 WRKY DNA -binding domain IPR003657  
ZF-HD PF04770 ZF-HD protein dimerisation region IPR006456  
ZIM PF06200 ZIM motif IPR010399  
BLAST conditions   back to top..
For those families that no DNA-binding domain profiles are available, we use their respective member sequences from existed databases as seed to blast search. And make manully investgation to detect the cut-off value.
Family Alfin-like BBR/BPC CCAAT-Dr1 CCAAT-HAP3 CCAAT-HAP5 GARP-G2-like GRF HRT LUG MBF1 NZZ/SPL PBF-2-like/Whirly ULT VOZ
Max E-value 3.00E-30 6.00E-36 8.00E-39 1.00E-06 4.00E-09 8.00E-04 2.00E-15 9.00E-19 2.00E-27 5.00E-36 2.00E-05 3.00E-08 4.00E-82 2.00E-93
Glossary   back to top..

Gene Name:
     The Gene Name was used to identified different members from indica.

Gene Model:
     A gene model represents the mRNA transcript of a locus (gene) and therefore contains information about features of the transcript such as exon-intron boundaries, splice sites, UTRs, etc. Due to the alternative splicing of mRNA transcripts, more than one gene model can derive from a locus (gene). Gene models are assigned with distinct identifiers in the database and are linked to the parent locus (gene).

Locus (Gene):
     A locus is a specific place on a chromosome where a gene is located, and could be taken equivalent as to a gene. in the database. Due to the potential alternative splicing, more than one gene models could be derived from one locus.

TF Family:
    The family the gene belongs to.

Chromosome:
     The chromosome the gene locates in.

Gene Structure:
     The gene structure picture is used to demonstrate the exons distribution along the gene. The gene length is the entire length, including exons and introns.

Annotation:
     Relative GO or UniGene information was selected and listed.

Protein Sequence Features:
    Graphic view. Relative information as supported evidences from InterPro, UniPro, RefSeq, and TransFac was selected.

Nucleic Location Signal:
     Nucleic location signals were scanned using PredictNLS.

Homology:
    List the homological peer(s) from japonica or indica, and arobidopsis.

Sequence:
     List the CDS sequence and protein sequence. One can download the sequence or blast them.

Details:
     List the relative information as supported evidences from EMBL, RIKEN, InterPro, UniPro, RefSeq, and TransFac

Download All Sequence ......    back to top..
All in FASTA format, text file.
indica:
Peptide sequences
CDS sequences
japonica:
Peptide sequences
CDS sequences
 
 

© Center for Bioinformatics(CBI), Peking University
2005
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