Plant Transcription factor database - Universität Potsdam
version: 3.0

Oryza sativa subsp. japonica Transcription factors

This section of PlnTFDB lists the putative complete set of transcriptional regulators in Oryza sativa subsp. japonica.

PlnTFDB currently contains 3017 protein models, 2722 distinct* protein sequences of Oryza sativa subsp. japonica (Proteins downloaded from: TIGR, release version 6.0), arranged in 79 gene families. The assortment of genes in each of the families is based on the presence of one or more characteristic domains previously described in the literature (identified through statistical analyses, see rules for the classification of TF families). To identify genes coding for transcription factors, previously constructed domain alignments (from the Pfam database version 23.0) or newly established alignments (PlnTFDB) were used to query the proteome of Oryza sativa subsp. japonica (Proteins downloaded from: TIGR, release version 6.0), using the hmmpfam programme of the HMMER suite, links to the domain alignments are provided. Additionally, 102 proteins were categorized as Orphans. These proteins contain one or more domain(s) whose presence, or combination, according to the literature, does not allow their classification into any of the defined families. Their role in the transcriptional regulation remains unclear.

Transcription Factor Families

Other Transcriptional Regulators

Or, you can write the sequence identifier you want to retrieve information for (e.g. LOC_Os01g01430.1, At1g08540). You can also use part of a sequence identifier (e.g. Os01g, At1g085):

Additionaly, you can use a protein sequence to query the Plant Transcription Factor protein Database using BLAST .

Citing PlnTFDB

We kindly ask users to cite the following paper when publishing results derived of the use of PlnTFDB:

Paulino Perez-Rodriguez; Diego Mauricio Riano-Pachon; Luiz Gustavo Guedes Correa; Stefan A. Rensing; Birgit Kersten; Bernd Mueller-Roeber. PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Research 2009; doi: 10.1093/nar/gkp805

* Distinct protein sequences were identified by the md5 algorithm implemented in MySQL. A md5 checksum was computed for each protein, different proteins would have distinct checksums, and identical proteins would have identical checksum.