Traffic analysis

Transcription Factor Nomenclature

There is currently no coherent effort in the grasses for a rational and organized naming of transcription factors (TFs). The use of GenBank accession numbers, EST names or locus identifiers provides an impractical mechanism, which often leads to ambiguities, for example because of multiple entries in GenBank or of several ESTs for the same protein. Thus, we have adopted a uniform nomenclature for TFs from the grasses, following the lead from Arabidopsis. This proposal was done in consultation with the Maize Genetics Nomenclature Committee, the TIGR rice annotation group and by the SUCEST-FUN sugarcane annotation group.
Nomenclature criteria adopted here: Each transcription factor will have an organism identifier (Zm for maize, Sb for sorghum, Os for rice and cane for sugarcane), followed by letters that represent the TF family (e.g., MYB, bHLH, HD, bZIP) and by a number that will start with "1". Since we realize that many TFs are known by their genetic names, this nomenclature will permit the use of synonyms. For example, KNOTTED could be named ZmHD1 (KN) and C1 would be ZmMYB1 (C1). In addition, whenever possible, we will try to have the numbers provide a historic perspective of which TFs have been first identified. In that regard, since KN and C1 correspond to the founding members of their respective families in maize, they are assigned the number "1". Whenever possible, an effort will also be made to capture phylogenetic relationships when numbering the TFs. We also realize that there are several TFs that have been already named with numbers, as for example "myb23" or "bZIP5". Whenever possible, we intend to keep the original numbers to ensure that we minimize confusion. However, we foresee that in some instances, the TFs may need to be re-named. In those cases, we will communicate the original author of the change and we will include a note in GenBank indicating to that effect. It should be noted that it is not our intention to alter the name of existing genes – the database deals primarily with proteins and when appropriate, the names of the genes (if already available) will be provided for cross- reference.
Maize Genetics Nomenclature Committee

GRASSIUS BLAST sets

Following sets are available for BLAST:
  1. All nt sequences: Contains AGRIS, GRASSIUS and all Maize nucleotide sequences (#3 + #5 + #7)
  2. ALL pep sequences: Contains peptide sequences from AGRIS, GRASSIUS and Maize (#4 + #6 + #8)
  3. GRASSIUS nt: Contains nucleotide sequence of all transcription factors in GRASSIUS
  4. GRASSIUS pep: Peptide sequences of all transcription factors in GRASSIUS
  5. AGRIS - TF nt: Contains nucleotide sequence of all transcription factors in AGRIS
  6. AGRIS - TF pep: Contains peptide sequence of all transcription factors in AGRIS

    7. All Maize sequence information was obtained from maizesequence.org. Data is as of 03-21-2008. More information describing the data is located here.
  7. Maize genes nt: Contains nucleotide sequences of genes predicted as protein-coding, evidence, hypothetical and transposon-like
  8. Maize gene translations: Protein translations of genes that are classified as protein-coding, evidence, hypothetical and transposon-like
  9. Maize BACs: Raw maize genome sequences for accessioned BACs, as stored in GenBank
  10. Maize BACs masked: RepeatMasked maize genome sequences for accessioned BACs
  11. Maize BAC contigs: Sequences for all individual contigs that make up the accessioned BACs
  12. Maize BAC contig masked: RepeatMasked sequences for individual BAC-contigs