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The most represented mature sequence was generally selected as representative ID by default.
c: Annotations were made based on Affymetrix gene annotation complemented with BLAST results using the public representative ID provided with the Affymetrix Gene Chip® wheat genome array.
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A TSS at position 3557930 is supported by one CAGE tag (Fantom3 representative tag ID 122BA39P0901, undefined tissue library) and this TSS is within TIAR.
Primers were designed for quantitative PCR (qPCR) from the most representative public ID sequence using Oligo5.0 software (Molecular Biology Insights, Inc., Cascade, CO).
Contrary to this, a false positive TSS at position 3580940 indicated by one CAGE tag (Fantom3 representative tag ID 119BA53D1906, macrophage tissue library) could not be confirmed by 5'-RACE in any of the 6 tissues.
Probe set sequences were also compared to the nonredundant Genbank database by BLAST (NCBI, Bethesda, MD, USA) to confirm the current most representative public ID and annotation for cattle.
Any two species can be compared with their representative gene ID from Phytozome.
Primer 3 was used to design primers for quantitative PCR from the most representative public ID sequence specified by Affymetrix annotation [ 35].
Phytozome sequence annotation did not support GO mapping annotation, but it did provide Pfam IDs; we mapped the representative Pfam IDs against GO terms.
Furthermore we have examined another 5 genomic positions where transcription is indicated by the existence of a single CAGE tag (Fantom3 representative tag IDs 120BA49K1606, 081AA66D1203, 069AE29I1002, 097AA30J2305 and 112BA90K2006).
Ortho script was also able to compute the most representative Pfam IDs of each species (exclusive domains relative to other species and most frequent domains).
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