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Likewise, we discovered novel cis-motifs with no description in PLACE database, except for CCA1 motif in rice.
The 1.5 kb sequences upstream of the start codon of selected genes in rice were scanned for putative conserved cis-elements identical with or similar to the motifs in PLACE database [ 88].
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A motif over-represented in light-induced promoters, GCCAC (SORLIP1AT in the PLACE database [ 46]), also is found to be highly enriched in guard cell ABA-regulated genes but not in leaves.
What this means is that developers can simply tell Factual what they know about an entity (i.e., a venue in a place database) and it will fill in the missing pieces (e.g., the category, the latitude/longitude info and venue's address).
Searching for known plant cis-regulatory DNA elements in the PLACE database [ 29] resulted in the identification of two distinct sequence motifs which might be involved in the regulation of ppcA expression levels (Fig. 3).
On the contrary, flower-specific motifs Flw_1, Flw_2, Flw_3 and Flw_5 (see Figure 4), root-specific motifs Rt_2 and Rt_4 (see Figure 1), seed-specific motif Sd_2 (see Figure 2) and shoot-specific motif Sht_2 (see Figure 5) did not match significantly to any known cis-acting regulatory element in the PLACE database, thus representing potentially new regulatory motifs in plants.
From the 20 motifs predicted in promoters of genes expressed in the analyzed PSs, 8 of them did not match significantly to either cis-regulatory elements in the PLACE database [ 13] or previous plant motifs reported in [ 12].
Oh, and that's the other thing Hopper had to create; in order to add all those interesting travel stories and photos to specific items in a place database, they needed one of those, too.
Most of the significantly overrepresented motifs in the promoter sequence of the OsEULD1B gene belong to the so-called ABRE elements (e.g. ABRELATERD1, ABRETAEM, ABREBNNAPA, ABADESI2) or are associated with the bZIP family of transcription factors according to their annotation in the PLACE database (HY5AT, ACGTTBOX).
The selected motifs were further compared with plant cis-acting regulatory elements in the PLACE database [ 13].
When we compared REG sequences with established cis-elements in the PLACE database, it was found that 27 out of 48 Arabidopsis PLACE entries are absent in the extracted REGs (Table 5).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com