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It's only fortunate juveniles that make it upstream in the first place (thanks largely to the aid of fish ladders), and then they face the danger of being chewed up by the turbines in hydropower dams on their way back down as adults.
In both collections there was a peak of association at or near the kdr L1014F SNP position, but in Ghana a second strongly associated SNP was present approximately 65 kb upstream in the first intron of the sodium channel gene.
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Of the remaining four cDNA, the TSS is identical in three, and 7 bp upstream in the fourth.
Bioinformatic analyses (MEME/MAST) were performed to determine the presence of enriched elements upstream or in the first intron of putative targets identified by our one-hybrid assay.
The combined yeast-based screening and MEME/MAST analysis were able to predict Gli transcription factor binding sites, and position mapping of these sequences upstream or in the first intron of promoters served to identify new putative target genes of Gli regulation.
An evolutionary highly conserved region of 400 bp upstream of the first in-frame AUG of the SPG4 gene was sufficient to provide basal expression in HeLa, HEK293 and SH-SY-5Y cells.
The position-dependent scoring matrix for the 14 bp motif was used as input to the MAST algorithm to search similar motifs in a 20 kb upstream region and in the first intron of 10 candidate genes, including ptc1, candidate genes were selected based on gene ontology associations, to cover a wide array of cellular and developmental processes.
For genes in operons, the sequence upstream of the first gene in the operon was used.
When the CM promoter is used as a BLAT/BLAST query against the 41 mammalian genomes investigated, only three regions appear: (1) upstream regions of nonprimate NBPF genes, (2) upstream regions of the majority of primate NBPF genes, and (3) in the fourth intron upstream of the first DUF1220 domain in NBPF genes, where it is not in the promoter position.
Most importantly, there is a long region devoid of in-frame STOP-codons upstream from the first predicted exon, and the ORF could be thus extended in the 5' direction (Fig. 3).
Moreover, autoregulatory binding sites are rather predicted downstream of TSSs than in the further upstream bins (excluding the first upstream bin).
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