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In rice, they matched sequences on chromosome 1.
Likewise, most loci on the same chicken chromosome matched sequences on a single Siberian jay LG, with the exceptions of three unlinked loci (SJ005, SJ020 and SJ034) and loci SJ009, SJ039, SJ101 and SJ076 on GgaZ that mapped to four different LGs, LGZ and LG1, LG2, and LG3, respectively.
Loci from the same Siberian jay LG matched sequences on a single chicken chromosome in the BLAST analysis, with the exception of loci SJ039, SJ101 and SJ076 on the autosomal LGs (LG1, LG2, and LG3, respectively) that mapped to chicken chromosome Z (GgaZ), whereas the other loci on these LGs mapped to the chicken autosomes.
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However, both of these ESTs detected matching sequences on multiple chromosomes in addition to those on the homoeologous group 4 chromosomes.
However, we cannot rule out that some of the genes with matching sequences on both arms arose from the duplication of individual genes or of chromosome segments.
As an example of using a comparative approach to elucidate the structure of the Matina 1-6 genome, Figure 5C illustrates duplicated sequences from Matina 1-6 linkagroupoup 10 that match sequences on Criollo chromosomes 4, 5, 8, and 10. Figure 5B shows a 2D comparison of Matina 1-6 chromosome 10 and Criollo chromosome 10.
Third, none of the genes having matching sequences on both arms for any of the chromosomes were included in this study for the reason that previous data had shown a limited number of genes in the centromeric regions to be present on both the long and short arm ditelosomic lines (Wicker et al. 2011).
For cloning using flanking att sites, a first round of PCR using a primer outside the flanking region and a mutagenic primer with at least 10 bp of matching sequence on either side of the desired mutation was used to generate a megaprimer.
For cloning using flanking restriction enzyme sites, a first round of PCR using a primer outside the flanking region and a mutagenic primer with at least 10 base pairs (bp) of matching sequence on either side of the desired mutation was used to generate a megaprimer.
The results of pattern matches were subsequently assessed to identify matched sequences located on the −500, −1000 and −3000 bp upstream sequences from the putative transcription start site for each TF encoding gene defined in the Glyma1 annotation.
Importantly, with our expansive data set, we confirmed that miR-203 utilizes the 5′ seed sequences to target perfectly matched sequences located on the 3′UTRs of its target genes.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com