The difference between spanning and flanking?

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In summary, spanning and flanking refer to sequences that extend across an entire region or are located on either side of a specific region, respectively. They are important in genetics and DNA sequencing as they provide information about gene location and organization, and can be used for primer design and further analysis. Spanning sequences can encompass various genetic features, while flanking sequences are specifically located on either side of a genomic feature. Tools such as BLAST and genome browsers are used to identify and analyze these sequences.
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sotellme
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What is the difference between Primers that span introns and primers that flank intron-exon border? Spanning intron does it mean that it covers the whole intron segment? Flanking the border does it also mean that it covers the whole border? :devil:


Any ideas would help alot!


Thanks.
 
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Spanning means inclusive of the intron. To flank means to be on either side, but not inclusive of the sequence in between.
 
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The difference between spanning and flanking refers to the location of the primers in relation to the intron-exon border. Spanning primers cover the entire intron segment, while flanking primers cover the border of the intron and exon. This means that spanning primers will amplify the entire intron, while flanking primers will only amplify the border region.

In terms of primer design, spanning primers are typically used when studying the expression of a specific gene, as they provide a more comprehensive view of the gene's structure. Flanking primers, on the other hand, are commonly used in genetic testing and sequencing to specifically target the intron-exon border and identify potential mutations or variations in that region.

It is important to note that spanning does not necessarily mean covering the entire intron sequence, as there may be other introns within the gene that are not targeted by the primer. Similarly, flanking does not always cover the entire border, as there may be other regions of the gene that are not included in the primer design.

In conclusion, the difference between spanning and flanking primers lies in the specific location they target within the gene, with spanning primers covering the entire intron segment and flanking primers targeting the border between introns and exons.
 

Related to The difference between spanning and flanking?

1. What is the difference between "spanning" and "flanking"?

Spanning refers to a sequence that extends across an entire region or interval, while flanking refers to sequences that are located on either side of a specific region.

2. How are spanning and flanking used in genetics and DNA sequencing?

Spanning and flanking sequences are important in genetic studies as they provide information about the location and organization of genes within a genome. They can also be used to design primers for PCR amplification or for identifying specific regions for further analysis.

3. Can you explain the concept of "spanning" in more detail?

Spanning sequences can refer to a variety of genetic features, including genes, exons, introns, regulatory regions, or entire chromosomes. These sequences provide a complete picture of the genetic information present in a given region.

4. How do "flanking" sequences differ from "intronic" sequences?

Flanking sequences refer to regions that are located on either side of a specific genomic feature, such as a gene or exon. Intronic sequences, on the other hand, are located within the gene itself, between exons. Flanking sequences are often used in genetic analysis, while intronic sequences may have important regulatory functions.

5. Are there any specific tools or techniques used to identify spanning and flanking sequences?

Yes, there are various bioinformatics tools and techniques used to identify and analyze spanning and flanking sequences, such as BLAST, Primer-BLAST, and genome browsers. These tools allow researchers to compare sequences, design primers, and visualize genomic features.

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