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Sequence-Tagged Sites (STS)


Sequence-Tagged Site (STS)

is a relatively short, easily PCR-amplified sequence (200 to 500 bp) which can be specifically amplified by PCR and detected in the presence of all other genomic sequences and whose location in the genome is mapped.

The STS concept was introduced by Olson et al (1989). In assessing the likely impact of the Polymerase Chain Reaction (PCR) on human genome research, they recognized that single-copy DNA sequences of known map location could serve as markers for genetic and physical mapping of genes along the chromosome. The advantage of STSs over other mapping landmarks is that the means of testing for the presence of a particular STS can be completely described as information in a database: anyone who wishes to make copies of the marker would simply look up the STS in the database, synthesize the specified primers, and run the PCR under specified conditions to amplify the STS from genomic DNA.

STS-based PCR produces a simple and reproducible pattern on agarose or polyacrylamide gel. In most cases STS markers are co-dominant, i.e., allow heterorozygotes to be distinguished from the two homozygotes.

The DNA sequence of an STS may contain repetitive elements, sequences that appear elsewhere in the genome, but as long as the sequences at both ends of the site are unique and conserved, researches can uniquely identify this portion of genome using tools usually present in any laboratory.

Thus, in broad sense, STS include such markers as microsatellites (SSRs, STMS or SSRPs), SCARs, CAPs, and ISSRs.


Polymorphic loci present in nuclear DNA and organellar DNA that consist of repeating units of 1-10 base pairs, most typically, 2-3 bp in length, also called Simple Sequence Repeats (SSR), Sequence-Tagged Microsatellite Sites (STMS) or Simple Sequence Repeats Polymorphisms (SSRP). SSRs are highly variable and evenly distributed throughout the genome. This type of repeated DNA is common in eukaryotes. These polymorphisms are identified by constructing PCR primers for the DNA flanking the microsatellite region. The flanking regions tend to be conserved within the species, although sometimes they may also be conserved in higher taxonomic levels.

SSR markers

Sequence Characterized Amplified Region (SCAR)

DNA fragments amplified by the Polymerase Chain Reaction (PCR) using specific 15-30 bp primers, designed from nucleotide sequences established in cloned RAPD (Random Amplified Polymorphic DNA) fragments linked to a trait of interest. By using longer PCR primers, SCARs do not face the problem of low reproducibility generally encountered with RAPDs. Obtaining a co-dominant marker may be an additional advantage of converting RAPDs into SCARs.

SCAR markers

Cleaved Amplified Polymorphic Sequences (CAPS)

STS polymorphisms that can be detected by differences in restriction fragment lengths caused by SNPs or INDELs that create or abolish restriction endonuclease recognition sites in PCR amplicons produced by locus-specific oligonucleotide primers. In other words this technique aims to convert and amplified band that does not show variation by length of PCR product into a polymorphic one. More about CAPS in Overview of CAPS technology.

Inter-simple Sequence Repeats (ISSRs)

STS polymorphisms that are found between microsatellite repeats. Primers can be designed based on a microsatellite repeats exclusively, in which case this technique will target multiple loci due to known abundance of repeat sequences in the genome. Alternatively, primers can be extended outside or inside the ISSR in which case a unique region most likely will be amplified.

ISSR markers


» Olson M et al. A common language for physical mapping of the human genome. Science. 1989 Sep 29;245(4925):1434-5. PMID: 2781285


» The NCBI Electronic PCR (e-PCR) compputational tool

» "Sequence Tagged Sites"[Majr] in PubMed

Simple Sequence Repeats (SSR)


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Last updated: 2017-11-09T11:33:30Z