We included two additional variables, total intron length and intron number, which are expected to influence the observed intron FPKM of a gene.
The minimum and maximum intron length was set to 5 bp and 50,000 bp respectively.
In addition, for IP molecular markers, the data here can be searched including: chromosome number, intron start, intron end, intron length, forward sequence, reverse sequence, forward Tm, reverse Tm, forward GC, and reverse GC.
Analysis of exon/intron composition including intron length and number, of GBSS1 provided another distinct fingerprinting method for grasses.
Additionally, the expression level, total intron length and the number of introns had a significant positive effect, whereas the gene length and expression breadth had a significant negative correlation with the number of reads mapping to introns (Table 3 and supplementary table S10).
In this study, we identified 524,170 simple sequence repeat (SSR), 267,636 intron length polymorphism (ILP), and 11,872 potential intron polymorphism (PIP) markers from 16 tree species based on recently available genome sequences.
Introns of plant tubulin genes are useful molecular tools to study IME (Intron Mediated Enhancement of gene expression) and to define plant genetic and evolutionary relationships through ILP (Intron Length Polymorphism).
Genomic analysis revealed that the LycCD4-1 gene consisted of nine exons and eight introns and exhibited a similar exon-intron organization to other species CD4 genes except for a different intron length.
A genefinder, for instance, ought to combine splice-site consensus, codon bias, exon/ intron length preferences and open reading frame analysis into one scoring system.
Kita, T. et al. Development of intron length polymorphism markers in genes encoding diketide-CoA synthase and curcumin synthase for discriminating Curcuma species.
For each gene, mean intron length was determined based on the transcript with the largest number of exons among transcripts with FPKM > 1.
