IN SCHOOL ARTICLE Discovering the Distribution of Palindromic Sequences in the SMAD4 Gene using Large and Medium Deletions and the Resulting RNA Structure Predictions
BibTeX
@MISC{Ninh_inschool,
author = {Andrew Ninh and Lisa Battig},
title = {IN SCHOOL ARTICLE Discovering the Distribution of Palindromic Sequences in the SMAD4 Gene using Large and Medium Deletions and the Resulting RNA Structure Predictions},
year = {}
}
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Abstract
The SMAD4 gene codes for cell-signaling proteins that prevent abnormal vascular growths. DNA palindromes are inversely proportional sequences that play roles in gene expression through the formation of stem-loops and disease/tumor detection. Previous research approximated that there were 100 palindromes in every 1000 base pairs of a randomly generated sequence. A Java program was written to mutate fasta sequences based on ARUP’s SMAD4 database, information from NCBI, and random locations and another was written to find palindromes in the DNA sequences and output their lengths. These lengths were plotted sequentially using the Mathematica software. By measuring shifts in each mutated plot superimposed on the wild type plot, the number of pixels shifted between peaks was recorded and, using a scale which was measured to be 12 pixels per 100 palindromes, converted into the number of palindromes deleted. The amount of base pairs (bp) deleted was proportional to the amount of palindromes deleted. The relationship between bp and palindromes is described by the equation p=round(-0.242996+0.425309*l) such that p represents the number of palindromes and l represents the length of a sequence. This linear regression shows that palindromes are evenly distributed throughout the SMAD4 gene assuming the distribution follows a Poisson distribution. Out of every 1000 bp, there are approximately 420 palindromes in the SMAD4 mRNA which is approximately 475 palindromes in SMAD4’s Primary Assembly genomic region. The SMAD4 gene exhibits 275 (137.5%) more palindromes than the randomly generated palindromic distribution projected by previous research. Finding the distribution of palindromes in RNA molecules can lead to future research and classification of key regions that determine the shape of secondary, tertiary, and quaternary structures.
Keyphrases
smad4 gene school article medium deletion palindromic sequence resulting rna structure prediction previous research base pair primary assembly genomic region arup smad4 database proportional sequence linear regression tumor detection mathematica software cell-signaling protein gene expression equation round palindromic distribution fasta sequence smad4 mrna abnormal vascular growth dna sequence rna molecule poisson distribution smad4 gene code random location quaternary structure future research smad4 gene exhibit java program wild type plot key region dna palindrome
