Computational tRNA Identification & Sequence Data Analysis Lab Report

This lab report details two experiments conducted in a molecular biology course. The first experiment focuses on computational identification of tRNAs using the tRNAscan-SE program, analyzing the sequence of Homo sapiens chromosome 21 to identify tRNA genes and anticodons. The experiment discusses the role of tRNAs in protein translation and the methodology used to analyze the genomic context. The second experiment involves comparison of multiple sequence data using diagonal plots, specifically analyzing human 28S ribosomal RNA pseudogenes and alu repeat region sequences using Dotlet. The report concludes with an understanding of repeated domains and their potential role in protein evolution and interactions, referencing relevant studies and databases used in the analysis. Desklib provides access to similar lab reports and study resources for students.

LAB REPORT: MOLECULAR BIOLOGY
COURSE NAME
FEBRUARY 10, 2019
STUDENT NAME
STUDENT ID

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Contents
EXPERIMENT: 1........................................................................................................................................2
DISCUSSION.........................................................................................................................................2
EXPERIMENT: 2_COMPARISON OF MULTIPLE SEQUENCE DATA USING DIAGONAL PLOTS.3
DISCUSSION.........................................................................................................................................3
REFERENCES................................................................................................................................................4

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EXPERIMENT: 1
PART A
1. DNA SEQUENCE – 5” A-A-T-C-G-C-T-T-A•C.G-A 3”
mRNA SEQUENCE – 3” AAUCGCUUACGA 5”
2. mRNA SEQUENCE – 5” AGCAUUCGCUAA 3” ( Anti-parallel to DNA sequence).
mRNA codon sequence – AGC AUU CGC UAA
3. tRNA sequence – AAUCGCUUACGA
tRNA anticodon- AAU CGC UUA CGA
DISCUSSION
4. A)
The anticodons can be defined as the respective complementary codons of a particular gene
sequence (three base pairs acting as a codon).
4 B) These anticodons are localized in tRNAs facilitating incorporation of amino acids
accompanied by mRNA during the translation process. mRNA act as instructing material and
tRNA as per instruction brings amino acids (Hoernes et al., 2015, p 854).
When a tRNA brings an amino acid the anticodon localized in tRNA get paired with mRNA
codon. The cellular mechanisms have an inherent capacity to prevent errors and place the right
amino acid for protein to be synthesized. We choose the CM000683|CM000683.2 Homo sapiens
chromosome 21 with the highest bit score, downloaded the fasta sequence did the scanning via
http://lowelab.ucsc.edu/tRNAscan-SE/ , found that total length of sequence is 5052 bp ,
anticodon count is zero , total number of tRNAs found is zero , tRNA pseudo genes is zero and
tRNAs with introns is also zero . No anticodons were detected. Apart from isotype prediction
based on anticodon analysis, the scoring was analyzed to find out the highest scoring isotype

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model. For closer inspection, the disagreement between the two isotypes is also reported (Hatori
et al., 2000, p 311). The scores of all isotype-specific models for each identified tRNA are shown
for comparison. There is no disagreement between two prediction methods as it helps for
comparison studies and the release of data can be proven by two scientific methods
Tarsius_syrichta_KE950676v1.trna1GlyGCC; Sus_scrofa_chr4.trna507-GlyGCC and
Sarcophilus_harrisii_chr4_GL857181_random.trna38-GlyGCC in these cases we found that
genomic context is in between 0 – 43 percentage which is identified by the GENSCAN.
EXPERIMENT: 2_COMPARISON OF MULTIPLE SEQUENCE DATA USING DIAGONAL
PLOTS.
DISCUSSION
rRNA (Ribosomal RNA) molecules represent the sub-cellular unit of ribosomes that have a
significant role in protein synthesis. We are using here human 28S ribosomal RNA pseudogenes
and alu repeat region sequence. This sequence is distally located and connected to rDNA cluster
at upstream region exactly at 4kb region of the first promoter. The same sequence has been
reported in primates too (Gonzalez & Sylvester, 1997, p 432). The sequential difference in
between the target gene in this case and rDNA intergenic spacer is the absence of polypurine and
polypyrimidine. From the literature, it is evident that rDNA clusters are free from any type of
interruptions and no connections exist with the distal section (Lowe & Chan, 2016, W55). In this
experiment, we understood to use Diagonal Plot Analysis by using Dotlet with the help of the

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https://myhitsåsb-sib.ch. Followed by the next steps for the comparison, GenBank on the search
bar typed accession number U67616 copy the fasta sequence for U67616, paste it in a notepad
Diagonal Plot analysis by the Dotlet to generate a plot of our sequence of interest. According to
the analysis, several repeated domains are present in the N-terminal part we can see repeated
regions, followed by C terminal also have repeated regions. Exons are introns also present but
exon-intron boundaries are as sharp. The diagonal is not perfect but partition shows that at the C
terminal one shift is present. Few residues might exhibit low complexity. So conclude that
amino acid repeats helping in the evolution and protein-protein interactions.
REFERENCES
Gonzalez, I.L. and Sylvester, J.E., 1997. Beyond ribosomal DNA: on towards the
telomere. Chromosoma, 105(7-8), pp.431-437.
Hattori, M., Fujiyama, A., Taylor, T.D., Watanabe, H., Yada, T., Park, H.S., Toyoda, A., Ishii,
K., Totoki, Y., Choi, D.K. and Soeda, E., 2000. The DNA sequence of human
chromosome 21. Nature, 405(6784), p.311.
Hoernes, T.P., Clementi, N., Faserl, K., Glasner, H., Breuker, K., Lindner, H., Hüttenhofer, A.
and Erlacher, M.D., 2015. Nucleotide modifications within bacterial messenger RNAs
regulate their translation and are able to rewire the genetic code. Nucleic acids
research, 44(2), pp.852-862.
Lowe, T.M. and Chan, P.P., 2016. tRNAscan-SE On-line: integrating search and context for
analysis of transfer RNA genes. Nucleic acids research, 44(W1), pp.W54-W57.