1. Identify the open reading frame in the following DNA sequence, the protein th
ID: 92497 • Letter: 1
Question
1. Identify the open reading frame in the following DNA sequence, the protein that this gene encodes for, its function, and the source.
ATGAAGAAGGTTTCTACGCTTGACCTGTTGTTCGTTGCGATCATGGGTGTTTCGC
CGGCCGCTTTTGCCGCCGACCTGATCGACGTGTCCAAACTCCCCAGCAAGGCTGCCCAGGGCGCGCCCGG
CCCGGTCACCTTGCAAGCCGCGGTCGGCGCTGGCGGTGCCGACGAACTGAAAGCGATCCGCAGCACGACC
CTGCCCAACGGCAAGCAGGTCACCCGCTACGAGCAATTCCACAACGGCGTACGGGTGGTCGGCGAAGCCA
TCACCGAAGTCAAGGGTCCCGGCAAGAGCGTGGCGGCGCAGCGCAGCGGCCATTTCGTCGCCAACATCGC
TGCCGACCTGCCGGGCAGCACCACCGCGGCGGTATCCGCCGAGCAGGTGCTGGCCCAGGCCAAGAGCCTG
AAGGCCCAGGGCCGCAAGACCGAGAATGACAAAGTGGAACTGGTGATCCGCCTGGGCGAGAACAACATCG
CCCAACTGGTCTACAACGTCTCCTACCTGATTCCCGGCGAGGGACTGTCGCGGCCGCATTTCGTCATCGA
CGCCAAGACCGGCGAAGTGCTCGATCAGTGGGAAGGCCTGGCCCACGCCGAGGCGGGCGGCCCCGGCGGC
AACCAGAAGATCGGCAAGTACACCTACGGTAGCGACTACGGTCCGCTGATCGTCAACGACCGCTGCGAGA
TGGACGACGGCAACGTCATCACCGTCGACATGAACAGCAGCACCGACGACAGCAAGACCACGCCGTTCCG
CTTCGCCTGCCCGACCAACACCTACAAGCAGGTCAACGGCGCCTATTCGCCGCTGAACGACGCGCATTTC
TTCGGCGGCGTGGTGTTCAAACTGTACCGGGACTGGTTCGGCACCAGCCCGCTGACCCACAAGCTGTACA
TGAAGGTGCACTACGGGCGCAGCGTGGAGAACGCCTACTGGGACGGCACGGCGATGCTCTTCGGCGACGG
CGCCACCATGTTCTATCCGCTGGTGTCGCTGGACGTGGCGGCCCACGAGGTCAGCCACGGCTTCACCGAG
CAGAACTCCGGGCTGATCTACCGCGGGCAATCAGGCGGAATGAACGAAGCGTTCTCCGACATGGCCGGCG
AGGCTGCCGAGTTCTATATGCGCGGCAAGAACGACTTCCTGATCGGCTACGACATCAAGAAGGGCAGCGG
TGCGCTGCGCTACATGGACCAGCCCAGCCGCGACGGGCGATCCATCGACAACGCGTCGCAGTACTACAAC
GGCATCGACGTGCACCACTCCAGCGGCGTGTACAACCGTGCGTTCTACCTGTTGGCCAATTCGCCGGGCT
GGGATACCCGCAAGGCCTTCGAGGTGTTCGTCGACGCCAACCGCTACTACTGGACCGCCACCAGCAACTA
CAACAGCGGCGCCTGCGGGGTGATTCGCTCGGCGCAGAACCGCAACTACTCGGCGGCTGACGTCACCCGG
GCGTTCAGCACCGTCGGCGTGACCTGCCCGAGCGCGTTGTAA
a. Go to the National Center for Biotechnology Information (NCBI) website http://www.ncbi.nlm.nih.gov/. Click on BLAST on the right-hand side under “Popular Resources.” BLAST is a program that will allow you to find the protein sequence for the DNA sequence (gene) you submit. Next click on blastx
b. Paste the DNA sequence into the box under “Entry Query Sequence.” Scroll down and click BLAST. The search may take a few seconds; the page will keep updating until the search is completed. You do not need to enter any parameters in the boxes before you click BLAST.
What would be the amino acid sequence of this protein after it was transcribed using BLAST? I found out that the protein was called elastase
Explanation / Answer
From the DNA (GENE) sequence mentioned above, affter following the procedure in NCBS website, the enzyme is found to be "elastase".
This DNA is having the whole sequence with open reading frame. As we know that a open reading frame is some sequence which is starting with a "start codon", here in case of DNA it is, TAC, as the reference goes back to mRNA, where it is fMethionine, coded by AUG sequence. Same AUG in case of DNA would be the alternative sequence, TAC.
Now moving on with ORF, it is having an initiation codon and this must be ending with a "stop codon". As we know the mRNA stop codns are UAA, UGA and UAG. So the same codons coded from DNA would be ATT, ACT and ATC respectively.
Now looing at the sequence, we first need to cut it in 3 codons each. Here the 'Query Length' is 1497 nucleotides, and if we carefully look into the sequence of this Pseudomonas aeruginosa locus CP008866, we can find 4 ORFs.
TAC (start codon, in mRNA AUG) GAG CAA TTC CAC AAC GGC GTA CGG GTG GTC GGC GAA GCC ATC (stop codon, in mRNA UAG),
The same sequence is highlighted with the ORFs.
ATG AAG AAG GTT TCT ACG CTT GAC CTG TTG TTC GTT GCG ATC ATG GGT GTT TCG CCG GCC GCT TTT GCC GCC GAC CTG ATC GAC GTG TCC AAA CTC CCC AGC AAG GCT GCC CAG GGC GCG CCC GGC CCG GTC ACC TTG CAA GCC GCG GTC GGC GCT GGC GGT GCC GAC GAA CTG AAA GCG ATC CGC AGC ACG ACC
CTG CCC AAC GGC AAG CAG GTC ACC CGC
TAC GAG CAA TTC CAC AAC GGC GTA CGG GTG GTC GGC GAA GCC ATC
ACC GAA GTC AAG GGT CCC GGC AAG AGC GTG GCG GCG CAG CGC AGC GGC CAT TTC GTC GCC AAC ATC GCT GCC GAC CTG CCG GGC AGC ACC ACC GCG GCG GTA TCC GCC GAG CAG GTG CTG GCC CAG GCC AAG AGC CTG AAG GCC CAG GGC CGC AAG ACC GAG AAT GAC AAA GTG GAA CTG GTG ATC CGC CTG GGC GAG AAC AAC ATC GCC CAA CTG GTC
TAC AAC GTC TCC
TAC CTG ATT CCC GGC GAG GGA CTG TCG CGG CCG CAT TTC GTC ATC
GAC GCC AAG ACC GGC GAA GTG CTC GAT CAG TGG GAA GGC CTG GCC CAC GCC GAG GCG GGC GGC CCC GGC GGC AAC CAG AAG ATC GGC AAG
TAC ACC
TAC GGT AGC GAC
TAC GGT CCG CTG ATC GTC AAC GAC CGC TGC GAG ATG GAC GAC GGC AAC GTC ATC ACC GTC GAC ATG AAC AGC AGC ACC GAC GAC AGC AAG ACC ACG CCG TTC CGC TTC GCC TGC CCG ACC AAC ACC
TAC AAG CAG GTC AAC GGC GCC TAT TCG CCG CTG AAC GAC GCG CAT TTC TTC GGC GGC GTG GTG TTC AAA CTG
TAC CGG GAC TGG TTC GGC ACC AGC CCG CTG ACC CAC AAG CTG
TAC ATG AAG GTG CAC TAC GGG CGC AGC GTG GAG AAC GCC
TAC TGG GAC GGC ACG GCG ATG CTC TTC GGC GAC GGC GCC ACC ATG TTC TAT CCG CTG GTG TCG CTG GAC GTG GCG GCC CAC GAG GTC AGC CAC GGC TTC ACC GAG CAG AAC TCC GGG CTG ATC
TAC CGC GGG CAA TCA GGC GGA ATG AAC GAA GCG TTC TCC GAC ATG GCC GGC GAG GCT GCC GAG TTC TAT ATG CGC GGC AAG AAC GAC TTC CTG ATC
GGC
TAC GAC ATC AAG AAG GGC AGC GGT GCG CTG CGC
TAC ATG GAC CAG CCC AGC CGC GAC GGG CGA TCC ATC GAC AAC GCG TCG CAG
TAC
TAC AAC GGC ATC GAC GTG CAC CAC TCC AGC GGC GTG
TAC AAC CGT GCG TTC
TAC CTG TTG GCC AAT TCG CCG GGC TGG GAT ACC CGC AAG GCC TTC GAG GTG TTC GTC GAC GCC AAC CGC
TAC TAC TGG ACC GCC ACC AGC AAC
TAC AAC AGC GGC GCC TGC GGG GTG ATT
CGC TCG GCG CAG AAC CGC AAC TAC TCG GCG GCT GAC GTC ACC CGG GCG TTC AGC ACC GTC GGC GTG ACC TGC CCG AGC GCG TTG TAA
As we know that this gene encodes for the protein "elastase", now we can define its function. This enzyme is a protease, functionally it breaks down a protein. It cleaves the peptide bonds in elastin, so that the elastin could be easily get digested.
Here the sequence is shown to be coming from the bacterium Pseudomonas aeruginosa. Naturally it has founded from Pancreas.
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