Using the webpate http://bioinfoc.ch/sawicgi/sawi.cgi?remap , please determine t
ID: 74010 • Letter: U
Question
Using the webpate http://bioinfoc.ch/sawicgi/sawi.cgi?remap , please determine the location of the two internal EcoRV sites in the sequence and explain what single nucleotide changes can remove the two EcoRV sites without changing the amino acid sequence.
1 ATGTGCCACC AGCAGCTGGT GATCAGCTGG TTCAGCCTGG TGTTCCTGGC
51 CAGCCCCCTG GTGGCCATCT GGGAGCTGAA GAAGGACGTG TACGTGGTGG
101 AGCTGGACTG GTACCCCGAC GCCCCCGGCG AGATGGTGGT GCTGACCTGC
151 GACACCCCCG AGGAGGACGG CATCACCTGG ACCCTGGACC AGAGCAGCGA
201 GGTGCTGGGC AGCGGCAAGA CCCTGACCAT CCAGGTGAAG GAGTTCGGCG
251 ACGCCGGCCA GTACACCTGC CACAAGGGCG GCGAGGTGCT GAGCCACAGC
301 CTGCTGCTGC TGCACAAGAA GGAGGACGGC ATCTGGAGCA CCGATATCCT
351 GAAGGACCAG AAGGAGCCCA AGAACAAGAC CTTCCTGAGG TGCGAGGCCA
401 AGAACTACAG CGGCAGGTTC ACCTGCTGGT GGCTGACCAC CATCAGCACC
451 GACCTGACCT TCAGCGTGAA GAGCAGCAGG GGCAGCAGCG ACCCCCAGGG
501 CGTGACCTGC GGCGCCGCCA CCCTGAGCGC CGAGAGGGTG AGGGGCGACA
551 ACAAGGAGTA CGAGTACAGC GTGGAGTGCC AGGAGGACAG CGCCTGCCCC
601 GCCGCCGAGG AGAGCCTGCC CATCGAGGTG ATGGTGGACG CCGTGCACAA
651 GCTGAAGTAC GAGAACTACA CCAGCAGCTT CTTCATCAGG GATATCATCA
701 AGCCCGACCC CCCCAAGAAC CTGCAGCTGA AGCCCCTGAA GAACAGCAGG
751 CAGGTGGAGG TGAGCTGGGA GTACCCCGAC ACCTGGAGCA CCCCCCACAG
801 CTACTTCAGC CTGACCTTCT GCGTGCAGGT GCAGGGCAAG AGCAAGAGGG
851 AGAAGAAGGA CAGGGTGTTC ACCGACAAGA CCAGCGCCAC CGTGATCTGC
901 AGGAAGAACG CCAGCATCAG CGTGAGGGCC CAGGACAGGT ACTACAGCAG
951 CAGCTGGAGC GAGTGGGCCA GCGTGCCCTG CAGC
Explanation / Answer
sequence_1.remap
SEQUENCE_1
PvuII
1 GCTGCAGGGCACGCTGGCCCACTCGCTCCAGCTGCTGCTGTAGTACCTGTCCTGGGCCCT 60
----:----|----:----|----:----|----:----|----:----|----:----|
1 CGACGTCCCGTGCGACCGGGTGAGCGAGGTCGACGACGACATCATGGACAGGACCCGGGA 60
61 CACGCTGATGCTGGCGTTCTTCCTGCAGATCACGGTGGCGCTGGTCTTGTCGGTGAACAC 120
----:----|----:----|----:----|----:----|----:----|----:----|
61 GTGCGACTACGACCGCAAGAAGGACGTCTAGTGCCACCGCGACCAGAACAGCCACTTGTG 120
121 CCTGTCCTTCTTCTCCCTCTTGCTCTTGCCCTGCACCTGCACGCAGAAGGTCAGGCTGAA 180
----:----|----:----|----:----|----:----|----:----|----:----|
121 GGACAGGAAGAAGAGGGAGAACGAGAACGGGACGTGGACGTGCGTCTTCCAGTCCGACTT 180
181 GTAGCTGTGGGGGGTGCTCCAGGTGTCGGGGTACTCCCAGCTCACCTCCACCTGCCTGCT 240
----:----|----:----|----:----|----:----|----:----|----:----|
181 CATCGACACCCCCCACGAGGTCCACAGCCCCATGAGGGTCGAGTGGAGGTGGACGGACGA 240
PvuII EcoRV
241 GTTCTTCAGGGGCTTCAGCTGCAGGTTCTTGGGGGGGTCGGGCTTGATGATATCCCTGAT 300
----:----|----:----|----:----|----:----|----:----|----:----|
241 CAAGAAGTCCCCGAAGTCGACGTCCAAGAACCCCCCCAGCCCGAACTACTATAGGGACTA 300
301 GAAGAAGCTGCTGGTGTAGTTCTCGTACTTCAGCTTGTGCACGGCGTCCACCATCACCTC 360
----:----|----:----|----:----|----:----|----:----|----:----|
301 CTTCTTCGACGACCACATCAAGAGCATGAAGTCGAACACGTGCCGCAGGTGGTAGTGGAG 360
361 GATGGGCAGGCTCTCCTCGGCGGCGGGGCAGGCGCTGTCCTCCTGGCACTCCACGCTGTA 420
----:----|----:----|----:----|----:----|----:----|----:----|
361 CTACCCGTCCGAGAGGAGCCGCCGCCCCGTCCGCGACAGGAGGACCGTGAGGTGCGACAT 420
DinI
421 CTCGTACTCCTTGTTGTCGCCCCTCACCCTCTCGGCGCTCAGGGTGGCGGCGCCGCAGGT 480
----:----|----:----|----:----|----:----|----:----|----:----|
421 GAGCATGAGGAACAACAGCGGGGAGTGGGAGAGCCGCGAGTCCCACCGCCGCGGCGTCCA 480
481 CACGCCCTGGGGGTCGCTGCTGCCCCTGCTGCTCTTCACGCTGAAGGTCAGGTCGGTGCT 540
----:----|----:----|----:----|----:----|----:----|----:----|
481 GTGCGGGACCCCCAGCGACGACGGGGACGACGAGAAGTGCGACTTCCAGTCCAGCCACGA 540
541 GATGGTGGTCAGCCACCAGCAGGTGAACCTGCCGCTGTAGTTCTTGGCCTCGCACCTCAG 600
----:----|----:----|----:----|----:----|----:----|----:----|
541 CTACCACCAGTCGGTGGTCGTCCACTTGGACGGCGACATCAAGAACCGGAGCGTGGAGTC 600
EcoRV
601 GAAGGTCTTGTTCTTGGGCTCCTTCTGGTCCTTCAGGATATCGGTGCTCCAGATGCCGTC 660
----:----|----:----|----:----|----:----|----:----|----:----|
601 CTTCCAGAACAAGAACCCGAGGAAGACCAGGAAGTCCTATAGCCACGAGGTCTACGGCAG 660
661 CTCCTTCTTGTGCAGCAGCAGCAGGCTGTGGCTCAGCACCTCGCCGCCCTTGTGGCAGGT 720
----:----|----:----|----:----|----:----|----:----|----:----|
661 GAGGAAGAACACGTCGTCGTCGTCCGACACCGAGTCGTGGAGCGGCGGGAACACCGTCCA 720
NaeI
721 GTACTGGCCGGCGTCGCCGAACTCCTTCACCTGGATGGTCAGGGTCTTGCCGCTGCCCAG 780
----:----|----:----|----:----|----:----|----:----|----:----|
721 CATGACCGGCCGCAGCGGCTTGAGGAAGTGGACCTACCAGTCCCAGAACGGCGACGGGTC 780
781 CACCTCGCTGCTCTGGTCCAGGGTCCAGGTGATGCCGTCCTCCTCGGGGGTGTCGCAGGT 840
----:----|----:----|----:----|----:----|----:----|----:----|
781 GTGGAGCGACGAGACCAGGTCCCAGGTCCACTACGGCAGGAGGAGCCCCCACAGCGTCCA 840
BtrI
841 CAGCACCACCATCTCGCCGGGGGCGTCGGGGTACCAGTCCAGCTCCACCACGTACACGTC 900
----:----|----:----|----:----|----:----|----:----|----:----|
841 GTCGTGGTGGTAGAGCGGCCCCCGCAGCCCCATGGTCAGGTCGAGGTGGTGCATGTGCAG 900
BalI BalI PvuII
901 CTTCTTCAGCTCCCAGATGGCCACCAGGGGGCTGGCCAGGAACACCAGGCTGAACCAGCT 960
----:----|----:----|----:----|----:----|----:----|----:----|
901 GAAGAAGTCGAGGGTCTACCGGTGGTCCCCCGACCGGTCCTTGTGGTCCGACTTGGTCGA 960
PvuII
961 GATCACCAGCTGCTGGTGGCACAT 984
----:----|----:----|----
961 CTAGTGGTCGACGACCACCGTGTA 1020
# Enzymes that cut Frequency Isoschizomers
BalI 2 MlsI,MluNI,MscI,Msp20I
BtrI 1 BmgBI,AjiI
DinI 1 EgeI,EheI,SfoI
EcoRV 2 Eco32I
NaeI 1 PdiI
PvuII 4
# Enzymes which cut less frequently than the MINCUTS criterion
# Enzymes < MINCUTS Frequency Isoschizomers
# Enzymes which cut more frequently than the MAXCUTS criterion
# Enzymes > MAXCUTS Frequency Isoschizomers
# Enzymes that do not cut
AhaIII* BsrBI BssNAI Bst1107I BstZ17I Ecl136II Eco47III Eco53kI
EcoICRI HpaI MstI* NruI PmaCI PmeI PsiI ScaI
SmaI SnaBI SspI StuI SwaI ZraI
Protein sequence for the given nucleotide sequence is
sequence_1.remap
These are the outputs which you get from Remap. EcoRV is a blunt cutter having a restriction site GATATC. GAC codes for asparatic acid whereas ATC codes for Isoleucine. Alternative codons which whch code for both these amino acids are
GAC/GAU for Asp
ATT/ATC/ATA/AUC for Ile
Hence if we remove T by U (Thymine by Uracil) then EcoRV will not be able to identify the site. But there will be no change in the amino acid sequence.
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