Question: Finding the start codon
0
gravatar for Mimmi Ahlmén
2.1 years ago by
Mimmi Ahlmén20 wrote:

I'm trying to find the start codon in this set of bases in a gene. I'm totally new in this field so you'll have to forgive my probably very basic question. This is on the reverse strand, so should it be read in the opposite way? I used ACT to find this gene.

>CDS CDS undefined product 93737:94594 reverse
GTGAATTCATTGAATAAAACTGGTCTTCTTTACATTGTTCCAACACCTATTGGAAATTTA
        10        20        30        40        50        60
TCTGATATTACTTATCGAGCTGTAGAAACACTAAAAAATGTTAATTTAATAGCAGCTGAA
        70        80        90       100       110       120
AATATTCATCATACTAATATTTTACTACAACATTACAACGTTAAAAATATTTTAATATCT
       130       140       150       160       170       180
TTAAATAAAAATAATGAAAAAAAACAAAGTGATTATGTAATTAACGAACTAAAAAAAGGA
       190       200       210       220       230       240
AAAAAAATTGCCTTAGTATCTGATGCAGGGACACCAGTTATTAACGATCCAGGTTATTTT
       250       260       270       280       290       300
TTAGTAAAAAAATGCTGTTTTTTAAACATTAAAATCATTCCTCTCCCAGGACCTTGTGCA
       310       320       330       340       350       360
GCTATTACAGCACTGAGTGCTTCTGGAATATCTACTAATCGTTTTTGCTATGAAGGATTT
       370       380       390       400       410       420
CTGCCTTCTAAAAAAAAAATAAGACGTGATTTATTAAAATCTTTAAAAAAAGAAATAAGG
       430       440       450       460       470       480
ACAATAATTTTTTATGAATCGAAACATAGAATACTTGAAAGTATAAAAGATATTATAGAA
       490       500       510       520       530       540
ACAATAGATGAAAATAGATATTTAGTAATCGCAAGAGAAATTACAAAAAAATGGGAGTAT
       550       560       570       580       590       600
ATATACGGTGCAAAAGCTAATATAATTCTGTCTTGGCTGAAAGAAGATCAAAGTCGTTAT
       610       620       630       640       650       660
AAAAAAGGCGAAATAGTAATTATTATAGATGGTTTTAAAGAATTAAAAAATAAAGATATT
       670       680       690       700       710       720
TCAGCAAAAGCAATAAATACATTGACAATCTTAAGAAATTTTCTTTCATTAAAACAATCA
       730       740       750       760       770       780
GTATTTATTACTTCTAAAATACATAAAATAAAAAAAAATGATTTATATCAACATGCAATA
       790       800       810       820       830       840
AAAGAAAAAGATAAGTGA
       850
artemis • 1.1k views
ADD COMMENTlink modified 2.1 years ago by caggtaagtat1.3k • written 2.1 years ago by Mimmi Ahlmén20

Sequence is generally presented in 5'--> 3' direction no matter what strand it is on (watson/crick). So ATG would still be a start codon (that is a naive generalization). Generally decreasing coordinates are used to indicate that the sequence is from reverse strand.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by GenoMax93k

OK, thanks! So in this case the start codon is GTG? I used GenemarkS to predict this ORF.

ADD REPLYlink written 2.1 years ago by Mimmi Ahlmén20
1

Yes, ATG is not the only valid start codon.

ADD REPLYlink written 2.1 years ago by Joe18k
0
gravatar for caggtaagtat
2.1 years ago by
caggtaagtat1.3k
caggtaagtat1.3k wrote:

Hi, I also think its the correct way, since there is a stopcodon TGA at the end. Therefore per definition of a CDS sequence, the GTG would be your start codon, which could be for example the case, if this is a gene from E.coli.

ADD COMMENTlink written 2.1 years ago by caggtaagtat1.3k
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