Terminators and other stem-loop structures
This is a plot of the Bacillus subtilis
UTP-glucose-1-phosphate uridylyltransferase gene
against itself.
The cursor is positioned at the location of
a translation terminator, which in this case
is a stem-loop in the RNA molecule. This means
that the sequence is locally similar to its
reversed complement, hence the appearance of
small perpendiculars to the main diagonal.
This is also clearly shown in the alignment window.
- BSGTABX (L12272):
AAGCTTGTTTAAAAATGGTTTATCCGATATCATAAAAATGTGTAAAAACATATTGAAAAGGGTAAATAGAGAATAGTTTA
ACCATAAATTTTTTCGATCATAAGGAAGGTGCCTTTTAAATGAAAAAAGTACGTAAAGCCATAATTCCAGCAGCAGGCTT
AGGAACACGTTTTCTTCCGGCTACGAAAGCAATGCCGAAAGAAATGCTTCCTATCGTTGATAAACCTACCATTCAATACA
TAATTGAAGAAGCTGTTGAAGCCGGTATTGAAGATATTATTATCGTAACAGGAAAAAGCAAGCGTGCGATTGAGGATCAT
TTTGATTACTCTCCTGAGCTTGAAAGAAACCTAGAAGAAAAAGGAAAAACTGAGCTGCTTGAAAAAGTGAAAAAGGCTTC
TAACCTGGCTGACATTCACTATATCCGCCAAAAAGAACCTAAAGGTCTCGGACATGCTGTCTGGTGCGCACGCAACTTTA
TCGGCGATGAGCCGTTTGCGGTACTGCTTGGTGACGATATTGTTCAGGCTGAAACTCCAGGGTTGCGCCAATTAATGGAT
GAATATGAAAAAACACTTTCTTCTATTATCGGTGTTCAGCAGGTGCCCGAAGAAGAAACACACCGCTACGGCATTATTGA
CCCGCTGACAAGTGAAGGCCGCCGTTATCAGGTGAAAAACTTCGTTGAAAAACCGCCTAAAGGCACAGCACCTTCTAATC
TTGCCATCTTAGGCCGTTACGTATTCACGCCTGAGATCTTCATGTATTTAGAAGAGCAGCAGGTTGGCGCCGGCGGAGAA
ATTCAGCTCACAGACGCCATTCAAAAGCTGAATGAAATTCAAAGAGTGTTTGCTTACGATTTTGAAGGCAAGCGTTATGA
TGTTGGTGAAAAGCTCGGCTTTATCACAACAACTCTTGAATTTGCGATGCAGGATAAAGAGCTTCGCGATCAGCTCGTTC
CATTTATGGAAGGTTTACTAAACAAAGAAGAAATCTAAACAAAAAGGCTATTGGACATTCATCCAATAGCCTTTTTTTAT
TTCAACATCAAAGTCAATGTATGCTCTTCATTATCAACTGCGAAGACCTGATCAACGGCCTGCCGCAAAAATTAATAATC
CCAGACAAACACACTGATTGTAGAGTTAAACAAACTAAATGAAAACATAAATACAAACATGCAGATTAAATAGTAAATAT
CTTGTATTCAATGCAAGCTAAGTAAACACCACTTGCTAAAAGAACAATGACTAAACAACCAGCATTACAAAT
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