All retroviruses contain three large genes: gag, pol, and env. The gag gene codes for several structural proteins that form the viral particle (virion) capsid and perform other functions. The pol gene codes for several enzymes, including Reverse Transcriptase. We will be analysing env sequences, which are about 2.5 kilobases (Kb) long. The env gene codes for two viral envelope glycoproteins that are positioned on the virion surface and interact with host cell-surface receptors.
You will be analysing an alignment of 62 env sequences of HIV-1, HIV-2, and various SIVs. The alignment has been made for you because aligning this many long sequences can require considerable computation time.
Click here to open the provided alignment.
When viewing the alignment, note that there are many large gaps, which is characteristic of an alignment of a rapidly evolving gene in divergent species.
The sequences are labelled in the format: virus type; followed by the common name of the primate species for the SIV sequences, or the group or subtype for HIV-1 and HIV-2 sequences; finally followed by the accession number.
This alignment contains sequences from various African primate species known to be infected with different SIVs. There are also three non-African species, all from Asia, that have been infected with SIVs in captivity: the pig-tailed macaque, the rhesus macaque and the stump-tailed macaque. The SIVs from all of these primate species are referred to by the three-letter code given with each picture. For example, the SIV from the sooty mangabey is called SIVSMM and the sequence in the alignment or tree is labelled SIV-SMM.
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Mona monkey Cercopithecus mona mona [denti] MON [DEN] |
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de Brazza's monkey Cercopithecus neglectus DEB |
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Tantalus monkey Chlorocebus tantalus TAN |
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Syke's monkey Cercopithecus albogularis SYK |
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Greater spot- nosed monkey Cercopithecus nictitans GSN |
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Green monkey Chlorocebus sabaeus SAB |
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Mustached guenon Cercopithecus cephus MUS |
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Vervet monkey Chlorocebus pygerythrus VER |
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Grivet Chlorocebus aethiops GRV |
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L'Hoest's monkey Cercopithecus lhoest LST |
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Sooty mangabey Cercocebus atys SMM |
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Red-capped mangabey Cercocebus torquatus RCM |
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Sun-tailed monkey Cercopithecus solatus SUN |
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Mandrill Mandrillu sphinx MND |
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Drill Mandrillus leucophaeus DRL |
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Pig-tailed macaque Macaca nemestrina MNE |
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Stump-tailed macaque Macaca arctoides STM |
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Rhesus macaque Macaca mulatta MAC |
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Common chimpanzee Pan troglodytes CPZ |