#9748 Query about ' GO:0075713 establishment of integrated provira

CALIPHO
closed-fixed
Jane Lomax
viruses (30)
5
2014-02-05
2012-09-26
Pascale Gaudet
No

Hello,

I am trying to annotate to 'integration of viral DNA into host genome', and so I came across another term, ' GO:0075713 establishment of integrated proviral latency', that has 'integration of viral DNA into host genome' as an exact synonym.

First - those terms should not be exact synonyms, especially when you look at the parents.

Second - is there a term to describe 'integration of viral DNA into host genome' ?

Thanks,

Pascale

Discussion

  • David Hill
    David Hill
    2012-09-26

    • assigned_to: nobody --> jl242
     
  • Jane Lomax
    Jane Lomax
    2012-11-06

    • milestone: --> CALIPHO
     
  • Jane Lomax
    Jane Lomax
    2012-11-06

    I'm pretty sure they are synonymous, Pascale. Unless you can think of steps other than integration which are required to establish latency?

     
  • Pascale Gaudet
    Pascale Gaudet
    2012-11-06

    Hi Jane,

    They are not synonymous. You can have latency without integration and integration without latency. We need all possibilities.

    Thanks,

    Pascale

     
  • Jane Lomax
    Jane Lomax
    2012-11-07

    Hi Pascale - so there are these terms for latency without integration:

    establishment of episomal latency
    ---[i] establishment of latency as a circular episome
    ---[i] establishment of latency as a linear episome

    but I'm not sure what you mean by 'integration without latency'? Could you give an example?

    Are there gps other than integrases that are involved with integration of viral DNA? Just trying to figure out how 'integration of viral DNA into host genome' would differ from the viral integrase function term (which I've just noticed is called 'prophage integrase activity' - will broaden that to 'provirus integrase activity').

    Which species are you annotating btw?

    Sorry - that's a lot of questions! These terms are all quite new and haven't really been used for much annotation yet so I'd like to get them right (I think they probably have a bit of a phage bias right now).

    cheers,

    Jane

     
  • Jane Lomax
    Jane Lomax
    2014-01-13

    Hi Pascale

    We're just trying to get the viral terms finished and this is still outstanding...when does integration happen without latency? Can you give us some references/species? Then we'll fix the terms.

    thanks,

    Jane

     
  • Jane Lomax
    Jane Lomax
    2014-02-04

    Okay, this is finally sorted. The new terms is:

    viral genome integration into host DNA ; GO:0044826

    and there are some new functions as well:

    retroviral integrase activity ; GO:0044823
    retroviral 3' processing activity ; GO:0044824
    retroviral strand transfer activity ; GO:0044825

    I've removed the synonym from GO:0075713.

    Let me know if you spot any problems,

    Jane

     
  • Jane Lomax
    Jane Lomax
    2014-02-05

    • status: open --> closed-fixed