Are "Unknowns" Unknown TEs or generally unknown repeats?

[isabelladistefano]

Dear Shujun,

I am summarising TEs in three species and wonder whethter to include the Unknown results as Unknown TEs or any type of repeat region?

They are SO:0000657
http://sequenceontology.org/browser/current_svn/term/SO:0000657 which say the "children" could be:

nested_repeat (SO:0001649)
direct_repeat (SO:0000314)
inverted_repeat (SO:0000294)
long_terminal_repeat (SO:0000286)
non_LTR_retrotransposon_polymeric_tract (SO:0000433)
flanking_repeat (SO:0002192)
X_element_combinatorial_repeat (SO:0001484)
tandem_repeat (SO:0000705)
knob (SO:0002257)
Y_prime_element (SO:0001485)
telomeric_repeat (SO:0001496)
centromeric_repeat (SO:0001797)
terminal_repeat (SO:0002201)
dispersed_repeat (SO:0000658)
engineered_foreign_repetitive_element (SO:0000293)

I have read the QandA, but I am wondering if EDTA only picks up certain types of these "children"

Best wishes,

Isabella

[oushujun]

HI Isabella, It's unknown repeat, which could be TEs or non-TE repeats but EDTA could not find information to further classify them. Shujun

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On Fri, Sep 22, 2023 at 11:11 AM isabelladistefano ***@***.***> wrote: Dear Shujun, I am summarising TEs in three species and wonder whethter to include the Unknown results as Unknown TEs or any type of repeat region? They are SO:0000657 http://sequenceontology.org/browser/current_svn/term/SO:0000657 which say the "children" could be: nested_repeat (SO:0001649) direct_repeat (SO:0000314) inverted_repeat (SO:0000294) long_terminal_repeat (SO:0000286) non_LTR_retrotransposon_polymeric_tract (SO:0000433) flanking_repeat (SO:0002192) X_element_combinatorial_repeat (SO:0001484) tandem_repeat (SO:0000705) knob (SO:0002257) Y_prime_element (SO:0001485) telomeric_repeat (SO:0001496) centromeric_repeat (SO:0001797) terminal_repeat (SO:0002201) dispersed_repeat (SO:0000658) engineered_foreign_repetitive_element (SO:0000293) I have read the QandA, but I am wondering if EDTA only picks up certain types of these "children" Best wishes, Isabella — Reply to this email directly, view it on GitHub <#390>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NAV7VRH5RDFTDX4UETX3WTBLANCNFSM6AAAAAA5DIDOOQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[isabelladistefano]

Thank you.

As this list from SO only mentions RNA transposons, does this mean that these particular Unknowns are definitely not of a DNA transposon nature?

Best wishes,

Isabella

[oushujun]

No, it can also be DNA transposons but there isn’t any evidence to tell. All TEs can belong under the dispersed repeat child SO. Thanks, Shujun

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On Sat, Sep 23, 2023 at 8:58 AM isabelladistefano ***@***.***> wrote: Thank you. As this list from SO only mentions RNA transposons, does this mean that these particular Unknowns are definitely not of a DNA transposon nature? Best wishes, Isabella — Reply to this email directly, view it on GitHub <#390 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NANOMQRTUN7AABRSODX33MG5ANCNFSM6AAAAAA5DIDOOQ> . You are receiving this because you commented.Message ID: ***@***.***>