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Question: can lnc-RNA target coding RNA?
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Hello everyone, I have two divergent RNA transcripts one is coding and the other is non-coding .. is there any tool one can use to precisely calculate the complementarity between the non-coding and coding transcript if any?

thanks much TA

ADD COMMENTlink 20 months ago ta_awwad • 210 • updated 19 months ago EagleEye 6.4k
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ADD COMMENTlink 19 months ago EagleEye 6.4k
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I'm actually trying to use triplexator to find TTS and TFOs for a specific lncRNA. In the above mentioned papers I see in the second one they used triplexator tool to get TTS and TFOs for MEG3 lncRNA. I'm interested in knowing whether they have given the whole FATSA sequence of MEG3 as input or selected any region? From which database I can get the FASTA sequence of a lncRNA?

ADD REPLYlink 13 months ago
Vasu
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Sorry for late response, I forgot to reply.

Yes, compete sequence from MEG3 was used for the prediction. You can get DNA FASTA sequence of any lncRNA from GENCODE, "Fasta files" section from this link. Also UCSC and ENSEMBL can be an option to extract DNA FASTA sequences.

ADD REPLYlink 13 months ago
EagleEye
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thanks a lot for the answer.

ADD REPLYlink 13 months ago
Vasu
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Could you please tell which command to use in linux to get FASTA sequence of MEG3/ any other lncRNA from gencode fasta file.

ADD REPLYlink 12 months ago
Vasu
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This should work

awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' gencode.v29.lncRNA_transcripts.fa | grep MEG3 | tr "\t" "\n"
ADD REPLYlink 12 months ago
genomax
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Thanks a lot for the command.

ADD REPLYlink 12 months ago
Vasu
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@EagleEye Do I need to use all the transcript (MEG3) sequences as input for triplexator?

ADD REPLYlink 12 months ago
Vasu
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What do you mean by "all transcript sequences" ? Are you referring to different isoforms ?

ADD REPLYlink 12 months ago
EagleEye
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What I mean is, MEG3 has multiple transcript IDs right. Do I need to use all or any specific transcript sequence is fine?

ADD REPLYlink 12 months ago
Vasu
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You must investigate all the transcript isoforms individually using triplexator.

ADD REPLYlink 12 months ago
EagleEye
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