How to find out the gene of specific long non-coding RNA (LncRNA) as I have sequence and chromosome number?

05 June 2023 1 3K Report

HELLO ALL, I need help with the following matter

I have sequences and chromosome numbers of the Arabidopsis thaliana long non-coding RNA (lncRNA) now I want to find the gene of the lncRNA, basically I want to order the knockout mutant from the stock center like ABRC.

The problem is that I don’t know how to order/purchase the specific LncRNA knockout mutant seeds.

Daniela Liebsch

maybe the easiest is to go to TAIR (www.arabidopsis.org) and blast your sequence against the genome (tools->blast). Paste the sequence and select the dataset to blast (i guess genomic locus sequences or genes of the newest annotation), at least if your lncRNA is annotated as gene you should find it there among the hits with the AGI identifier. Later you can use http://signal.salk.edu/cgi-bin/tdnaexpress to find a potential T-DNA insertion line. Good luck.

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