Where to find rRNA, tRNA, snoRNA, snRNA sequences for Arabidopsis?
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7.8 years ago
biolab ★ 1.4k

Hi everyone,

As my title states, I am looking for a database that has extensive collection of Arabidopsis structural RNAs. Your help will be much appreciated! THANKS!

trna snrna snorna rrna • 5.6k views
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Entering edit mode
7.8 years ago
PoGibas 5.0k

Ensembl Plants. You can get Arabidopsis t.** gtf here.

In this example you get CDS, exons, start/stop_codons

curl -s "ftp://ftp.ensemblgenomes.org/pub/release-24/plants/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.24.gtf.gz" | gunzip -c | 
    cut -f 2 | sort | uniq -c

    193 miRNA
   1178 ncRNA
 475382 protein_coding
   1274 pseudogene
     15 rRNA
     71 snoRNA
     13 snRNA
   6277 transposable_element
    697 tRNA
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Thanks a lot! pgibas

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