Where to find rRNA, tRNA, snoRNA, snRNA sequences for Arabidopsis?

Question

[biolab]

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!

Answer 1

[PoGibas]

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

[biolab]

Thanks a lot! pgibas