Where to find rRNA, tRNA, snoRNA, snRNA sequences for Arabidopsis?
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7.0 years ago
biolab ★ 1.3k

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!

rrna trna snorna snrna • 5.3k views
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7.0 years ago
PoGibas 5.0k

Ensemble Plants (http://plants.ensembl.org/info/website/ftp/index.html). You can get Arabidopsis t. gtf here: ftp://ftp.ensemblgenomes.org/pub/release-24/plants/gtf/arabidopsis_thaliana/

# 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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