some text 0%
Some Status Text

3USS was developed to automatically identify alternative 3’UTRs (shorter or longer with respect to a reference transcriptome) in RNA-seq experiments. In addition, the tool tries to distinguish putative novel (not already known) 3’UTRs, comparing them to the annotated ones in various databases.
When a user uploads data from two samples, their alternative 3’UTRs are compared, highligthing those shared in diverse cell types or occurring in specific biological conditions.

Although the tool was thought for managing RNA-seq assembled transcripts, it provides another utility that aids to easily retrieve 3’UTR genomic coordinates and nucleotide sequences of already annotated transcripts.

Retrieving alternative 3'UTRs (compared to the Reference) from RNA-seq assembled transcripts

[ Ex_1 (GEO data): input files - results ] [ Ex_2: input files - results ]

Upload your RNA-seq transcriptome assembly file

(Uploading two files, a comparison of the results will be also performed)
RNA-Seq GTF transcriptome assembly file (also as .zip or .gz)


Select the Reference Transcriptome used for the RNA-seq analysis

(The recommended way is to directly upload your reference annotation file, used by Cuffcompare or Cuffmerge to produce your input file. Alternatively, you can select the corresponding genome assembly and the annotation database from menus)
  Organism (genome assembly):
 
Upload your Reference Annotation GTF file (also as .zip or .gz)  
 or
Select the Database:      

Please enter your email address, if you prefer to receive a link to the result page via email

Retrieving 3'UTRs of already Annotated transcripts

[ Ex_3: input files - results ]

Upload a transcript annotation file

Transcript Annotation GTF file (also as .zip or .gz)      

Select the organism and genome assembly

Organism :     

Please enter your email address, if you prefer to receive a link to the result page via email