Retrieving RNA sequence from corresponding genomic coordinates

Question

[Aishwarya Kulkarni]

I have some genomic coordinates and I want to retrieve their RNA sequence especially the ones for reverse complement ones (since RNA sequence would not be strand specific). Where could I find such tool or package?

[Neilfws]

what organism?

[Aishwarya Kulkarni]

Human genome hg19
 

Answer 1

[Anima Mundi]

Hello,

you can also go to the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables), upload your input file as a custom track ("add custom track" button), select your genome, choose "sequence" as output format, press "get output" and choose "mRNA" from the following menu. This would output your mRNA sequences in FASTA format.

[Aishwarya Kulkarni]

Thanks this is most useful! It's just that I cannot see the mRNA option once I click get sequence, all I get is:

 All upper case. 
 All lower case. 
 Mask repeats:  to lower case  to N 
 Reverse complement (get '-' strand sequence) 

[Anima Mundi]

I see, then you can create an intersection with "mRNA and EST" (track "Human RNAs"), either to retrieve just the sequences overlapping between your data and human mRNAs, or also to get the complete mRNA sequences with at least partial overlap with your custom track.

Answer 2

[arnstrm]

See this thread for details:

Extract Cds Fastas From A Gff Annotation + Reference Sequence