extracting 5'UTR of each gene
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This has been answered here:
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
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Which organism are you working with ?
A simple solution would be to download homer and then install the genome of your interest, which comes with the annotations like
exons,introns,3'UTR,5'UTRetc. With a simple grep, you could extract all the5'UTRsand you could use homer for motif analysis.As @genomax2 suggested, you can easily get the required sequences from Ensembl. Follow the turorial here.
Provided your genome is available - Ensembl (BioMart) or UCSC (Table Browser). Tools to use are in respective brackets.
retrieval of upstream non-coding sequences