How to get the longest fasta sequence including all possible switching isoforms of a gene out of isoforms I am working with RNA-seq data without a reference genome/transcriptome and am instead using a Trinity de novo transcriptome assembly.
I analyzed both isoform and gene expression abundances using RSEM.
And got differentially expressed GENES via DESeq2.
In the next step I want to get fasta sequences of differentially expressed genes to use them in the subsequent BlastX/Blast2Go analyses.

Considering the fact that my Trinity created assembly is based on isoform id:

How can I extract the gene sequence out of it? Is that a right thing to combine all the isoforms of a single gene in order to generate the longest possible isoform assembly? 

If so, how can I do it to have a union-exon (combined form of all the exons present in the isoforms of an individual gene) sequence used in my Blast analysis? 

If not, how should I proceed with the data type available?
Trinity assembled file includes the isoform column as:

TRINITY_DN1780_c0_g1_i2 
TRINITY_DN1780_c0_g1_i1 
TRINITY_DN1780_c0_g1_i3 
TRINITY_DN1780_c0_g1_i4 
TRINITY_DN1780_c0_g1_i5


and the DESeq2 produces the output (gene differentials) as:

TRINITY_DN1780_c1_g1
From your question it isn't clear if you are trying to identify the isoforms that have a very high or very low differential expression value, or if you are trying to correctly find an orthlog for your top hits using BLAST. 

If your question is about isoform-level quantification, identifying DE at the isoform level is challenging and DESeq2 is only designed for gene-level analyses. That is why it is only outputting genes rather than a specific isoform.