This appears to work in the way I interpret your description, though there is at least one ambiguity in there so I may have dwiw'd the wrong way.

#! perl -slw
use strict;

my $re_resgen = qr[(.)(,(?:\w+),(?:\w+),ResGen)];

while (<DATA>) {
    s[$re_resgen][my $t=$1; $t.='"' unless $t eq '"'; $t.$2]e;
    print;
}

=pod output

c:\test>234040
001 GENE1="Rattus norvegicus serum and glucocorticoid-regulated kinase
+ (sgk) mRNA, complete cds",NM_019232,333,ResGen,ATP binding|pr
otein serine/threonine kinase|protein amino acid phosphorylation,,,,29
+517

002 GENE2="ESTs, Weakly similar to putative serine/threonine protein k
+inase MAK-V [M.musculus]",NM_144755,331,ResGen,,,,,246273

003 GENE3="Thiosulfate sulphurtransferase (rhodanese)",X56228,329,ResG
+en,mitochondrion|sulfate transport| thiosulfate sulfurtransfer
ase,,,,25274

004 GENE4="Spleen tyrosine kinase",NM_012758,327,ResGen,ATP binding|pr
+otein tyrosine kinase|intracellular signaling cascade|protein
amino acid phosphorylation,,,,25155

005 GENE5="Spleen kinase 24,NM_012758,,ResGen,ATP binding|protein tyro
+sine kinase|intracellular signaling cascade|protein amino acid
 phosphorylation,,,,25155

=cut

__DATA__
001 GENE1="Rattus norvegicus serum and glucocorticoid-regulated kinase
+ (sgk) mRNA, complete cds,NM_019232,333,ResGen,ATP binding|protein se
+rine/threonine kinase|protein amino acid phosphorylation,,,,29517
002 GENE2="ESTs, Weakly similar to putative serine/threonine protein k
+inase MAK-V [M.musculus]",NM_144755,331,ResGen,,,,,246273
003 GENE3="Thiosulfate sulphurtransferase (rhodanese)",X56228,329,ResG
+en,mitochondrion|sulfate transport| thiosulfate sulfurtransferase,,,,
+25274
004 GENE4="Spleen tyrosine kinase,NM_012758,327,ResGen,ATP binding|pro
+tein tyrosine kinase|intracellular signaling cascade|protein amino ac
+id phosphorylation,,,,25155
005 GENE5="Spleen kinase 24,NM_012758,,ResGen,ATP binding|protein tyro
+sine kinase|intracellular signaling cascade|protein amino acid phosph
+orylation,,,,25155
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