This should suit your needs (it only adds the " if the pattern matches otherwise it leaves it alone.):
use strict;
use warnings;

while ( <DATA> ) {
  s/([^"])(,\w*,\w*,ResGen,)/$1"$2/;
  print;
}

__DATA__
GENE1="Rattus norvegicus serum and glucocorticoid-regulated kinase (sg
+k) mRNA, complete cds,NM_019232,333,ResGen,ATP binding|protein serine
+/threonine kinase|protein amino acid phosphorylation,,,,29517
GENE2="ESTs, Weakly similar to putative serine/threonine protein kinas
+e MAK-V [M.musculus]",NM_144755,331,ResGen,,,,,246273
GENE3="Thiosulfate sulphurtransferase (rhodanese)",X56228,329,ResGen,m
+itochondrion|sulfate transport|thiosulfate sulfurtransferase,,,,25274
GENE4="Spleen tyrosine kinase,NM_012758,327,ResGen,ATP binding|protein
+ tyrosine kinase|intracellular signaling cascade|protein amino acid p
+hosphorylation,,,,25155
GENE5="Spleen kinase 24,NM_012758,,ResGen,ATP binding|protein tyrosine
+ kinase|intracellular signaling cascade|protein amino acid phosphoryl
+ation,,,,25155

[download]
This assumes a lot from your data. Mainly that the only thing possible between the commas lie in the character class [A-Za-z0-9_]

-enlil

In reply to Re: Need method to create Regular expression for known pattern in the middle of a line by Enlil
in thread Need method to create Regular expression for known pattern in the middle of a line by Ya

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