First remove non-ACGTacgt, then split on acgt:
$s = 'G_I1E2_GTGGAG^303CTGgacgCCCTGC_I2E3_TACA';;
$s =~ tr[ACGTacgt][]cd;;
print for split '[acgt]+', $s;;
GGTGGAGCTG
CCCTGCTACA
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