The patch function will do what you want:
x = linspace(1, 300, 300); % Create Data
y = randi([20 80], 1, 300);
figure(1)
patch([1 100 100 1], [0 0 99 99], 'w')
hold on
p2 = patch([100 153 153 100], [0 0 99 99], 'b')
plot(x, y, '-k')
hold off
axis([1 300 0 99])
set(p2, 'FaceAlpha', 0.5) % Adjust Patch Transparency
The one caveat is to plot the patches first regardless of the transparency or other settings, and plot the data last. This plots the data on top of the patches:
