28 mortars were fired from from the Gaza Strip earlier in the day, injuring at least five Israelis.
In a statement issued by the Israeli military, it said that the sites targeted by army fighter jets overnight included sheds used to store drones, a rocket manufacturing workshop, advanced naval weaponry, military compounds, training facilities and a munitions manufacturing site.
"This afternoon, the United States called for an emergency meeting of the UN Security Council to discuss the latest attacks on Israel out of the Gaza Strip by Hamas and other militants", the release said.
The attempt to leave Gaza by sea, which comes amid a barrage of mortars and rockets being fired at southern Israel on Tuesday from Gaza, is being called a "reverse flotilla" because it is the first public attempt to break out of the blockade and not into it.
The Israeli military said most of the projectiles were intercepted, but three soldiers were wounded, raising the chances of further Israeli retaliation.
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Calm returned to the Gaza Strip and nearby Israeli communities Wednesday after the exchange of fire on Tuesday that stretched into the night.
The armed wings of Hamas and Islamic Jihad claimed responsibility for the firing and said it was in response to Israel's killing of dozens of Palestinians since 30 March, mainly in Gaza border protests.
The attack came a few days after violent confrontation between Palestinian protesters and Israeli forces along the Gaza border, which left dozens of Palestinians dead.
France and Britain have criticised the draft resolution for a lack of specific details, diplomats said, adding the U.S. viewed it as biased against Israel. Israel says it holds Gaza's Hamas rulers responsible for the bloodshed. One mortar shell landed in a kindergarten shortly before it opened, wounding one person.
A member of Hamas was killed on Monday amid an attempt to breach the border and carry out an attack, while on Sunday three members of Islamic Jihad were killed after placing an explosive device on the border fence, the IDF said.
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Other residents reported machine- gun fire from Gaza.
Israel's military said it was not seeking an escalation, but warned Hamas. No Israelis have been killed.
In 2010, Israeli commandos killed nine Turkish activists when they raided a six-ship Flotilla trying to reach the Gaza Strip in defiance of the blockade.
The Israeli military said the boat was intercepted without incident, was taken to the Israeli port of Ashdod and the 17 people aboard would be sent back to Gaza.
Earlier this month, a large number of Palestinians gathered to protest on the Gaza Strip's eastern border to commemorate the Nakba anniversary and protest the relocation of the USA embassy from Tel Aviv to Jerusalem. At least one base belonging to Hamas and four for Islamic Jihad, an allied group, were struck, Gazan security sources said.
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But if there are no exemptions, she said, "We will respond in an intelligent, decisive and joint way", Merkel said in Lisbon. He says the USA action leaves the European Union with no choice but to proceed with a case in the World Trade Organization.
The Gaza Strip has been under Israeli blockade for more than a decade, with Israel saying it is necessary to prevent Hamas from obtaining means to attack.