Technology companies that work with the U.S. government could get hit as the shutdown over a border wall continues, some analysts say.

It's not the only way the government shutdown, which began on Dec. 22, could affect the technology industry, though. Two technology companies seeking to go public, Lyft and Uber, are awaiting feedback on confidential filings from the U.S. Securities and Exchange Commission, Bloomberg reported on Wednesday, and unprocessed paperwork has been forming a backlog for the agency, an attorney told CNBC this week.

Software companies that could get hit the hardest are those whose fiscal quarters end in December, and those that derive a meaningful percentage of revenue from government business, Morgan Stanley analysts led by Keith Weiss wrote in a note distributed to clients on Jan. 3. The analysts assembled a list of software companies with high government exposure and put cybersecurity company ForeScout on top, as they believe it generates 28 percent of its revenues from federal, state and local government agencies. Pivotal was the second on the list, at 19 percent. (Morgan Stanley later corrected its note, lowering Pivotal's exposure to under 10 percent, putting it further down the list.)

Many companies don't specify how much money they get from government business. But some do. Red Hat, which was recently acquired by IBM, has gotten one-tenth of a percent of its revenue in its three most recent fiscal years from the government, for example.

Oracle and Microsoft don't disclose the scale of their revenue from government customers, but Morgan Stanley estimates that Oracle receives 15 percent of its revenue comes from government agencies, while Microsoft gets 9 percent. But while Oracle's fiscal second quarter ended on Nov. 30, Microsoft's ended on Dec. 31.

"If it prolongs, we could see delays in govt, contracts, which could push revenue forward not just for MSFT," Bernstein Research analysts led by Mark Moerdler wrote in a note distributed to clients on Wednesday.

Microsoft and Oracle declined to comment on how they could be affected by the shutdown

Storage hardware company NetApp picks up around 10 percent to 15 percent of its revenue from the U.S. public sector, Susquehanna Financial Group analysts led by Mehdi Hosseini estimated in a Jan. 4 note.

"A shutdown can directly impact a seasonally soft Jan Q (for Federal)," the analysts wrote. NetApp's fiscal third quarter ends on Jan. 27. NetApp didn't respond to a request for comment.

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