While applying for the government job, every individual need to keep in mind the Eligibility Criteria as prescribed by that particular department in the Government. And as long as the degree is genuine and from an Institute that is recognised by the Govt. of India or that particular state, The Govt. of India doesn't differentiate between the University you got your degree and certificates from be it Anna University or a Deemed University.

Coming to Private Organisations like MNCs, few companies look for candidates for B schools, IIMs and IITs. And thats not the case for all the jobs. It is for few designations. 

So its difficult to analyse.