Dear Rohit, all the sub section/provision although talks about trust& universities but they all have their different meaning in the act....if u carefully read the provision u will find their different meaning....refer below extracts;
Section 139 (4A):
Its speaks about a person (and not the trust) who receives any income derived from property held under Trust
Section 139 (4C): it speaks about ;
1. trust or institution referred to in sub-clause (v) of clause (23C) of section 10 (reproduced below)
(v) 49any trust (including any other legal obligation) or institution wholly for public religious purposes or wholly for public religious and charitable purposes, 50[which may be approved by the prescribed authority51], having regard to the manner in which the affairs of the trust or institution are administered and supervised for ensuring that the income accruing thereto is properly applied for the objects thereof;
2. any university or other educational institution referred to in 33[sub-clause (iiiad) or] sub-clause (vi) of clause (23C) of section 10 (reproduced below)
(iiiad) any university or other educational institution43 existing43 solely43 for educational purposes and not for purposes of profit if the aggregate annual receipts of such university or educational institution do not exceed the amount of annual receipts as may be prescribed44;
(vi) any university or other educational institution53 existing53 solely53 for educational purposes and not for purposes of profit, other than those mentioned in sub-clause (iiiab) or sub-clause (iiiad) and which may be approved54 by the prescribed authority55
(iiiab) any university or other educational institution43 existing43 solely43 for educational purposes and not for purposes of profit, and which is wholly or substantially financed by the Government;
Section 139 (4D): it speaks about: Every university, college or other institution referred to in clause (ii) and clause (iii) of sub-section (1) of section 35, which is not required to furnish return of income or loss under any other provision of this section (reproduced below)
ii) 59[an amount equal to 59a[one and one-fourth] times of any sum paid] to a 59b[scientific research association] which has as its object the undertaking of scientific research or to a university, college or other institution to be used for scientific research :
60[Provided that such association, university, college or other institution for the purposes of this clause—
(A) is for the time being approved, in accordance with the guidelines, in the manner and subject to such conditions as may be prescribed; and
(B) such association, university, college or other institution is specified as such, by notification61 in the Official Gazette, by the Central Government;]
iii) 66[an amount equal to one and one-fourth times of 66a[any sum paid] to a university], college or other institution to be used for research in social science or statistical research :
67[Provided that 67a[such university], college or other institution for the purposes of this clause—
(A) is for the time being approved, in accordance with the guidelines, in the manner and subject to such conditions as may be prescribed; and
(B) 67a[such university], college or other institution is specified as such, by notification68 in the Official Gazette, by the Central Government.]
69[Explanation.—The deduction, to which the assessee is entitled in respect of any sum paid to a 69a[scientific research association], university, college or other institution to which clause (ii) or clause (iii) applies, shall not be denied merely on the ground that, subsequent to the payment of such sum by the assessee, the approval granted to the association, university, college or other institution referred to in clause (ii) or clause (iii) has been withdrawn;]