Institutes which use IIT JEE Extended Merit List (EML) besides IIT JEE AIR for their admissions:

Dasvidaniya

IIST, Trivandrum, Kerala (Indian Institute of Space Technology) – 156 seats http://www.iist.ac.in
IISER Mohali, Punjab – 100 seats http://www.iisermohali.ac.in/
IISER Pune, Maharashtra – 100 seats http://www.iiserpune.ac.in/
IISER Kolkata, West Bengal - – 100 seats website: www.iiserkol.ac.in
IISER Bhopal, Madhya Pradesh - – 100 seats
IISER Trivandrum, Kerala – 100 seats
The various disciplines in the 5 Years' Integrated Masters Programme at various IISERs are:

Biology Chemistry Mathematics Physics

Optional/inter-disciplinary courses being taught are:

Computer Science Earth Sciences
IIMS (Navi Mumbai, Kolkata, Mumbai) – 300 seats http://iims.dgshipping.com/
1. 3 year B.Sc. (Nautical Sciences) - T.S.Chanakya, Navi Mumbai - 120 seats
2. 4-year Marine Engg Degree at MERI, Kolkata – 160 seats
3. 3-year Polyvalent B.Sc. (Maritime Sciences) Degree at MERI, Mumbai – 30 seats Out of these 10 seats are reserved for foreign nationals in T.S. Chanakya, MERI, Kolkata and MERI, Mumbai for which the details can be directly obtained from Indian Institute of Maritime Studies.
RGIPT (Rajiv Gandhi Institute of Petroleum Technology) Rae Barelli, UP - 70 seats (35 seats each in 4yr BTech Petroleum Reservoir & Production Engg & 4yr BTech Petroleum Refining).