Jayarajan arrived at the court in an ambulance and surrendered before at 11 AM. He has been remanded in judicial custody for a month.
His counsel drew the attention of the court to his health condition and wanted him to be shifted to a hospital, which was turned down by the court saying for the time being he should be taken to Kannur Jail and the jail superintendent can take an appropriate decision later.
Earlier, the Thalassery district and sessions court had also rejected his anticipatory bail plea.
He is the 25th accused in the case relating to the murder of RSS functionary Manoj.
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Manoj was hacked to death in politically volatile Kathiroor in Kannur district on September 1, 2014, allegedly by a group of CPI(M) workers. CBI is investigating the case.
Earlier, talking to reporters, Jayarajan alleged that the RSS leadership had met Chief Minister Oommen Chandy and Home Minister Ramesh Chennithala to list him as an accused in the case.
Jayarajan was later shifted to Pariyaram medical college hospital cell on the advise of doctors who examined him.
When examined at the Kannur district hospital, it was found that he had some cardiac problems and was advised to be shifted to the nearest hospital.
Jayarajan was admitted to the hospital after being taken to the Kannur jail and completion of formalities there.
Meanwhile, CBI has filed an application in the sessions court, seeking his custody for three days from February 16.
The matter is likely to come up before the court on Monday.