JavaCard OS

I am trying to figure out what data communications look like on the low level serial channel when APDU SELECT is sent via T=0, T=1 or T=CL.
I have reference material showing me the APDU SELECT packet format. But I wonder before it's sent over the channel, is the byte sequence for SELECT encrypted?

SELECT command itself for a Java Card is described on the application layer in the corresponding specifications. On the low level only the protocol (T=0/1: ISO7816-3, T=CL: ISO14443) is described . The APDU structure is described in ISO7816-4. The commands described are not supported with the exception of the GET RESPONSE command.

But I wonder before it's sent over the channel, is the byte sequence for SELECT encrypted?

No. For a java card the SELECT command is never encrypted. It has a well defined structure.