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In ethereum whitepaper there are separate sections for Transaction and Message contents.
While I am able to find in an implementation a file called "transaction.go" which contains (more or less the same) fields mentioned in the whitepaper I cannot find such file for Message. Is the same data structure used for both (Transactions and Messages)?

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Yeap, the same data structure is used for both Transactions and messages.

The Transaction contains the message and the data field of the transaction represents the message

The transaction.go file contains a struct with the data field.

The data field has a representation of the transaction's messages

Empty data field = simple transaction

data field not empty= message

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