Crossword Genius

Delayed transit; intrastate whale in an accident (3,5,3,4)

Ross

I believe the answer is:

the train was late

I'm a little stuck... Click here to teach me more about this clue!

'an accident' is the definition.
I know nothing about this answer so I can't judge whether it can be defined by this definition.

'delayed transit intrastate whale' is the wordplay.
'intrastate whale' anagrams to 'THE TRAIN WAS LATE'.
But, I am unsure how this is indicated.

'in' acts as a link.

Can you help me to learn more?

I've seen this clue in the Sydney Morning Herald.
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