There was a bit of dialog between them that was short, but revealing:
In a deleted scene from II, after Sr. Roberto makes his clumsy retreat from Vito's office, Genco chuckles and tells Vito that Roberto will probably hide out in the Bronx--it bespeaks a certain brotherly closeness. Then he says, "Vito, Clemenza wants to speak to you..." Clemenza comes in--first doffing his hat and holding it before him--and introduces Vito to the young Hyman Roth, who he says is good at fixing trucks. Clemenza refers to Vito as "Mr. Corleone."
That scene shows a remarkable transition in young Clemenza. Previously, he was the de facto boss--he organized the rug theft and the dress heist. And, in another deleted scene, Vito has to wait in the dress truck while Clemenza dallies with a winsome young woman with whom he's exchanging dresses for sex. When he finally emerges from the building and Vito wants to know what took him so long, Clemenza replies that "she couldn't make up her mind." He then orders Vito to deliver some dresses to "Dadino." But after the Fanucci murder, Clemenza suddenly becomes the humble subordinate.