Ja is the voiced palatal and the third letter of its class, differing from the head of the class by voicing alone. It is common in the vocabulary, standing at the front of the words for birth and for conquest and of the large families of terms built on those roots, so a page of Sanskrit of almost any kind will carry it.
Its most consequential appearance is in a conjunct rather than alone. Joined to the palatal nasal that closes its own class, it writes the cluster that opens the Sanskrit word for knowledge, a term at the centre of Buddhist doctrinal vocabulary and consequently written in Siddham more often than almost any other. The conjunct has a shape of its own, and its pronunciation varies from region to region in India in ways that have nothing to do with how it is written.
Like the other letters of the class it takes the inherent short a and is read ja standing alone. The regularity that lets a reader predict its sound from its position, third slot, palatal class, voiced and unaspirated, is the property the East Asian students of the script valued most, because it made the table teachable to people who did not know the language.
The word for conquest built on this letter stands at the front of a long list of personal and monastic names, so a Siddham page carrying a colophon or a dedication is likely to use it even where the text itself does not. Names are a distinct layer of any manuscript and they are frequently the part hardest to establish, because nothing else in the text constrains them.