I think it is safe to say that he is definitely not a uchiha he probably acquired his sharigan via transplant.
Although he is not a uchiha he is probably a descendant of the senju clan because think about it the sharigan is a watered down version of the rinnegan and the rinnegan is both related to the uchiha and senju clans as it was possible for nagato who was a senju to gain the rinnegan. Also tobis eye is constantly open he doesnt seem able to shut off which you would thing he would do as keeping the sharigan open drains his chakra so it must be transplanted.
Who he is not He is not harishma as demonstrated when he was revived by orichmaru. He is not Orichmaru as Tobi appeared a couple of years ago during narutos birth but when we see the first series of naruto he is still searching for a sharigan. He is not obito for one obito is way to young madara is probably quite old probably over his 60s as you can see his wrinkles when he tries to reveal his face to sasuke or when part of his mask was destroyed by konan .
Other notes it could be possible that tobis mangekyou looks just the same as his 3 tomoe sharigan and his space time jutsu is his mangekyou sharigan if so he probably acquires his sharigan another way instead of killing his best friend as shisui and kakashi didnt not kill their best friend but still got the mangekyou but theirs differed from the usual amaretsu and susano.
na fist nagato was uzimaki not senju. second i
have been saying he wasnt an uchia but someone
that aided madara i think this last manga proves
that. i mean tobi has great medical skill and i
think he was the one who put senju cells in
madara. i dont think he is senju i think he also
used the cells and put them in him uchia and
senju. i also have been thinking that madara and
tobi had a hand in killing the uzimaki clan
because they are also part of the senju.
actually his sharingan is not always active b/c
when he was a filler member once sasori of the red
sand died his sharingan was not active so I think
he is an uchia but I am loving how the story is
Uzumaki clan (うずまき一族, Uzumaki
Ichizoku) was a prominent clan in Uzushiogakure.
They were also distant relatives of the Senju clan
and thus both clans were on good terms; an
alliance that extended onto their Hidden Villages
- Konohagakure and Uzushiogakure. http://naruto.wikia.com/wiki/Uzumaki