Well, the lists in the Bible vary—there are no two identical lists!
Gen. 49: Reuben, Simeon and Levi, Judah, Zebulun, Issachar, Dan, Gad, Asher, Naphtali, Joseph, Benjamin
Numbers 1: Reuben, Simeon, Judah, Issachar, Zebulun, Joseph (Ephraim, Manasseh), Benjamin, Dan, Asher, Gad, Naphtali
Ezekiel 48: Dan, Asher, Naphtali, Manasseh, Reuben, Judah, Levites (sons of Zadok), Benjamin, Simeon, Issachar, Zebulun, Gad
Revelation 7: Judah, Reuben, Gad, Asher, Naphtali, Manasseh, Simeon, Levi, Issachar, Zebulun, Joseph, Benjamin
The reason for this is sometimes the descendants down the line were named rather than the original person. They are all still considered by Jewish authorities to be literal lists (take a list of the names from Revelation to a local Rabbi to confirm).
Why might Ephraim not be specifically mentioned in Revelation (even though Joseph is, so that tribe is still covered)? That answer may be found in Isaiah 7:8: “"For the head of Aram is Damascus and the head of Damascus is Rezin (now within another 65 years Ephraim will be shattered, {so that it is} NO LONGER A PEOPLE).” Also see Hosea 4:17: "Ephraim is joined to idols; Let him alone." (& Hos. 7:1-16) -- v. 13 says, "Destruction is theirs, for they have rebelled against Me!"
Why might Dan not specifically be included? It could be because Judas was from the tribe of Dan. Acts 1:16 says, “Brethren, the Scripture had to be fulfilled, which the Holy Spirit foretold by the mouth of David concerning Judas, who became a guide to those who arrested Jesus.” That can be followed to Psalm 109:8-13: “Let his days be few; Let another take his office…LET HIS POSTERITY BE CUT OFF; IN A FOLLOWING GENERATION LET THEIR NAME BE BLOTTED OUT.” Or the answer could be found in Judges 17:1-18:31, where we are told the Danites turned to idol worship and Amos 8:11-14, which says, "They will fall and not rise again."
I could be off target here, but I do feel like it's a pretty good, educated guess taking these Scriptures into consideration.