Dear all, Does anybody know the meaning of int in the repeatname output by Repeatmasker? Such as the -int in HERVL-int. Thanks.
Dear all, Does anybody know the meaning of int in the repeatname output by Repeatmasker? Such as the -int in HERVL-int. Thanks.
The INT means the "internal" region that would be flanked by LTRs on both sides in a full length ERV or LTR element, e.g. http://www.girinst.org/2007/vol7/issue1/SHACOP4_I_MT.html
See also similar interpretation here "PREM2_ZM_I (the internal region of an LTR-retrotransposon in REPBASE)"
The internal region can also be suffixed by "_I".
The reason that LTRs and Internal regions are sepearate entries in Repbase/repeatmasker databases is so that defragmentation of full length LTR elements in the genome will not erroneous link, e.g. the 5' LTR of a query to the 3' of a genomic hit.
It actually means "integrase" sequence of the Human endogenous retrovirus. There are some entries in Repbase like "HERV-LTR" which means the "long terminal repeat" sequence of that element.
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I'm guessing: "interspersed". As in interspersed repeats.