What Does The Int Mean In Hervl-Int Output By Repeatmasker

Question

[Gangcai]

Dear all, Does anybody know the meaning of int in the repeatname output by Repeatmasker? Such as the -int in HERVL-int. Thanks.

[Neilfws]

I'm guessing: "interspersed". As in interspersed repeats.

Answer 1

[Casey Bergman]

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.

[SES]

The question was about the "-int" suffix not "_I." I don't know what database is being used here (I don't see this element in Repbase), though I agree that it probably refers to some internal region.

[SES]

I think the naming scheme has changed and this is the result of an older Repbase release.

Answer 2

[SES]

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.

[SES]

It means "internal." I tried to down vote myself and it wouldn't let me. :)