22 chromosome comments, definiton of HERV



Our definition of HERV

We defined endogenous retroviruses (included in our database) using this criteria:

Excluded were all other families classified as "LTR/retroviral" in the RepeatMasker output:

HERVs

HERV151HERV16HERV172HERV3HERV9
HERVEHERVFH213HERVHHERVHC2HERVR
HERVH_48HERVIHERVKHERVK11IHERVK13
HERVK14HERVK14CHERVK22HERVK3HERVKC4
HERVK_14HERVK_9HERVLHERVL18HERVL32
HERVL40HERVL68HUERS-P1HUERS-P3MERVL4
pTR55

  • 1 also known as HSRIRT
  • 2 now described also as HERVW
  • 3 now described also as HERVF
  • 4 Mouse Endogenous Retrovirus L; parts of HERVL or HERV16, that were due to S-W score named MERVL
  • 5 part of HERV9 internal sequence
  • LTRs of this HERV group are listed bellow. They were defined from Repbase and from frequencies of fusion with internal HERV sequencies obtained from the whole genome analysis. Their frequecies in close vicinity of corresponding coding sequences were significantly higher than random.

    LTRs

    LTR10ALTR10BLTR10CLTR10DLTR12
    LTR13LTR14LTR14ALTR14BLTR14C
    LTR15LTR16ALTR16A1LTR16BLTR16C
    LTR17LTR18ALTR18BLTR2LTR21A
    LTR21BLTR22LTR22ALTR22BLTR26
    LTR26ELTR3LTR32LTR33LTR33A
    LTR4LTR40aLTR40bLTR45BLTR47A
    LTR47BLTR5LTR7LTR8LTR9
    MER11AMER11BMER11CMER11DMER48
    MER9MLT2AMLT2BMLT2CAMLT2CB
    MLT2DMLT2EMLT2FAMLT2FBMLT2G
    MLT2HMLT2I

    Other elements from Repbase and RepeatMasker are not included in our database.



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