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. 2012 Dec 5;3:20. doi: 10.1186/1759-8753-3-20

Table 2.

Conserved retroviral pro-pol motifs in crocodilian ERV (CERV) sequences

CERV clade Motif Genera Motif sequence*
CERV1
PR2
Gammaretrovirus
(A/V)L(V/L)DTG(A/S)TFSM
 
PR3
Gammaretrovirus
LLG(Q/R)DLLTKL
 
RT1
Gammaretrovirus
YN(S/T)PILGV(L/P)K(A/V)
 
RT2
Gammaretrovirus
SVLDLKDAFFSI(P/S(L
 
RT3
Gammaretrovirus
(Q/R)LMWTVLPQGF(I/V)(A/V)AP
 
RT4
Gammaretrovirus
LL(H/Q)YVDD(I/L)L
Haplotype 58
PR2
Gammaretrovirus
VLLDGTATMSM
 
PR3
Gammaretrovirus
LLGRDLLCK
 
RT1
Gammaretrovirus
CNTPVLPVRKP
 
RT2
Epsilonretrovirus
TVIDLCAAFFPIPV
 
RT3
Gammaretrovirus
HTLNTQLPQGYTKSP
 
RT4
Gammaretrovirus
LVQYVDDIL
CERV2
RT2
Spumavirus
(A/T)AID(L/P)K(D/E)MF(C/Y)(H/Q)IPL
 
RT3
Spumavirus
F(E/K)G(C/H/R)VY(E/K)WKVC(P/S)(E/Q)GYKNSP
  RT4 Spumavirus (L/N)SYVDD(I/L)L

*Residues presented here are those that occurred in more than one sequence. Motifs are based on those defined by Sperber et al.[48]. For the complete alignments, see Additional file 1: Figure S1.