RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity

Table 2

3′-Repeats of plant SINE families [34].

SINE	Species	3′-Repeat	LINE tail	Reference for SINEs
	Green algae
SINEX-1_CR	Chlamydomonas reinhardtii	(ATT)𝑛	RandI-2/DualenCr3	[83]
SINEX-2_CR	Chlamydomonas reinhardtii	(CTTT)𝑛	RandI-2 (RandI-3)	[83]
SINEX-3_CR	Chlamydomonas reinhardtii	(A)𝑛	L1-1_CR	[83]
SINEX-4_CR	Chlamydomonas reinhardtii	(ATT)𝑛	RandI-2 (RandI-3)	[83]
SINEX-5_CR/SINEX-6_CR	Chlamydomonas reinhardtii	(ATT)𝑛	RandI-5	[83]
	Seed plants
Au	Angiosperms and a gymnosperm	(T)2–5	Nd	[76–79]
ZmSINE1 (Au-like)	Zea mays	(T)𝑛	Nd	[66]
SINE2-1_ZM (Au-like)	Zea mays	(T)3	Nd	[15]
SINE-5_Mad (Au-like)	Malus x domestica	(T)3	Nd	[15]
	Monocots
p-SINE1	Oryza sativa	(T)𝑛	Nd	[74]
p-SINE2	Oryza sativa	(T)𝑛	Nd	[75]
p-SINE3	Oryza sativa	(T)𝑛	Nd	[75]
ZmSINE2.1*/SINE2-1a_SBi	Zea mays, Sorghum bicolor	(T)𝑛	LINE1-1_ZM	[15, 66]
ZmSINE2.2*	Zea mays	(T)𝑛	LINE1-1_ZM	[66]
ZmSINE2.3*	Zea mays	(T)𝑛	LINE1-1_ZM	[66]
SINE2-1_SBi (ZmSINE2-like)	Sorghum bicolor	(T)𝑛	LINE1-1_ZM	[15]
SINE2-1c_SBi (ZmSINE2-like)	Sorghum bicolor	(T)𝑛	LINE1-1_ZM	[15]
ZmSINE3	Zea mays	(A)𝑛	LINE1-1_ZM	[66]
OsSN1/F524	Oryza sativa	(A)𝑛	Nd	[140]
OsSN2/SINE2-12_SBi	Oryza sativa, Sorghum bicolor	(A)𝑛	Nd	[15, 140]
OsSN3	Oryza sativa	(A)𝑛	Nd	[140]
SINE9_OS/SINE2-11_SBi (OsSN-like)	Oryza sativa, Sorghum bicolor	(A)𝑛	Nd	[15]
	Eudicots
TS	Nicotiana tabacum	(TTG)𝑛	RTE-1_STu	[35]
SB1-15 (S1/AtSN/RAthE/BoS)	Arabidopsis thaliana,  Brassicaceae (Cruciferae)	(A)𝑛	Nd	[68, 69, 141–144]
LJ_SINE-1	Lotus japonicus	(A)𝑛	Nd	[145]
LJ_SINE-2	Lotus japonicus	(A)𝑛	Nd	[145]
LJ_SINE-3	Lotus japonicus	(A)𝑛	Nd	[145]
MT_SINE-1	Medicago truncatula	(A)𝑛	Nd	[145]
MT_SINE-2	Medicago truncatula	(A)𝑛	Nd	[145]
MT_SINE-3	Medicago truncatula	(A)𝑛	Nd	[145]
SINE-1_Mad	Malus x domestica	(A)𝑛	Nd	[15]
SINE-2_Mad	Malus x domestica	(A)𝑛	Nd	[15]
SINE-4_Mad	Malus x domestica	(A)𝑛	Nd	[15]
SINE2-1_PTr	Populus trichocarpa	(A)𝑛	Nd	[15]
SINE2-2_PTr	Populus trichocarpa	(A)𝑛	Nd	[15]

*subfamilies. Nd: no data.