Review Article

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

Table 1

Identification of SINE/LINE pairs [34].

SINESpeciesPromoterLINE tailDescription of SINE/LINE pair

Mammals
MIR (CORE-SINEs:
Ther-1, Mon-1)
[9799]All mammalstRNAL2[15][100]
CORE-SINEs (MIR3/Ther-2)[15, 99]MammalstRNAL3[101][15, 34, 102]
CORE-SINEs (Mar-1/MAR1_MD)[15, 99]MarsupialstRNARTE-3_MD[15][15, 34, 102]
MAR4
(MAR4_MD, WALLSI3)
[15]Opossum and wallaby, Monodelphis domestica, Macropus eugenii (5′-end of RTE)RTE-2 (MD, ME)[15][15, 34]
RTESINE1[15]Opossum,
Monodelphis domestica
(5′-end of RTE)RTE-1_MD[15][34]
Ped-1[103]Springhare,
Pedetes capensis (Rodentia)
5S rRNABovB_Pca[103][103]
Ped-2[103]Springhare,
Pedetes capensis (Rodentia)
tRNA (ID SINE)BovB_Pca[103][103]
Bov-tA [104, 105]RuminantstRNAGluBov-B[105, 106][100, 104]
Bov-A2[104, 105]Ruminants(5′-end of BovB)Bov-B[105, 106][104]
SINE2-1_EC[15]Horse, Equus caballus tRNARTE-1_EC[15][15, 34]
Afro SINEs
(AFRO_LA, PSINE1)
[15, 107]All AfrotherianstRNARTE1 (LA, Pca)[15][34, 103, 108]
RTE1-N1_LA[15]Elephant,
Loxodonta africana
(5′-end of RTE)RTE1_LA[15][15]
SINE2-1_Pca[15]Hyrax, Procavia capensis tRNARTE1_Pca[15][15]

Birds and Reptiles
TguSINE1[15]Zebra finch,
Taeniopygia guttata
tRNAIleCR1-X[15][15]
Tortoise Pol III/SINE[31, 109111]Tortoises and turtles, Cryptodira tRNALysPsCR1[112][31, 113]
Sauria SINE[114, 115]Lizard, Anolis carolinensis tRNAAnolis Bov-B[114][114]
Anolis SINE 2[115]Lizard, Anolis carolinensis (Box A & B)Anolis LINE 2[115][115]
SINE2-1B_Acar/
SINE2-1_Acar
[15]Lizard, Anolis carolinensis tRNAVingi-2_Acar[116][15, 34]

Amphibians
V-SINEs (SINE2-1_XT)[15]Frog, Xenopus (Silurana) tropicalis tRNAL2-4_XT
(L2-3, L2-6, L2-2)
[15][15, 34]
CORE-SINEs (MIR_Xt)[15]Frog, Xenopus (Silurana) tropicalis tRNAL2-5_XT[15][34]

Fish
Sma I[117, 118]Chum and pink salmon, Oncorhynchus tRNALysSalL2[23][23, 31, 32]
Fok I [118]Charr, Salvelinus tRNALysSalL2[23][23, 31, 32]
SlmI[119]All salmonids, Salmonidae tRNALeuRSg-1[120][119]
CORE-SINEs (Hpa I) [102, 118]All salmonids, Salmonidae tRNARSg-1[120][31]
CORE-SINEs
(AFC, SINE2-1_AFC)
[102, 121, 122]Cichlid fish, Cichlidae tRNACiLINE2[121][121]
CORE-SINEs (UnaSINE1, UnaSINE2)[123]Eel, Anguilla japonica tRNAUnaL2[36, 123][36, 123]
HAmo SINE[124]Carp, Cyprinidae tRNAHAmoL2[124][124]   
DeuSINEs
(AmnSINE1, SINE3)
[21, 125]Mammals, chicken,
zebrafish, catfish
5S rRNACR1-4_DR (CR1-7, CR1-9, CR1-13)[15][21, 34, 125]
DeuSINEs
(LmeSINE1, SacSINE1)
[125]Coelacanth and dogfish shark,
Latimeria menadoensis,
Squalus acanthias
tRNACR1-4_DR-like[15][125]
DeuSINEs (OS-SINE1)[119, 125]Salmon and trout,
Oncorhynchus, Salmo
5S rRNARSg-1[120][125]
V-SINEs (HE1)[126, 127]Sharks and rays,
M. manazo, S. torazame,
H. japonicus, T. californica
tRNAHER1[126][126]
V-SINEs (DANA)[127129]Zebrafish, Danio rerio tRNACR1-3DR/ZfL3[15, 127][127]
V-SINEs (Lun1)[127]Lungfish,
Lepidosiren paradoxa
tRNALfR1[127][127]
SINEX-1_CM/SINE2-1_CM[130]Elephant shark, Callorhinchus milii tRNACR1-2_CMDQ524334[34, 130]

Chordates
DeuSINEs (BflSINE1)[125]Amphioxus,
Branchiostoma floridae
tRNACrack-16_BF[15][34]

Deuterostomes
SURF1/SINE2-4c_SP[15, 131]Sea urchin,
Strongylocentrotus purpuratus
tRNACR1-4_SP[15][34]
DeuSINEs (SINE2-3_SP)[15, 125]Sea urchin,
Strongylocentrotus purpuratus
tRNACR1Y_SP (CR1X_SP)[15][15, 34]
SINE2-8_SP
(SINE2-6, SINE2-4b)
[15]Sea urchin,
Strongylocentrotus purpuratus
tRNAL2-1_SP/CR1-3_SP[15][34]

Protostomes
Gecko[132]Mosquito, Aedes aegypti tRNAI-74_AAe (MosquI, I-58, I-59, I-62, I-64,
I_Ele10, 14, 35, 37)
[15, 133][34, 132]

Eumetazoans
Nve-Nin-DC-SINE-1 (*1)[134]Sea anemone,
Nematostella vectensis
tRNAL2-22_NV[15][134]
Nve-Nin-DC-SINE-2 (*1)[134]Sea anemone,
Nematostella vectensis
tRNACR1-5_NV[15][134]
Nve-Nin-DC-SINE-3 (*1)[134]Sea anemone,
Nematostella vectensis
tRNACR1-15_NV[15][134]
SINE2-1_NV[15]Sea anemone,
Nematostella vectensis
tRNACR1-16_NV[15][34]
SINE2-5_NV[15]Sea anemone,
Nematostella vectensis
tRNARex1-24_NV[15][34]

Fungi
Mg-SINE[135]Rice blast fungus,
Magnaporthe grisea
tRNAMgL/MGR583AF018033[32, 34]
SINE2-1_BG[15]Powdery mildew fungus,
Blumeria graminis
tRNATad1-24_BG (HaTad1-3, 1-5)[15][34]   

Amoebozoa
EdSINE1 (SINE-lile)[136]Amoeba, Entamoeba dispar UnknownR4-1_ED[15][34]
R4-N1_ED (SINE-lile)[15]Amoeba, Entamoeba dispar UnknownR4-1_ED[15][34]
EhLSINE1/ehapt2 (SINE-lile)[137, 138]Amoeba,
Entamoeba histolytica
UnknownEhLINE1/EhRLE1[30, 137][137]
EhLSINE2 (SINE-like)[137]Amoeba,
Entamoeba histolytica
UnknownEhLINE2/EhRLE3[30, 137][137]

Land plants
TS[35]Tobacco,
Nicotiana tabacum
tRNARTE-1_Stu[15][34]
ZmSINE2/SINE2_SBi[66]Maize, Zea mays;
Sorghum, Sorghum bicolor
tRNALINE1-1_ZM[15][34, 66]
ZmSINE3[66]Maize, Zea mays tRNALINE1-1_ZM[15][66]

Green algae
SINEX-1_CR[15, 83]Chlamydomonas reinhardtii UnknownRandI-2/
DualenCr3
[15, 139][34, 83]
SINEX-2_CR[15, 83]Chlamydomonas reinhardtii UnknownRandI-2 (RandI-3)[15, 139][83]
SINEX-3_CR[15, 83]Chlamydomonas reinhardtii tRNAL1-1_CR[15][15, 83]
SINEX-4_CR[15, 83]Chlamydomonas reinhardtii UnknownRandI-2 (RandI-3)[15, 139][34, 83]
SINEX-5_CR/SINEX-6_CR[83]Chlamydomonas reinhardtii tRNARandI-5[15][83]

(*1) Subfamilies.