SINE    Length
  (w/o tail)
         Taxon         
Distribution Copy number Structure
tRNA >80/75/70%
LINE [clade]
Tail
Features
Refs
5S-Sauria236 Reptilia reptiles green anole
(Anolis carolinensis)
1.6×102 5S???~~~     ACCTTT   Piskurek 2009
AC1
(SINE_FR2, SINE_TE)
380 Actinopterygii ray-finned fishes fugu & medaka2×102
(fugu)
3×103
(medaka)
tRNACORE???LINE~~~ Val Gly Glu   TGAR V-domain Ogiwara 2002
AcaNinDC
(Aca-Nin-DC-SINE)
513 Gastropoda gastropod molluscs sea hares Aplysia californica and A. kurodai 5.5×104 tRNA???CORELINE~~~ Arg Val I-3 [nimb] CA2-5 Deu-domain Piskurek 2011
ACar-1
(SINE2-1_ACar)
269 Reptilia reptiles green anole
(Anolis carolinensis)
3.9×104 tRNA???LINE~~~   Vingi_ACar [Vingi] A   Jurka 2010
AFC
(SINE_AFC)
310 Actinopterygii ray-finned fishes African cichlids2×103
2×104
tRNACORE???LINE~~~ Asn Arg CiLINE2 [L2] ATT CORE domain Takahashi 1998
AFC-2
(SINE2-1_AFC)
275 Actinopterygii ray-finned fishes African cichlids 2.4×103 0 tRNA???LINE~~~ Lys Asn Ile Tyr ? [L2] CCATTTA   Kojima 2010
AFC-3
(SINE3_AFC)
215 Actinopterygii ray-finned fishes African cichlids 8×102 0 tRNA???~~~ Phe Gly   ATT
CT2-3
  Jurka 2010
AfroLA
(AFRO_LA, PSINE1)
158 Mammalia mammals elephants and mammoths
(Proboscidea)
7×105
(mammoth)
tRNALINE~~~ Asn Gln Bov-B [RTE] T   Jurka 2006, Zhao 2009
AfroSINE
(AfroSINEn)
230 Mammalia mammals afrotherians8×105 tRNALINE~~~ Asn Bov-B [RTE] TTG   Nikaido 2003
Alu282 Mammalia mammals primates1.1×106
(human)
1.5×105
(galago)
7SL~7SL~~~   L1 [L1] A dimer Deininger 1981
Anolis SINE2 456 Reptilia reptiles Green anole
(Anolis carolinensis)
1.4×104 tRNA???LINE~~~   Anolis L2 [L2] TAAA   Piskurek 2009
Asu1 407 Insecta insects mosquito (Armigeres subalbatus) 5.1×103 tRNAANRt???~~~ Val Gly   AAAT   SINEBase
Asu2 313 Insecta insects mosquito (Armigeres subalbatus) 6 ×103 tRNA???~~~ Lys Thr Val   AAG   SINEBase
Au
(SINE2-1_ZM)
180 Angiospermae flowering plants Poaceae, Fabaceae, Solanaceae & Gramineae 1×104
(Aegilops)
1×102
(other plants)
tRNA???~~~     T   Fawcett 2006, Yasui 2001
Ava III 260 Actinopterygii ray-finned fishes Salmonoidei1×102 tRNACORE???~~~ Ile Met Ini   AT CORE domain Kido 1994, Matveev 2009
B1
(pB1, pB1dx, STR1)
135 Mammalia mammals rodents8×103-
6.5×105
7SL~~~   L1 [L1] A quasidimer Krayev 1980, Veniaminova 2007
B1-dID
(STRIDE*)
200 Mammalia mammals Gliridae, Sciuridae & Aplodontidae1.1×105
(dormouse) 4.5×104
(squirrel)
2.8×104
(beaver)
7SL~tRNA~~~   L1 [L1] A dimer Kramerov 2001, Veniaminova 2007
B2
(B2s, B2l, B3, SINEB2)
185 Mammalia mammals Muridae, Cricetidae, Spalacidae & Rhizomiidae3.5×105 tRNA???~~~ Thr Cys Ala Arg Lys L1 [L1] A T+ Krayev 1982
B4
(RSINE2, ID_B1)
278 Mammalia mammals different rodent families4×105
(mouse)
3.6×105
(rat)
tRNA~7SL~~~ Ala Val Thr L1 [L1] AC dimer Lee 1998, Veniaminova 2007
BflSINE1363 Leptocardii lancelets lancelet  0 tRNACORE???~~~     CCAAA CORE domain, α-domain Nishihara 2006
Bm1430 Insecta insects silkworm
(Bombyx mori)
1.5×105 tRNA???LINE~~~   Zenon_Bm [CR1] A   Adams 1986, Xu 2010
BmSE249 Insecta insects silkworm
(Bombyx mori)
5.2×103 tRNALINE~~~ Val R1 [R1] ATTT   Xu 2010
Bovc-Ta2 315 Mammalia mammals Bovidae
(cattle, goats & sheep)
2×104 tRNALINEtRNALINE~~~ Gly Cys Thr Asp
Gly Lys Thr
Bov-B [RTE] AT dimer Jurka 2005
Bov-tA
(Bov-tAn)
204 Mammalia mammals Bovidae
(cattle, goats & sheep)
2×105 tRNALINE~~~ Gly Lys Thr Asp Bov-B [RTE] AC   Lenstra 1993
BraS-I 134 Angiospermae flowering plants Brassicaceae 4.6×102
(Arabidopsis lyrata)
3.2×101
(Arabidopsis thaliana)
tRNA???~~~     A   Wenke 2011
C
(CSINEn)
325 Mammalia mammals Lagomorpha 5.4×105 tRNACORE???~~~   L1 [L1] A β-domain, (TC)n, T+ Cheng 1984, Krane 1991
CAN
(SINEC*, MVB2)
160 Mammalia mammals Carnivora2×105 tRNA???~~~ Ala L1 [L1] A (TC)n, T+ Lavrent'eva 1989, Vassetzky 2002
CELE45250 Nematoda roundworms Caenorhabditis elegans2×102 tRNA???~~~   RTE1 [RTE] T   Jurka 2005
CHRS
(CHR-1, CHR-2, CHRS-S, SINE2-1_BT, CHRL, CHRL_BT, SINE2-1_BT, SINE2-2_BT, SINE2-3_BT)
321
.(120-340)
Mammalia mammals cetaceans, hippopotamuses, ruminants & suiforms104-105 tRNA???~~~ Glu Pro Ala Gly L1 [L1] A quasioligomer; T+ Shimamura 1999, Nikaido 2001, Jurka 2005, Vassetzky 2013
Cisc-1290 Tunicata tunicates sea squirt
(Ciona spp.)
4×104 tRNACORE???~~~ Thr Trp Ile   CATT CORE domain Simmen 2000
CM-1
(SINEX-1_CM, SINE2-1_CM)
308 Chondrichthyes cartilaginous fishes ghost shark
(Callorhinchus milii)
6.5×104 tRNA???LINE~~~ Ala Cys Thr CR1-2_CM [CR1] ATT   Jurka 2005
CQ-1
(SINE2-1_CQ)
662 Insecta insects mosquito
(Culex pipiens)
5.5×102 tRNA???ANRt???~~~ Asn
  GATTA dimer Kojima 2011
CQ-2
(SINE2-2_CQ)
238 Insecta insects mosquito
(Culex pipiens)
1.4×103 tRNA???~~~ Arg Met Ini   T   Kojima 2011
CQ-3
(SINE3_CQ)
404 Insecta insects mosquito
(Culex pipiens)
2.5×103 tRNACORE???~~~     T α-domain Kojima 2011
CQ-4
(SINE4_CQ)
583 Insecta insects mosquito
(Culex pipiens)
1.4×102 tRNA???ANRt???~~~ Gly Thr Arg
Arg Trp Asn Thr Met
  GATTA dimer Kojima 2011
CQ-5
(SINE5_CQ)
237 Insecta insects mosquito
(Culex pipiens)
8.4×102 tRNACORE???ANRt???~~~     T dimer; α-domain Kojima 2011
CQ-6
(SINE6_CQ)
208 Insecta insects mosquito
(Culex pipiens)
3.1×103 tRNACORE???~~~     T α-domain Kojima 2011
Cre-1
(SINEX-1_CR)
520 Chlorophyta green algae Chlamydomonas reinhardtii 1×102 tRNA???~~~     ATT   Kapitonov 2004
Cre-3
(SINEX-3_CR)
496 Chlorophyta green algae Chlamydomonas reinhardtii 30 tRNA???LINE~~~   L1-1_CR [?] A   Kapitonov 2004
Cre-4
(SINEX-4_CR)
500 Chlorophyta green algae Chlamydomonas reinhardtii 30 tRNA???LINE~~~     ATT   Kapitonov 2004
Cry
(pol III/SINE, Hirt)
200 Reptilia reptiles Cryptodira
(straightneck turtles)
5×105 tRNALINE~~~ Thr Lys PsCR1 [CR1] AT   Endoh 1990, Sasaki 2004
CteNinDC
(Cte-Nin-DC-SINE)
333 Polychaeta polychaete annelida polychaete worms Capitella teleta and C. capitata 5.9×103 tRNA???CORE~~~     TCAC Deu-domain Piskurek 2011
CucuS-I 206 Angiospermae flowering plants Cucurbitaceae 7.1×102
(Cucumis sativus)
tRNA???LINE~~~   ? [L1] A   Wenke 2011
CucuS-II 98 Angiospermae flowering plants Cucurbitaceae 8.7×102
(Cucumis sativus)
tRNA???~~~ Cys   A   Wenke 2011
CYN-I
(t-SINE)
79 Mammalia mammals flying lemur
(Cynocephalus)
1×106
(with CYN-II & CYN-III)
tRNA~~~ Ile Thr L1 [L1] A simple Piskurek 2003, Schmitz 2003
CYN-II154 Mammalia mammals flying lemur
(Cynocephalus)
1×106
(with CYN-I & CYN-III)
tRNA~tRNA~~~   L1 [L1] A dimer Piskurek 2003, Schmitz 2003
CYN-III203 Mammalia mammals flying lemur
(Cynocephalus)
1×106
(with CYN-I & CYN-II)
tRNA~tRNA~tRNA~~~   L1 [L1] A trimer Piskurek 2003, Schmitz 2003
DANA370 Actinopterygii ray-finned fishes zebrafish
(Danio)
4.5×105 tRNACORE???LINE~~~ Asn Cys ZfL3 TGAA V-domain Izsvak 1996
DAS-I76 Mammalia mammals nine-banded armadillo
(Dasypus novemcinctus)
2.9×104 tRNA~~~ Ala Val Gly L1 [L1] A simple Borodulina 2005, Churakov 2005
DAS-IIa208 Mammalia mammals nine-banded armadillo
(Dasypus novemcinctus)
6.5×104
(with DAS-IIb)
tRNA~tRNA~~~
Ala
L1 [L1] A dimer Churakov 2005
DAS-IIb355 Mammalia mammals nine-banded armadillo
(Dasypus novemcinctus)
6.5×104
(with DAS-IIa)
tRNA???tRNA???~~~   L1 [L1] A dimer; T+ Churakov 2005
DAS-III387 Mammalia mammals nine-banded armadillo
(Dasypus novemcinctus)
2.2×105 tRNA???~~~ Ala Gly L1 [L1] A T+ Churakov 2005
DIP
(B2L_S)
190 Mammalia mammals Dipodidae & Zapodidae1×105 tRNA???~~~ Ala L1 [L1] A (TC)n, T+ Serdobova 1998
DR-1
(SINE_DR1)
244 Actinopterygii ray-finned fishes zebrafish
(Danio)
4.8×103 tRNA???LINE~~~   ? [L2] AAATGT   Jurka 2002
DR-2
(SINE2-1_DR, CypS-I)
174 Actinopterygii ray-finned fishes zebrafish
(Danio)
5×103 tRNA???~~~     A   Jurka 2002
EbuSINE1345 Myxini hagfish hagfish
(Eptatretus burgeri)
 0 tRNACORE???~~~     GAA Deu-domain Nishihara 2006
EbuSINE2345 Myxini hagfish hagfish
(Eptatretus burgeri)
 0 tRNACORE???~~~       Deu-domain Nishihara 2006
EC-1
(SINE2-1_EC)
398 Mammalia mammals horse
(Equus caballus)
7.7×103 tRNA???LINE~~~Glu Bov-B [RTE] AAC   Jurka 2008
ERE-A
(ERE-1x, ERE-4x)
251 Mammalia mammals horses
(Equus spp.)
9×104 tRNA???~~~   L1 [L1] A T+ Sakagami 1994, Jurka 2005, Vassetzky 2013
ERE-B
(ERE-2x, ERE-3x)
235
(176)
Mammalia mammals horse
(Equus caballus)
3.8×105 tRNA???~~~Glu L1 [L1] A quasidimer Jurka 2008, Vassetzky 2013
ERI-1
(Erine1)
126 Mammalia mammals hedgehogs
(Erinaceidae)
1×105 tRNA???~~~ Ala Gly Cys Thr L1 [L1] A (TC)n, T+ Borodulina 2001
ERI-2
(Erine2)
186 Mammalia mammals hedgehogs
(Erinaceidae)
1×105 tRNA???~~~   L1 [L1] A (TC)n, T+ Borodulina 2001
EuphS-I 83 Angiospermae flowering plants certain Euphorbiaceae 2.5×103
(Manihot esculenta)
1.3×102
(Ricinus communis)
tRNA~~~ Thr   A simple Wenke 2011
FabaS-I
(MT_SINE-1)
131 Angiospermae flowering plants barrel medic
(Medicago truncatula)
2.8×103 tRNA???~~~     A   Gadzalski 2011
FabaS-II
(SINE1_MT, MT-1)
116 Angiospermae flowering plants barrel medic
(Medicago truncatula)
2.2×103 tRNA???~~~   ? [L1] A   Jurka 2007
FabaS-III
(MT_SINE-3)
166 Angiospermae flowering plants barrel medic
(Medicago truncatula)
6.9×102 tRNA???LINE~~~   ? [L1] A   Gadzalski 2011
FabaS-IV 205 Angiospermae flowering plants barrel medic
(Medicago truncatula)
6.9×102
tRNA???tRNA~~~     A dimer Wenke 2011
FabaS-V 185 Angiospermae flowering plants certain Fabales 2.4×102
(Medicago truncatula)
~4×101
(Glycine max & Lotus japonicus)
tRNA???~~~ Thr, Gln, Glu. Pro   A   Wenke 2011
FabaS-VI 185 Angiospermae flowering plants certain Fabales 1.4×103
(Cajanus cajan)
4.6×102
(Medicago truncatula)
tRNA???~~~ Thr   A   Wenke 2011
FabaS-VII 124 Angiospermae flowering plants barrel medic
(Medicago truncatula)
6.9×103
tRNA???~~~ Ala, Val   A   Wenke 2011
FabaS-VIII 115 Angiospermae flowering plants barrel medic
(Medicago truncatula)
1.6×103
tRNA???~~~     A   Wenke 2011
FabaS-IX 120 Angiospermae flowering plants certain Fabales 3×103
(Glycine max)
2.8×102
(Cajanus cajan & Medicago truncatula)
tRNA???~~~     A   Wenke 2011
Fc-1
(tSINE_Fc)
105 Mammalia mammals Carnivora4×104-
6×104
(cat, dog, panda)
tRNA~~~ Lys Ile Met L1 [L1] A simple, T+ Jurka 2008
Feilai275 Insecta insects yellow fever mosquito
(Aedes aegypti)
6×104 tRNA???~~~ Leu Juan-A [Jockey] GAA   Tu 1999
FR-1
(SINE_FR1)
273 Actinopterygii ray-finned fishes fugu
(Takifugu rubripes)
3×102 tRNA???~~~     A   Smit 2002
GA-1
(SINE2-1_GA)
294 Actinopterygii ray-finned fishes stickleback
(Gasterosteus aculeatus)
3.4×102 tRNACORE???LINE~~~   ? [L2] CCATTTA CORE domain Kojima 2010
Gecko188 Insecta insects yellow fever mosquito
(Aedes aegypti)
7.2×103 tRNACORE???~~~ Val Gly MosquI [clade I] A
CCAA
etc.
α-domain Tu 2004
HaSE1
(HzIS1)
375 Insecta insects certain owlet moths
(Helicoverpa & Heliothis)
  tRNA???CORELINE~~~ Ala HaRTE1 [RTE] GAT Deu-domain Wang 2012
HaSE2
(HaSE2_DP)
284 Insecta insects certain owlet moths
(Helicoverpa, Heliothis & Spodoptera) & monarch butterfly (Danaus plexippus)
1.6×103
(Danaus plexippus)
tRNA???~~~     GAT   Wang 2012
HaSE3 354 Insecta insects certain owlet moths
(Helicoverpa, Heliothis, Trichoplusia & Mamestra)
  5S???CORELINE~~~   HaRTE1 [RTE] GAT Deu-domain Wang 2012
HE1340 Chondrichthyes cartilaginous fishes higher elasmobranches103-106 tRNACORE???LINE~~~ Gly Ala HER-1 [CR1] NATTCTAT V-domain Ogiwara 1999
Hpa I
(OM2)
200 Actinopterygii ray-finned fishes Salmonoidei102-104 tRNACORELINE~~~ Ile Thr Cys RSg-1 [L2] AT CORE domain Kido 1991, Matveev 2009
ID
(BC1, CAVID, MUSID, RDRE1_RN, RNALUIII, STRID1)
75 Mammalia mammals rodents2.5×104-
5×105
tRNA~~~ Ala Val Gly Thr L1 [L1] A simple Milner 1984
Idio1259 Cephalopoda cephalopod molluscs Japanese pygmy squid
(Idiosepius paradoxus)
 0 tRNACORE???~~~     CAAA Ceph-domain Akasaki 2010
Idio2425 Cephalopoda cephalopod molluscs Japanese pygmy squid
(Idiosepius paradoxus)
 0 tRNACORE???~~~     TGA Ceph-domain Akasaki 2010
IDL-Geo
(DIPODE1, DIPODE2)
190 Mammalia mammals Geomyidae & Heteromyidae1×105 tRNA~tRNA~~~ Ala Val Thr
L1 [L1] A dimer Gogolevsky 2006
ID-Spe
(STRID2, STRID3, STRID4)
126 Mammalia mammals Sciuromorpha1.9×105 tRNA???~~~ Ala Val Gly Cys L1 [L1] A quasidimer Churakov 2010
IscNinDC
(Isc-Nin-DC-SINE)
290 Arachnida arachnids hard-bodied ticks Ixodes scapularis and I. ricinus 2.2×104 tRNACORE???~~~     T Deu-domain, two A-boxes Piskurek 2011
Lam1230 Hyperoartia lampreys lamprey
(Lethenteron reissneri)
2.4×103 tRNACORE???~~~     GCA V-domain Ogiwara 2002
LgiNinDC
(Lgi-Nin-DC-SINE)
352 Gastropoda gastropod molluscs true limpets Lottia gigantea and L. scutum 3.1×103 tRNA???CORE???~~~ AlaThr Lys   CAT2-3 Deu-domain Piskurek 2011
Lj-1
(Lj_SINE-1)
135 Angiospermae flowering plants Lotus japonicus & Medicago truncatula 3.1×103
(Lotus japonicus)
3.9×101
(Medicago truncatula)
tRNA???~~~     A   Gadzalski 2011
Lj-2
(Lj_SINE-2)
191 Angiospermae flowering plants Lotus japonicus 3.3×102 tRNAtRNA???~~~     A dimer Gadzalski 2011
Lj-3
(Lj_SINE-3)
182 Angiospermae flowering plants Lotus japonicus 5.5×102 tRNA???LINE~~~ Arg ? [L1] A   Gadzalski 2011
LF
(LFSINE_Vert)
453 Vertebrata Mammalia Aves Reptilia Amphibia Sarcopterygii vertebrates mammals birds reptiles amphibians lobe-finned fishes coelacanths & tetrapods
(Sarcopterygii)
105
(Latimeria menadoensis)
3×102
(mammals)
tRNA???~~~     A   Bejerano 2006
Lm1
(SGRP1)
200 Insecta insects Locusta, Schistocerca & Chorthippus6×105
(locust)
tRNA???~~~ Leu   T   Bradfield 1985
LmeSINE1314 Sarcopterygii lobe-finned fishes coelacanth
(Latimeria menadoensis)
 0 tRNACORELINE~~~ Gly ? [L2] AACC Deu-domain, α-domain Nishihara 2006
Lun1291 Sarcopterygii lobe-finned fishes lungfish
(Lepidosiren paradoxa)
3×105 tRNACORE???LINE~~~ Gly LfR1 GAACCTAT V-domain; (TC)n Ogiwara 2002
Mac1
(WALLSI2)
311 Mammalia mammals kangaroos
(Macropodoidea)
4.5×104
(wallaby)
tRNACORE~~~     CA CORE domain Munemasa 2008
Mad-1
(SINE-1_Mad)
159 Angiospermae flowering plants apple
(Malus × domestica)
9.5×103 tRNAANRt~~~   L1 [L1] A dimer Jurka 2010
Mad-2
(SINE-2_Mad, SINE-4_Mad)
193 Angiospermae flowering plants apple
(Malus × domestica)
1×103 tRNA???~~~   L1 [L1] A   Kojima 2010
MamSINE1 286 Mammalia mammals mammals5×102
(platypus)
tRNACORE???~~~ Ile Ala RTE1 [RTE] CA β-domain Jurka 2005, Warren 2008
Mar1
(SINE1_MD)
246 Mammalia mammals marsupials
(Metatheria)
5×105
(opossum)
tRNACORELINE~~~   Bov-B [RTE] CAA CORE domain Gilbert 2000
Mar3
(WSINE1)
128 Mammalia mammals marsupials
(Metatheria)
5.3×104
(wallaby)
tRNACORE~~~ Thr L1 [L1] A CORE domain Munemasa 2008
MARE3 172 Mammalia mammals mammals1×102
(human)
1.4×103
(opossum)
tRNACORE~~~ Ile Lys   A β-domain Gentles 2007
MEG-RL
(Meg_PVa)
197 Mammalia mammals megabats
(Megachiroptera)
1×104 5S???~~~   L1 [L1] A quasioligomer Gogolevsky 2009
MEG-RS120 Mammalia mammals megabats
(Megachiroptera)
7×103 5S~~~   L1 [L1] A simple Gogolevsky 2009
MEG-T2212 Mammalia mammals megabats
(Megachiroptera)
4×103 tRNA???~~~ Val Ile Glu Gln Met L1 [L1] A   Gogolevsky 2009
MEG-TR182 Mammalia mammals megabats
(Megachiroptera)
5×103 tRNA5S~~~ Val Ala Met Ile Thr L1 [L1] AAT dimer Gogolevsky 2009
MEN259 Mammalia mammals squirrels Menetes & Callosciurus 1×105 tRNA~7SL~~~ Ala Thr Gly Val L1 [L1] A dimer Serdobova 1998
Mon1270 Mammalia mammals monotremes2×106
(platypus)
tRNACORELINE~~~ Arg Thr L2 [L2] TTA CORE domain Gilbert 2000, Warren 2008
MyrSINE83 Mammalia mammals anteaters
(Myrmecophagidae)
 0 tRNA~~~ Gly L1 [L1] A simple Nishihara 2007
NV-1
(SINE2-1_NV)
257 Anthozoa sea anemones and corals starlet sea anemone
(Nematostella vectensis)
95 tRNA???LINE~~~ Glu ? [L2] T   Jurka 2005
NV-2
(SINE2-2_NV)
324 Anthozoa sea anemones and corals starlet sea anemone
(Nematostella vectensis)
70 tRNACORE???~~~     ATTT V-domain Jurka 2005
NV-3
(SINE2-3_NV)
376 Anthozoa sea anemones and corals starlet sea anemone
(Nematostella vectensis)
60 tRNA???CORE???~~~     A α-domain Jurka 2005
NymS-I 131 Angiospermae flowering plants spatterdock
(Nuphar advena)
  tRNALINE~~~   L1 [L1] A   Wenke 2011
Oegop371 Cephalopoda cephalopod molluscs Oegopsida1×104 tRNACORE???~~~     AGC Ceph-domain Akasaki 2010
OK405 Cephalopoda cephalopod molluscs Octopodidae8.5×104 tRNA???~~~     AT (TR)n Ohshima 1994
Opo-1
(SINE-1_MD, SINE-2_MD)
193 Mammalia mammals American marsupials2.8×105 tRNACORE???~~~ Ser Trp Thr   A CORE domain Gilbert 2000, Munemasa 2008
OR1390 Cephalopoda cephalopod molluscs Octopus spp.3.3×104 tRNA???~~~ Thr Arg   AT   Ohshima 1994
OR2270 Cephalopoda cephalopod molluscs Octopus spp.2.8×104 tRNACORE???~~~ Arg   AT CORE domain Ohshima 1994
OS469 Actinopterygii ray-finned fishes Salmonoidei  0 5StRNACORELINE~~~   RSg-1 [L2] TAAA dimer; Deu-domain, β-domain Nishihara 2006, Matveev 2009
OsSN1
(F524)
285 Angiospermae flowering plants rice
(Oryza sativa)
5.7×102 tRNA???~~~ Ala Val Thr   A   Jiang 2002, Tsuchimoto 2008
OsSN2
(SINE9_OS, SINE2-11_SBi, SINE2-12_SBi)
283 Angiospermae flowering plants rice & sorghum
(Oryza sativa & Sorghum bicolor)
1.2×103
(rice)
2.2×102
(sorghum)
tRNA???~~~     A   Gentles 2005, Tsuchimoto 2008
OsSN3
(CASINE)
176 Angiospermae flowering plants rice
(Oryza sativa)
7.1×102 tRNA???~~~ Ala L1 [L1] A   Jiang 2002, Tsuchimoto 2008
Otri 252 Insecta insects mosquito
Ochlerotatus triseriatus
  tRNACORE???~~~     A α-domain Luchetti 2013
Pca-1
(SINE2-1_Pca)
330 Mammalia mammals hyrax
(Procavia capensis)
9.3×103 tRNA???LINE~~~ Gly Glu Asp Pro Bov-B [RTE] AAC   Jurka 2009
Ped-1231 Mammalia mammals springhare
(Pedetes capensis)
6×104 5SLINE~~~   Bov-B [RTE] CAA   Gogolevsky 2008
Ped-2185 Mammalia mammals springhare
(Pedetes capensis)
2.5×105 tRNALINE~~~ Ala Phe Cys Ile Val Met Lys Bov-B [RTE] CAA   Gogolevsky 2008
PinS-I 227 Pinophytaconifers coniferous plants spruces
(Picea spp.)
2.7×102
tRNA???~~~     A   Wenke 2011
PoaS-I 156 Angiospermae flowering plants purple false brome
(Brachypodium distachyon)
1.4×102
tRNA???~~~     A   Wenke 2011
PoaS-II 156 Angiospermae flowering plants purple false brome
(Brachypodium distachyon)
1.4×102
tRNALINE~~~   L1 [L1] A   Wenke 2011
PRE-1246 Mammalia mammals pigs and peccaries106
(pig)
tRNA???~~~ Thr Lys L1 [L1] A quasidimer Singer 1987
p-SINE1
(p-SINE2, p-SINE3, SINE1R5_OS, SINE1OS, SINE6_OS, SINE8_OS, SINE16_OS)
115 Angiospermae flowering plants rice
(Oryza genus)
6×103
(rice)
tRNA???~~~     T   Mochizuki 1992, Motohashi 1997
PTr-1
(SINE2-1_PTr, SaliS-I)
187 Angiospermae flowering plants black cottonwood
(Populus trichocarpa)
4.1×103 tRNA???LINE~~~   ? [L1] A   Jurka 2010
PTr-2
(SINE2-2_PTr, SaliS-II)
161 Angiospermae flowering plants black cottonwood
(Populus trichocarpa)
4×103 tRNA???LINE~~~   ? [L1] A   Jurka 2010
PTr-3183 Angiospermae flowering plants black cottonwood
(Populus trichocarpa)
2.6×102 tRNA???LINE~~~   ? [L1] A   SINEBase
Ras1281 Actinopterygii ray-finned fishes Rasbora pauciperforata 2×102 tRNACORE???~~~ Val   YAAA V-domain Ogiwara 2002
Rhin-1190 Mammalia mammals bat families Rhinolophidae & Hipposideridae  0 tRNA???~~~ Ile Ala Met L1 [L1] A T+ Borodulina 2005
RSINE1 139 Mammalia mammals mouse & rat3×104
(mouse)
1.6×104
(rat)
tRNA???~~~ Ala L1 [L1] AC   Jurka 2005
Ruka230 Arachnida arachnids ixodid ticks6×104
(Rhipicephalus appendiculatus)
tRNA???~~~ Glu Pro Gly   TCAA   Sunter 2008
SacSINE1454 Chondrichthyes cartilaginous fishes dogfish shark
(Squalus acanthias)
 0 tRNACORELINE~~~ Arg Lys Asn ? [L2] T Deu-domain Nishihara 2006
SaliS-III 168 Angiospermae flowering plants black cottonwood
(Populus trichocarpa)
4.9×102
tRNA???~~~     A   Wenke 2011
SaliS-IV 185 Angiospermae flowering plants black cottonwood
(Populus trichocarpa)
3.2×102
tRNA???LINE~~~   ? [L1] A   Wenke 2011
SaliS-V 268 Angiospermae flowering plants black cottonwood
(Populus trichocarpa)
7×102
tRNA???tRNA???LINE~~~ Ala
? [L1] A dimer Wenke 2011
Sauria
(Squam1, ACA, AFE, POM, VIN)
350 Reptilia reptiles scaled reptiles
(Squamata)
1.3×105 tRNA???~~~     ACCTTT   Kosushkin 2006, Piskurek 2006
SB1
(S1)
171 Angiospermae flowering plants Brassica oleracea 330 tRNA???~~~   ? [L1] A   Deragon 1994
SB2
(RAthE1, SN2)
149 Angiospermae flowering plants Arabidopsis thaliana & Brassica oleracea 144
(Arabidopsis)
165
(Brassica)
tRNA???~~~   ? [L1] A   Lenoir 2001, Myouga 2001
SB3
(RAthE2, RBolE2)
297 Angiospermae flowering plants Arabidopsis thaliana & Brassica oleracea 58
(Arabidopsis)
510
(Brassica)
tRNA???~~~   ? [L1] A   Lenoir 2001
SB4
(RAthE3, SN1)
159 Angiospermae flowering plants Arabidopsis thaliana 64 tRNA???~~~   ? [L1] A   Deragon 2006
SB5
(Bos a, ab, b, ai)
162 Angiospermae flowering plants Arabidopsis thaliana & Brassica oleracea 7
(Arabidopsis) 645
(Brassica)
tRNA???LINE~~~   ? [L1] A   Deragon 2006
SB6
(ATSINE4)
297 Angiospermae flowering plants Arabidopsis thaliana & Brassica oleracea 32
(Arabidopsis) 735
(Brassica)
tRNA???~~~   ? [L1] A   Deragon 2006
SB7352 Angiospermae flowering plants Arabidopsis thaliana & Brassica oleracea 3
(Arabidopsis) 210
(Brassica)
tRNA???~~~   ? [L1] A   Deragon 2006
SB895 Angiospermae flowering plants Brassica oleracea 215 tRNA???~~~   ? [L1] A   Deragon 2006
SB9
(Bos c, f)
212 Angiospermae flowering plants Brassica oleracea 395 tRNA???~~~   ? [L1] A   Deragon 2006
SB10
(Bos d, e)
159 Angiospermae flowering plants Brassica oleracea 455 tRNA???LINE~~~   ? [L1] A   Deragon 2006
SB11
(Bos G)
170 Angiospermae flowering plants Brassica oleracea 100 tRNA???~~~   ? [L1] A   Deragon 2006
SB12
(Bos i1)
170 Angiospermae flowering plants Brassica oleracea 150 tRNA???LINE~~~   ? [L1] A   Deragon 2006
SB13
(Bos i2)
225 Angiospermae flowering plants Brassica oleracea 55 tRNA???~~~ Pro ? [L1] A   Deragon 2006
SB14
(Bos j, k)
156 Angiospermae flowering plants Brassica oleracea 285 tRNA???~~~ Glu ? [L1] A   Deragon 2006
SB15
(Bos l)
206 Angiospermae flowering plants Brassica oleracea 40 tRNA???~~~   ? [L1] A   Deragon 2006
SBi-1
(SINE2-1_SBi)
282 Angiospermae flowering plants Sorghum bicolor1×102 tRNA???~~~     T   Bao 2010
ScroS-I 210 Angiospermae flowering plants Common monkey-flower
(Mimulus guttatus)
1×103
tRNA???~~~     A   Wenke 2011
Sepia312 Cephalopoda cephalopod molluscs cuttlefish
(Sepiida)
1.7×105 tRNACORE???~~~       Ceph-domain Akasaki 2010
Sepioth1 292 Cephalopoda cephalopod molluscs Sepioteuthinae & Loliginidae 1.8×105 tRNACORE???~~~       Ceph-domain Akasaki 2010
Sepioth2A293 Cephalopoda cephalopod molluscs Sepioteuthinae9×104 tRNACORE???~~~       Ceph-domain Akasaki 2010
Sepioth2B229 Cephalopoda cephalopod molluscs Sepioteuthinae & Loliginidae9.4×104 tRNACORE???~~~     (CCAAA)2CCA Ceph-domain Akasaki 2010
SINE type II
(GarnAlu)
260 Mammalia mammals bush babies and lorises
(Lorisiformes)
3×105 tRNA~7SL~~~ Thr L1 [L1] A dimer Daniels 1983, Roos 2004
SINE type III
(Garnel1)
78 Mammalia mammals bush babies and lorises
(Lorisiformes)
2×105 tRNA~~~   L1 [L1] A simple Daniels 1991, Roos 2004
Sine200
(SINEX-1/2)
190 Insecta insects mosquito Anopheles gambiae2×103 tRNA???~~~ Val   AAG   Holt 2002
SINE3
(AmnSINE1)
561 Amniota Mammalia Aves Reptilia Amphibia amniotes mammals birds reptiles amphibians Amniota1×104
(zebrafish)
5StRNACORELINE~~~   ? [L2] ACATT
ATT
dimer; Deu-domain; TSD Kapitonov 2003, Nishihara 2006
SK241 Cephalopoda cephalopod molluscs squid
(Loligo bleekeri)
 0 tRNA???~~~ Lys Ile Ala Cys   ACTTT   Ohshima 1993
SlmI227 Actinopterygii ray-finned fishes Salmonoidei3×104 tRNA???LINE~~~   RSg-1 [L2] AT   Matveev 2007
SlmII465 Actinopterygii ray-finned fishes Salmonoidei1×104 tRNA???~~~     AT   Matveev 2007
Sma I
(Fok I, pol III/SINE, SMAIDIV, SINE_SM)
150 Actinopterygii ray-finned fishes Salmonoidei1×102-
3×104
tRNA???LINE~~~ Arg Thr Ala SalL2 [L2] AT   Kido 1991, Matveev 2009
Smα
(Sjα, T2)
332 Trematoda parasitic flatworms Schistosomatidae1×103 tRNA???~~~ Arg   AT   Spotila 1989
SolS-I 179 Angiospermae flowering plants Solanaceae 2×103
(potato)
1.4×103
(N. benthamiana)
6.3×102
(tomato)
tRNAtRNA???~~~     A dimer Wenke 2011
SolS-II
(SINE2-1_STu)
216 Angiospermae flowering plants Solanaceae 1.7×103
(potato, tomato)
2.2×103
(N. benthamiana)
tRNA???LINE~~~ Cys ? [L1] A   Wenke 2011
SolS-IIIa 231 Angiospermae flowering plants Solanaceae 1.3×103
(potato)
1×103
(tomato)
tRNA???~~~     A   Wenke 2011
SolS-IIIb 246 Angiospermae flowering plants Solanaceae 1.6×102
(potato, N. benthamiana)
1×102
(tomato)
tRNA???~~~     A   Wenke 2011
SolS-IV 193 Angiospermae flowering plants Solanaceae 1×103
(potato)
4.7×102
(N. benthamiana)
3.7×102
(tomato)
tRNA???~~~     A   Wenke 2011
SolS-V 107 Angiospermae flowering plants Solanaceae 1.2×103
(potato)
5.4×102
(tomato)
4.3×102
(N. benthamiana)
tRNA???~~~     A   Wenke 2011
SolS-VI 225 Angiospermae flowering plants Solanaceae 9.5×102
(N. benthamiana)
1×102
(potato)
tRNA???LINE~~~   ? [L1] A   Wenke 2011
SolS-VII 211 Angiospermae flowering plants Solanaceae 3×102
(N. benthamiana)
3.4×101
(tomato)
tRNA???LINE~~~ Tyr
? [L1] A   Wenke 2011
SOR157 Mammalia mammals shrews
(Soricidae)
1×105 tRNA???~~~ Ala Val L1 [L1] A quasidimer Borodulina 2001
SP-1
(SINE2-1_SP)
246 Echinoidea sea urchins Strongylocentrotus purpuratus9.9×102 tRNA???~~~ Ile Val Thr Ala Gly   ATT   Kapitonov 2005
SP-2
(SINE2-2_SP)
231 Echinoidea sea urchins Strongylocentrotus purpuratus2.9×102 tRNA???~~~ Ala Thr Gly Ile Val   ATT   Kapitonov 2005
SP-3
(SINE2-3_SP)
353 Echinoidea sea urchins Strongylocentrotus purpuratus1.4×102 tRNA???CORE???~~~ Thr Gln Asn Phe Arg Ile Lys   GAA Deu-domain, α-domain Kapitonov 2005
SP-4
(SURF1, SINE2-4_SP)
262 Echinoidea sea urchins Strongylocentrotus purpuratus2.1×103 tRNACORE???~~~ Arg   ATT CORE domain Nisson 1988
SP-5
(SPEC1, SINE2-5_SP)
225 Echinoidea sea urchins Strongylocentrotus purpuratus1.3×103 tRNACORE???~~~ Arg   ATT CORE domain Carpenter 1982
SP-6
(SINE2-6_SP)
342 Echinoidea sea urchins Strongylocentrotus purpuratus4.5×102 tRNACORE???LINE~~~ Thr Lys Ile ? [L2] ATT CORE domain Kapitonov 2005
SP-7
(SINE2-7_SP)
199 Echinoidea sea urchins Strongylocentrotus purpuratus4×103 tRNA???CORE???~~~     ACC α-domain Kapitonov 2005
SP-D-Geo
(DIPODE3)
225 Mammalia mammals Geomyidae & Heteromyidae6.1×104 7SL~tRNA~~~   L1 [L1] A dimer Churakov 2010
Squam-2191 Reptilia reptiles scaled reptiles
(Squamata)
5.6×102
(anole)
tRNA???~~~ Ala Lys Val Cys Tyr Phe Thr Gly   A   Grechko 2011
SS-1
(SINE1_SS, SUSINE2)
121 Mammalia mammals pig
(Sus scrofa)
1.9×105 tRNA???~~~   L1 [L1] A   Jurka 2005
STRIDM199 Mammalia mammals thirteen-lined ground squirrel
(Spermophilus tridecemlineatus)
5.4×103 tRNAtRNA???~~~ Ala Val Gly Thr
Ala Val Gly
L1 [L1] A dimer Bao 2010
TAL
(SINE_UT)
237 Mammalia mammals moles
(Talpidae)
1×105 tRNA???~~~   L1 [L1] A (TC)n, T+ Borodulina 2001
Talua252 Insecta insects termites
(Isoptera)
1×105 tRNA???~~~ Leu   A   Luchetti 2009
Talub277 Insecta insects termites
(Isoptera)
2×104 tRNA???~~~ Glu   A   Luchetti 2011
Taluc387 Insecta insects termites
(Isoptera)
7.9×104 tRNACORE???~~~ Ile   (GAA)n
(CAA)n
(CTAA)n
(TTA)n(TA)n
quasidimer in H. sjoestedti; α-domain Luchetti 2011
Talud261 Insecta insects termites
(Isoptera)
6.3×104 tRNA???LINE~~~ Val Pro Thr ? [CR1] (CTTT)n   Luchetti 2011
TguSINE1124 Aves Estrildidae9.4×102 tRNALINE~~~ Ile Lys Ala ? [CR1] RTTYTGTG   Smit 2009
Ther-1
(MIR)
252 Vertebrata Mammalia Aves Reptilia vertebrates mammals birds reptiles mammals, birds & reptiles4×105
(human)
1×105
(mouse, rat)
tRNACORELINE~~~ Cys L2 [L2] ATT CORE domain Smit 1995, Gilbert 2000
Ther-2
(MIR3)
220 Mammalia mammals marsupials & placentals8×104
(human)
tRNACORELINE~~~ Gly L3 [CR1] TCTATGA CORE domain Gilbert 2000, Jurka 2005
TS158 Angiospermae flowering plants Solanaceae & Convolvulacea5×104
(tobacco)
tRNA???~~~ Ile Thr Met Asp Asn Val   TTG   Yoshioka 1993
Tu type I
(TUBE2, TUBE3, TUBE5)
179 Mammalia mammals tree shrews
(Scandentia)
102 tRNA~7SL~~~   L1 [L1] A dimer; some with (TC)n Nishihara 2002
Tu type II
(TUBE4)
278 Mammalia mammals tree shrews
(Scandentia)
102 tRNA~7SL~7SL~~~   L1 [L1] A trimer Nishihara 2002
Tu type III
(TUBE1, TUS)
242 Mammalia mammals tree shrews
(Scandentia)
2×105 tRNA???~~~ Gly L1 [L1] A (R)n-(Y)n Nishihara 2002
TUB
(TUB1, TUB2, TUB3, TUB4)
131 Mammalia mammals tree shrews
(Scandentia)
2.5×105 tRNA???~~~   L1 [L1] A (TC)n, T+ Jurka 2008
Twin 217 Insecta insects mosquito
(Culex spp.)
5×102 tRNA???~tRNA~~~     A dimer; T+ Feschotte 2001
UCON3 168
Euteleostomi Mammalia Aves Reptilia Amphibia Sarcopterygii Actinopterygii vertebrates mammals birds reptiles amphibians lobe-finned fishes ray-finned fishes
Euteleostomi102 tRNA???~~~     A   Jurka 2006
UnaSINE1208 Actinopterygii ray-finned fishes eel
(Anguilla japonica)
2.5×105 tRNACORELINE~~~ Tyr Arg UnaL2 [L2] TGTAA CORE domain; T+ Kajikawa 2002
VES
(Ves2, Ves3, Ves4)
191 Mammalia mammals bat families Vespertilionidae, Molossidae, Phyllostomidae & Emballonuridae105 tRNA???~~~ Cys Ala Phe Tyr Ile Thr L1 [L1] A (TC)n, T+ Borodulina 1999
vic-1
(ALPINE1, ALPINE2, SINE_VV)
117 Mammalia mammals Camelidae105 tRNA~~~ Ala Val Ile Thr Phe Lys Cys L1 [L1] A simple Lin 2001
VitaS-I 93 Angiospermae flowering plants grapevine
(Vitis vinifera)
1.3×103
tRNA???~~~     A   Wenke 2011
WallSI4 233 Mammalia mammals wallaby
(Macropus eugenii)
1×105 tRNACORE???~~~ Arg Gly   CCCTAT CORE domain Thompson 2006
Xt-1
(MIR_Xt)
208 Amphibia amphibians Xenopus tropicalis4×105 tRNACORELINE~~~   ? [L2] T2-4C2-3 CORE domain Jurka 2005
Xt-2
(SINE2-1_XT)
318 Amphibia amphibians Xenopus tropicalis6×102 tRNACORELINE~~~ Gly Ala ? [L2] A V-domain Jurka 2005
All SINE elements originally published in Repbase have been reproduced with permission from the Genetic Information Research Institute, which reserves all rights in the material.