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Table 1 Squam3 SINE in scaled reptiles. Major subfamilies are described by the proportion and estimated number of full-length copies, the mean sequence similarity, and the tail repeat unit. Certain parameters of genome assemblies are given in the left columns (the level column indicates the chromosome-, scaffold-, and contig-levels levels of assembly: , , and , respectively)

From: New Ther1-derived SINE Squam3 in scaled reptiles

  Family Species Squam3 SINE Genome assembly
subfamily copies lengthw/o tail, nt similarity tail level ‘N’ N50 Reference
Squamata Gekkota Gekkonidae Gekko japonicus 3A (21%) 54,829 224 60% (TAAA)n 4% 707,733 [14]
3B (10%) 26,109 238 75% (CTT)n
3B3 (69%) 180,151 271 81% (CTT)n
Paroedura picta 3A (12%) 17,761 221 57% (TAAA)n 9% 4,106,116 [15]
3B (19%) 28,122 238 61% (CTT)n
3B3 (57%) 84,367 267 74% (CTT)n
Eublepharidae Eublepharis macularius 3A (50%) 68,299 224 60% (TAAA)n 2% 663,762 [16]
3B (50%) 63,045 239 85% (GTT)n
Lacertoidea Lacertidae Darevskia valentini 3A (48%) 25,848 218 63% (TAAA)n 16% 658,539 [17]
3B (52%) 28,003 238 91% (CTT)n
Lacerta agilis 3A (16%) 17,446 219 62% (TAAA)n 0% 86,565,987 [18]
3B (84%) 91,590 238 92% (CTT)n
Lacerta bilineata 3A (39%) 24,123 219 63% (TAAA)n 0% 368,212 [19]
3B (61%) 37,732 238 75% (CTT)n
Lacerta viridis 3A (39%) 24,836 219 61% (TAAA)n 0% 662,519
3B (61%) 38,847 238 94% (CTT)n
Podarcis muralis 3A (35%) 16,967 220 61% (TAAA)n 0% 92,398,148 [20]
3B (65%) 31,440 238 88% (CTT)n
Zootica vivipara 3A (38%) 10,036 220 61% (TAAA)n 3% 92,810,032 [21]
3B (62%) 16,374 238 89% (CTY)n
Teiidae Salvator merianae 3A (53%) 4892 221 54% (TAAA)n 2% 55,382,274 [22]
3B (47%) 4338 234 85% (CTT)n
Serpentes Colubridae Pantherophis guttatus 3C 12,936 226 64% (TAAA)n 5% 16,790,024 [23]
Pantherophis obsoletus 3C 12,961 226 63% (TAAA)n 3% 14,519,768 [24]
Ptyas mucosa 3C 19,524 226 63% (TAAA)n 3% 15,963,960 [25]
Thamnophis elegans 3C 16,934 226 64% (TAAA)n 0% 440,193 [26]
Thamnophis sirtalis 3C 12,410 226 63% (TAAA)n 21% 647,592 [27]
Thermophis baileyi 3C 15,914 228 65% (TAAA)n 8% 2,413,955 [28]
Elapidae Emydocephalus ijimae 3C 15,782 226 62% (TAAA)n 0% 18,937 [29]
Hydrophis cyanocinctus 3C 15,094 226 64% (TAAA)n 4% 7437 [30]
Hydrophis hardwickii 3C 15,782 228 62% (TAAA)n 4% 5391 [31]
Hydrophis melanocephalus 3C 14,271 226 63% (TAAA)n 11% 59,810 [29]
Laticauda colubrina 3C 19,118 226 63% (TAAA)n 13% 3,139,541
Laticauda laticaudata 3C 27,835 226 61% (TAAA)n 0% 39,330
Naja naja 3C 10,813 226 64% (TAAA)n 6% 224,088,900 [32]
Notechis scutatus 3C 27,122 226 63% (TAAA)n 5% 5,997,050 [33]
Ophiophagus hannah 3C 11,613 226 63% (TAAA)n 13% 241,519 [34]
Pseudonaja textilis 3C 17,187 226 65% (TAAA)n 2% 14,685,528 [35]
Pythonidae Python bivittatus 3A (43%) 9349 221 58% (TAAA)n 4% 213,970 [36]
3C (57%) 12,393 237 75% (A)n
Viperidae Crotalus horridus 3C 15,006 226 63% (TAAA)n 12% 23,829 [37]
Crotalus pyrrhus 3C 15,556 226 64% (TAAA)n 0% 5299 [38]
Crotalus viridis viridis 3C 18,694 226 63% (TAAA)n 6% 179,897,795 [39]
Protobothrops flavoviridis 3C 20,667 226 64% (TAAA)n 3% 467,050 [40]
Protobothrops mucrosquamatus 3C 20,184 228 64% (TAAA)n 8% 424,052 [41]
Vipera berus berus 3C 19,964 226 64% (TAAA)n 14% 126,452 [42]
Shinisauria Shinisauridae Shinisaurus crocodilurus 3A 165,288 225 58% (TAAA)n 8% 1,469,749 [43]
Anguimorpha Anguidae Dopasia gracilis 3A 35,118 225 71% (TAAA)n 3% 1,273,270 [44]
Varanoidea Varanidae Varanus komodoensis 3A 108,651 229 66% (TAAA)n 1% 23,831,982 [45]
Iguania Agamidae Pogona vitticeps 3A 4542 221 53% (TAAA)n 4% 2,290,546 [46]
Dactyloidae Anolis carolinensis 3A 457 217 54% (TAA)n 5% 150,641,573 [47]
Rhynchocephalia Sphenodon punctatus 10% 3,052,611 [12]
Testudines Trachemys scripta elegans 1% 147,425,149 [48]
Crocodilia Crocodylus porosus 5% 84,437,661 [49]
Aves Gallus gallus 1% 91,315,245 [50]