Sines Mono Di/Trimers




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Table S4

SINEs

Mono-

Di/Trimers

Distribution

References

pB1

7SL




rodents

Quentin, 1994

pB1D10

7SL







Quentin, 1994

ID

tRNA







Milner et al. 1984

BC1

tRNA







Milner et al. 1984
















pB1D7

7SL




Mouse-related clade/Ctenohystrica

Quentin, 1994

pB1D9

7SL







Quentin, 1994

B1F

7SL







giri Repbase

B1F1

7SL







giri Repbase

B1F2

7SL







giri Repbase

ID-B1




ID-B1




Lee et al. 1998; this publication
















4.5SH

7SL




Myodonta

Schoeniger and Jelinek, 1986

B2

tRNA




Muridae, Cricetidae, and Spalacidae

Krayev et al. 1982

Serdobova and Kramerov, 1998



RSINE1

7SL




Muridae

giri Repbase

B3

tRNA







Lee et al. 1998

B1_Mur

7SL







giri Repbase

B4




ID-B1




Lee et al. 1998
















IDL-Geo




ID-ID

Geomyoidea

Gogolevsky and Kramerov, 2006

SP-D-Geo




pB1D10-ID




this publication
















B1dID




B1-dID

Ctenodactylomorphi

Huchon et al. 2007
















B1L

7SL




Squirrel-related clade

Veniaminova et al. 2007; this publication

B1L-dID




B1L-dID




Kramerov et al. 2001; this publication

pB1D10-dID




pB1D10-dID




Veniaminova et al. 2007
















B2_Mm

tRNA




mouse

giri Repbase

BC1-Mm

tRNA







giri Repbase

B1_Mus

7SL







giri Repbase
















B2-Rn

tRNA




rat

giri Repbase

BC1-Rn

tRNA







giri Repbase

B1-Rn

7SL







giri Repbase

ID-Rn

tRNA







giri Repbase
















DIP

tRNA




Dipodidae and Zapodidae

Serdobova and Kramerov, 1998
















Ped-1

5S-rRNA




springhare

Gogolevsky et al. 2008

Ped-2

tRNA



















GPIDL

tRNA




guinea pig

Kim et al. 1994; Kass et al. 2009

BC1_Cp

tRNA




guinea pig

giri Repbase

pB1D-dID




pB1D-dID

Detected in guinea pig

this publication

ID-pB1D7




ID-pB1D7

Octodontidae; detected in guinea pig

Veniaminova et al. 2007
















twinID-Spe




ID-ID

detected in ground squirrel (Spermophylus

this publication

tri-Spe




B1L-B1L-ID

tridecemlineatus)

this publication

ID-Spe




ID-dID




this publication
















MEN




ID-B1L

Menetes, Callosciurus

Serdobova and Kramerov, 1998

Table S4. Compilation of SINEs in rodents and corresponding references. Di- and trimeric structures are indicated and taxonomic distributions given.

References

1. Bains W, Temple-Smith K. 1989. Similarity and divergence among rodent repetitive DNA sequences. J Mol Evol. 28:191-199.

2. Gogolevsky KP, Kramerov DA. 2006. Short interspersed elements (SINEs) of the Geomyoidea superfamily rodents. Gene 373:67-74.

3. Gogolevsky KP, Vassetzky NS, Kramerov DA. 2008. Bov-B-mobilized SINEs in vertebrate genomes. Gene 407:75-85.

4. Huchon D, Chevret P, Jordan U, Kilpatrick CW, Ranwez V, et al. 2007. Multiple molecular evidences for a living mammalian fossil. Proc Natl Acad Sci USA 104:7495-7499.

5. Kass DH, Schaetz BA, Beitler L, Bonney KM, Jamison N, et al. 2009. Guinea pig ID-like families of SINEs. Gene 436:23-29.

6. Kim J, Martignetti JA, Shen MR, Brosius J, Deininger P. 1994. Rodent BC1 RNA gene as a master gene for ID element amplification. Proc Natl Acad Sci USA 91:3607-3611.

7. Kramerov DA, Vassetzky NS. 2001 Structure and origin of a novel dimeric retroposon B1-dID. J Mol Evol. 52:137-143.

8. Krayev AS, Markusheva TV, Kramerov DA, Ryskov AP, Skryabin KG, Bayev AA, Georgiev GP. 1982. Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 seqencing. Nucleic Acids Res. 10:7461-7475.

9. Lee IY, Westaway D, Smit AF, Wang K, Seto J, et al. 1998. Complete genomic sequence and analysis of the prion protein gene region from three mammalian species. Genome Res. 8:1022-1037.

10. Milner RJ, Bloom FE, Lai C, Lerner RA, Sutcliffe JG. 1984. Brain-specific genes have identifier sequences in their introns. Proc Natl Acad Sci USA 81:713-717.

11. Quentin Y. 1994. A master sequence related to a free left Alu monomer (FLAM) at the origin of the B1 family in rodent genomes. Nucleic Acids Res. 22:2222-2227.

12. Schoeniger LO, Jelinek WR. 1986. 4.5S RNA is encoded by hundreds of tandemly linked genes, has a short half-life, and is hydrogen bonded in vivo to poly(A)-terminated RNAs in the cytoplasm of cultured mouse cells. Mol Cell Biol. 6:1508-1519.

13. Serdobova IM, Kramerov DA. 1998. Short retroposons of the B2 superfamily: evolution and application for the study of rodent phylogeny. J Mol Evol. 46:202-214.



14. Veniaminova NA, Vassetzky NS, Kramerov DA. 2007. B1 SINEs in different rodent families. Genomics 89:678-686.


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