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A New Class of SINEs with snRNA Gene-Derived Heads.

Kojima KK - Genome Biol Evol (2015)

Bottom Line: SINEU-2 is the only SINE family that was active after the split of crocodiles and gharials.All SINEU families, especially SINEU-3, are preferentially inserted into a family of Mariner DNA transposon, Mariner-N4_AMi.A group of Tx1 non-long terminal repeat retrotransposons designated Tx1-Mar also show target preference for Mariner-N4_AMi, indicating that SINEU was mobilized by Tx1-Mar.

View Article: PubMed Central - PubMed

Affiliation: Genetic Information Research Institute, Los Altos, CA kojima@girinst.org.

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Crocodile lineage-specific insertions of SINEU-2 with 5′ extensions. Crp represents the crocodile scaffold sequence and Gav represents the gharial scaffold sequence. SINEU-2 sequences are colored in green with their 5′ extension in blue, and putative TSD sequences characterized based on the corresponding “empty” sites in gharial are in red. (A) SINEU-2A with 5′ extension. Intron sequence for AKHW01109664, which encodes a protein annotated as amisp024556, from alligator is shown. Scaffold-6053 is a crocodile sequence that has the sequence similar to the 5′ extension sequences of SINEU-2A. (B) SINEU-2B with 5′ extension. The 5′ extension sequences show similarity to the consensus of Mariner-N4_AMi.
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evv100-F2: Crocodile lineage-specific insertions of SINEU-2 with 5′ extensions. Crp represents the crocodile scaffold sequence and Gav represents the gharial scaffold sequence. SINEU-2 sequences are colored in green with their 5′ extension in blue, and putative TSD sequences characterized based on the corresponding “empty” sites in gharial are in red. (A) SINEU-2A with 5′ extension. Intron sequence for AKHW01109664, which encodes a protein annotated as amisp024556, from alligator is shown. Scaffold-6053 is a crocodile sequence that has the sequence similar to the 5′ extension sequences of SINEU-2A. (B) SINEU-2B with 5′ extension. The 5′ extension sequences show similarity to the consensus of Mariner-N4_AMi.

Mentions: By the comparison of orthologous loci of crocodile and gharial, SINEU-2 insertions were found in the crocodile genome at whose orthologous loci in the gharial genome SINEU-2 are absent (fig. 2). Gharial-specific SINEU-2 insertions were also detected (supplementary fig. S2, Supplementary Material online). Both types of target site alterations (TSD and TST) were observed aside from the cases where no nucleotide was altered upon integration.Fig. 2.—


A New Class of SINEs with snRNA Gene-Derived Heads.

Kojima KK - Genome Biol Evol (2015)

Crocodile lineage-specific insertions of SINEU-2 with 5′ extensions. Crp represents the crocodile scaffold sequence and Gav represents the gharial scaffold sequence. SINEU-2 sequences are colored in green with their 5′ extension in blue, and putative TSD sequences characterized based on the corresponding “empty” sites in gharial are in red. (A) SINEU-2A with 5′ extension. Intron sequence for AKHW01109664, which encodes a protein annotated as amisp024556, from alligator is shown. Scaffold-6053 is a crocodile sequence that has the sequence similar to the 5′ extension sequences of SINEU-2A. (B) SINEU-2B with 5′ extension. The 5′ extension sequences show similarity to the consensus of Mariner-N4_AMi.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494074&req=5

evv100-F2: Crocodile lineage-specific insertions of SINEU-2 with 5′ extensions. Crp represents the crocodile scaffold sequence and Gav represents the gharial scaffold sequence. SINEU-2 sequences are colored in green with their 5′ extension in blue, and putative TSD sequences characterized based on the corresponding “empty” sites in gharial are in red. (A) SINEU-2A with 5′ extension. Intron sequence for AKHW01109664, which encodes a protein annotated as amisp024556, from alligator is shown. Scaffold-6053 is a crocodile sequence that has the sequence similar to the 5′ extension sequences of SINEU-2A. (B) SINEU-2B with 5′ extension. The 5′ extension sequences show similarity to the consensus of Mariner-N4_AMi.
Mentions: By the comparison of orthologous loci of crocodile and gharial, SINEU-2 insertions were found in the crocodile genome at whose orthologous loci in the gharial genome SINEU-2 are absent (fig. 2). Gharial-specific SINEU-2 insertions were also detected (supplementary fig. S2, Supplementary Material online). Both types of target site alterations (TSD and TST) were observed aside from the cases where no nucleotide was altered upon integration.Fig. 2.—

Bottom Line: SINEU-2 is the only SINE family that was active after the split of crocodiles and gharials.All SINEU families, especially SINEU-3, are preferentially inserted into a family of Mariner DNA transposon, Mariner-N4_AMi.A group of Tx1 non-long terminal repeat retrotransposons designated Tx1-Mar also show target preference for Mariner-N4_AMi, indicating that SINEU was mobilized by Tx1-Mar.

View Article: PubMed Central - PubMed

Affiliation: Genetic Information Research Institute, Los Altos, CA kojima@girinst.org.

Show MeSH